Tracefinder User Guide For General Quantitation, Version 4.1 Manual Trace Finder

2017-05-02

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Contents
Preface
Introduction
Getting Started
Using the Acquisition Mode
Using the Analysis Mode for Quantitation Batches
Using the Analysis Mode for Target Screening Batches
Using the Analysis Mode for Unknown Screening Batches
Using the Report Designer
Using the Audit Viewer
Using Quick Acquisition
Using Copy Down and Fill Down
Moving Data Review Panes

Thermo

TraceFinder

User Guide

Software Version 4.1

Optimized for General Quantitation

XCALI-97838 Revision A May 2016

TraceFinder, Aria, Q Exactive, FreeStyle, LCquan, ToxID, ExactFinder, Prelude, ISQ, and mzVault are

trademarks, and Exactive, Thermo Scientific, TSQ Quantum, TSQ Endura, TSQ Quantiva, TurboFlow, and

Xcalibur are registered trademarks of Thermo Fisher Scientific Inc. in the United States.

NIST is a registered trademark of the National Institute of Standards and Technology in the United States.

The following are registered trademarks in the United States and other countries: Windows, Active Directory,

Excel, and Microsoft are registered trademarks of Microsoft Corporation. Waters and ACQUITY are registered

trademarks of Waters Corporation.

ChemSpider is a trademark of ChemZoo, Inc.

All other trademarks are the property of Thermo Fisher Scientific Inc. and its subsidiaries.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the

product operation. This document is copyright protected and any reproduction of the whole or any part of this

document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this

document is for reference purposes only. System configurations and specifications in this document supersede

all previous information received by the purchaser.

This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This

document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of

Sale shall govern all conflicting information between the two documents.

Release history: Revision A, May 2016

Software version: Microsoft Windows 7 Professional SP1; (Thermo) Foundation 3.1 SP3; Xcalibur 4.0;

LC Devices 3.0; GC Devices 3.2

For Research Use Only. Not for use in diagnostic procedures.

Thermo Scientific TraceFinder User Guide iii

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

Accessing Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii

License Activation and Deactivation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .ix

Special Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . x

Contacting Us . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .xi

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1

About the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

TraceFinder Summary of Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

TraceFinder Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Reporting Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Chapter 2 Getting Started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .9

Installing the TraceFinder Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Installing the NIST and QED Libraries. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Launching the NIST Library Browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Launching a Qualitative Explorer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Thermo Scientific FreeStyle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Thermo Xcalibur Qual Browser. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Converting Legacy Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Converting Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Converting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Converting Method Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Converting Batch Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Converting Compound Databases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Choosing a Mode or Console . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Chapter 3 Using the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .35

Working with Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Opening and Navigating the Acquisition Mode . . . . . . . . . . . . . . . . . . . . . . 36

Creating and Submitting Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Contents

iv TraceFinder User Guide Thermo Scientific

Real Time Status Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

Real Time Status – Acquisition Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77

Real Time Status – Instrument Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Real Time Status – Queues Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Instrument Controls Page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Real-Time Trace Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Chapter 4 Using the Analysis Mode for Quantitation Batches . . . . . . . . . . . . . . . . . . . . . . . .93

Working in the Batch View for Quantitation Batches . . . . . . . . . . . . . . . . . . . . 94

Samples Page for Quantitation Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94

Auto Samples Page for Quantitation Batches. . . . . . . . . . . . . . . . . . . . . . . . 131

Reference Sample Page for Quantitation Batches. . . . . . . . . . . . . . . . . . . . . 133

Threshold Samples Page for Quantitation Batches. . . . . . . . . . . . . . . . . . . . 134

Working in Data Review for Quantitation Batches . . . . . . . . . . . . . . . . . . . . . 135

Sample View for Quantitation Batches . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136

Compound View for Quantitation Batches . . . . . . . . . . . . . . . . . . . . . . . . . 151

Compound Details for Quantitation Batches . . . . . . . . . . . . . . . . . . . . . . . 164

Comparative View for Quantitation Batches . . . . . . . . . . . . . . . . . . . . . . . . 192

Qualitative View for Quantitation Batches . . . . . . . . . . . . . . . . . . . . . . . . . 200

Column Parameters for Compound Results and Sample Results . . . . . . . . . 214

Working in the Report View for Quantitation Batches . . . . . . . . . . . . . . . . . . 226

Working in the Local Method View for Quantitation Batches . . . . . . . . . . . . 232

Chapter 5 Using the Analysis Mode for Target Screening Batches . . . . . . . . . . . . . . . . . .235

Working in the Batch View for Target Screening Batches . . . . . . . . . . . . . . . . 236

Samples Page Features for Target Screening Batches . . . . . . . . . . . . . . . . . . 237

Creating a New Target Screening Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . 251

Editing a Target Screening Batch. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258

Submitting a Target Screening Batch. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261

Working in Data Review for Target Screening Batches . . . . . . . . . . . . . . . . . . 270

Samples Pane. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272

Compounds Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273

Chromatogram Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286

Spectrum Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286

Working in the Report View for Target Screening Batches . . . . . . . . . . . . . . . 298

Working in the Local Method View for Target Screening Batches. . . . . . . . . . 304

Chapter 6 Using the Analysis Mode for Unknown Screening Batches. . . . . . . . . . . . . . . .307

Working in the Batch View for Unknown Screening Batches . . . . . . . . . . . . . 308

Samples Page Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308

Creating a New Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320

Editing a Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328

Submitting a Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330

Working in Data Review for Unknown Screening Batches . . . . . . . . . . . . . . . 340

Contents

Thermo Scientific TraceFinder User Guide v

Working in the Report View for Unknown Screening Batches . . . . . . . . . . . . 374

Working in the Local Method View for Unknown Screening Batches. . . . . . . 380

Chapter 7 Using the Report Designer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .383

Editing a Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 384

Toolbar Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 396

Home Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 396

Insert Toolbar – General Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397

Insert Toolbar – Quantitation Reports . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398

Insert Toolbar – Target Screening Reports . . . . . . . . . . . . . . . . . . . . . . . . . 400

Insert Toolbar – Unknown Screening Reports. . . . . . . . . . . . . . . . . . . . . . . 401

Page Layout Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403

Plot Display Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404

Quantitation and Target Screening Plots. . . . . . . . . . . . . . . . . . . . . . . . . . . 404

Unknown Screening Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 420

Quick Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 432

Chapter 8 Using the Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .433

Audit Trail Log Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433

Audit Log File Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434

Audit Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 442

Appendix A Using Quick Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .445

Appendix B Using Copy Down and Fill Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .447

Appendix C Moving Data Review Panes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .451

Contents

vi TraceFinder User Guide Thermo Scientific

Thermo Scientific TraceFinder User Guide vii

Preface

This guide describes how to use the Thermo TraceFinder™ 4.1 application with compatible

Thermo Scientific™ GC/MS and LC/MS analytical instruments.

To suggest changes to the documentation or to the Help

Complete a brief survey about this document by clicking the button below.

Thank you in advance for your help.

Accessing Documentation

The TraceFinder application includes complete documentation. For system requirements,

refer to the Release Notes on the software DVD.

To view the TraceFinder manuals

From the Microsoft™ Windows™ taskbar, choose Start > All Programs > Thermo

TraceFinder > Manuals.

–or–

From the application, choose Help > Manuals.

Contents

•Accessing Documentation

•License Activation and Deactivation

•Special Notices

•Contacting Us

Preface

Accessing Documentation

viii TraceFinder User Guide Thermo Scientific

To view user documentation from the Thermo Fisher Scientific website

1. Go to thermofisher.com.

2. Click the Services & Support tab.

3. On the right, click Manuals & Protocols.

4. In the Refine Your Search box, search by the product name.

5. From the results list, click the title to open the document in your web browser, save it, or

print it.

To return to the document list, click the browser Back button.

To view TraceFinder Help

Open the TraceFinder application and choose Help > TraceFinder Help.

• To find a particular topic, use the Contents, Index, or Search panes.

• To create your own bookmarks, use the Favorites pane.

Preface

License Activation and Deactivation

Thermo Scientific TraceFinder User Guide ix

License Activation and Deactivation

Use the Thermo Scientific Product Licensing wizard to activate or deactivate the license for

the TraceFinder application. To activate the license, you must have an activation code from

Thermo Fisher Scientific. Before you transfer a license to another computer, deactivate the

license.

When you first start the TraceFinder application, a dialog box displays the number of days

remaining in your 120-day free evaluation license. If your evaluation license has expired, the

License Activation wizard opens.

Two types of licenses are available:

• 120-Day Evaluation Version (free of charge)

• Full Version Single License

The evaluation version is full-featured and automatically expires 120 days after activation.

Any attempt to set back the system date automatically terminates this version. You can

purchase and then activate the full version of the application at any time, during or after the

free evaluation, without reinstalling the software.

Each activation key is valid only for a single license. Any additional installation generates a

different license and requires a different activation key.

For software download and licensing questions, contact support at

ThermoMSLicensing@thermo.com.

Use the License Activation wizard to activate or deactivate the license for the application. To

activate the license, you must have an activation code from Thermo Fisher Scientific. You

must deactivate the license before you transfer it to another computer.

To start the license activation or deactivation process

1. Open the application.

2. Choose Help > About TraceFinder and Licensing to display the License Activation

wizard.

3. Click Activate (Deactivate) to start the activation or deactivation process, as applicable.

Note You can open the License Activation wizard at any time during your evaluation

period by choosing Help > About TraceFinder and Licensing from the TraceFinder

menu and then clicking Activate. If you already have a permanent license, a message tells

you that your product is fully licensed.

IMPORTANT The 120-day evaluation license includes the basic TraceFinder 4.1 features

and the unknown screening features. When you purchase a permanent license, you have

the option to purchase the unknown screening features. Your permanent license might not

include the unknown screening features.

Preface

Special Notices

xTraceFinder User Guide Thermo Scientific

The License Activation wizard opens.

4. Follow the instructions in the License Activation wizard.

For additional instructions, click Help in the wizard.

Special Notices

Make sure you follow the special notices presented in this guide. Special notices appear in

boxes; those concerning safety or possible system damage also have corresponding caution

symbols.

IMPORTANT Highlights information necessary to prevent damage to software, loss of

data, or invalid test results; or might contain information that is critical for optimal

performance of the system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

Preface

Contacting Us

Thermo Scientific TraceFinder User Guide xi

Contacting Us

There are several ways to contact Thermo Fisher Scientific for the information you need. You

can use your smartphone to scan a QR code, which opens your email application or browser.

(U.S.) 1 (800) 532-4752 (U.S.) 1 (800) 532-4752

(U.S.) 1 (561) 688-8731 (U.S.) 1 (561) 688-8736

us.customer-support.analyze

@thermofisher.com

us.techsupport.analyze

@thermofisher.com

To find global contact information or customize your request

1. Go to thermofisher.com.

2. Click Contact Us and then select the type of support you need.

3. At the prompt, type the product name.

4. Use the phone number or complete the online form.

To find product support, knowledge bases, and resources

Go to thermofisher.com/us/en/home/technical-resources.

To find product information

Go to thermofisher.com/us/en/home/brands/thermo-scientific.

Note To provide feedback for this document:

• Send an email message to Technical Publications (techpubs-lcms@thermofisher.com).

• Complete a survey at surveymonkey.com/s/PQM6P62.

Preface

Contacting Us

xii TraceFinder User Guide Thermo Scientific

Thermo Scientific TraceFinder User Guide 1

Introduction

This chapter describes general features of the TraceFinder application.

About the TraceFinder Application

The TraceFinder application targets the general quantitation market. It supports a focused

quantification workflow for specific nonbioanalytical laboratory use, instrument control, and

method development functionality. TraceFinder is the primary application for the TSQ

Quantum™ XLS triple quadrupole mass spectrometers.

The application can export mass data in the Acquisition List to XML format so that other

systems’ applications, such as for the TSQ 8000, TSQ Quantum™, ISQ, and Q Exactive™,

can import the files into their databases.

The application can import the following file types:

• Sample lists in .csv or .xml format

See Defining a Sample List in Chapter 3, “Using the Acquisition Mode.”

• Compounds from files that use the database (.xml or .cdb) format

Refer to Chapter 2, “Using Compound Databases in the Method Development Mode,”

in the TraceFinder Lab Director User Guide.

• Batches, methods, or templates from the TraceFinder 2.0, 2.1, 3.0, 3.1, 3.2, 3.3, or 4.0

applications.

See Converting Legacy Data.

Contents

•About the TraceFinder Application

•TraceFinder Summary of Features

•TraceFinder Workflow

•Reporting Features

1 Introduction

About the TraceFinder Application

2TraceFinder User Guide Thermo Scientific

• Processing (.pmd) and instrument (.meth) method files from the Xcalibur™ data system

The TraceFinder Lab Director User Guide provides detailed information for creating the

following methods.

The application checks the accuracy and precision of data against systems that have previously

been certified against a standard processing program, such as the Statistical Analysis System

(SAS).

Supported File Types

The application supports the following file types:

• Comma-separated values (.csv): A set of file formats used to store tabular data in which

numbers and text are stored in plain textual form that can be read in a text editor. Lines in

the text file represent rows of a table, and commas in a line separate fields in the tables

row.

• Extensible Markup Language (.xml): A generic framework for storing any amount of text

or any data whose structure can be represented as a tree. The only indispensable

syntactical requirement is that the document has exactly one root element (also called the

document element). This means that the text must be enclosed between a root start-tag

and a corresponding end-tag.

• Instrument method (.meth): A proprietary file format for the Xcalibur data system suite

with specific instructions that enable scientific instruments to perform data acquisition.

• Processing method (.pmd): A proprietary file format for the Xcalibur data system suite

with specific instructions on processing data that was acquired through the instruments

attached to the system.

• Raw data (.raw): The file type for acquired samples on the system.

• Compound database (.cdb): The file type for TraceFinder or ExactFinder™ compound

database data.

• Library (.db): A library used for target screening.

Quantitative

processing methods

Chapter 4, “Using the Method Development Mode for

Quantitation Methods”

Targe t s cre en in g

processing methods

Chapter 5, “Using the Method Development Mode for Target

Screening Methods”

Unknown screening

processing methods

Chapter 6, “Using the Method Development Mode for

Unknown Screening Methods”

Instrument methods Chapter 3, “Using Instrument Methods in the Method

Development Mode”

1 Introduction

TraceFinder Summary of Features

Thermo Scientific TraceFinder User Guide 3

TraceFinder Directory Structure

The application creates folders for batches, methods, and templates in the

…\TraceFinderData directory. Within each batch folder, the application creates folders for

data, methods, and reports.

You can create batches in the TraceFinderData\4.0\Projects folder, or you can create

subfolders within the Projects folder for your batches. You can create as many subfolders as

you want for your batches, but you cannot create a batch within another batch folder.

Figure 1. Example batch directory structure

TraceFinder Summary of Features

The TraceFinder system provides a workflow-oriented approach to high-throughput

quantitation, using tools that automate and speed up the processes of method creation,

loading samples, automatically generating data, manually reviewing and editing results, and

finalizing the data review and reporting process.

The TraceFinder software package includes data acquisition, processing, reviewing, and

reporting capabilities designed to assist analysts in general quantitation applications. The

application has a fully automated acquisition mode and a manual data analysis mode. You can

use the data acquisition system to create and submit batches and monitor real-time review of

results.

IMPORTANT TraceFinder 4.1 uses the same data as TraceFinder 4.0. By default, the application

stores the method, project, template, and compound database data for the 4.1 release in the

TraceFinderData\4.0 folder.

IMPORTANT You cannot rename or move the folders created by the TraceFinder

application.

1 Introduction

TraceFinder Summary of Features

4TraceFinder User Guide Thermo Scientific

The application uses a comprehensive processing method to provide improved handling of

ion ratio calculations, reviewing, and reporting. In addition, it can compare the mass spectra

and integrate the processes of data review and reporting.

Key features include the following:

• Role-based authorization for Security, LabDirector, ITAdmin, Supervisor, Technician,

and QAQC (quality assurance) roles

• Administrator Console for user security, role-based permissions, and data repositories

• Configuration console for report configuration, detection and acquisition defaults,

adduct definitions, screening library selection, and customized columns and flags

• Method Development mode for editing instrument methods, setting processing and error

flag parameters, and setting reporting options

• Acquisition mode that guides you in creating batches and running samples

• Analysis mode with batch views, data review, local method views, and reporting views

• Database-capable method development

• Quantification, target screening, and unknown screening workflows

• Spreadsheet-based report designer

Features of the common workflow core include the following:

• Acquisition and processing

•Peak detection

• Quantification to include calibration

• Error analysis and flag setting

•Reporting

• Data persistence

• Raw data file handling

1 Introduction

TraceFinder Workflow

Thermo Scientific TraceFinder User Guide 5

TraceFinder Workflow

The application is structured with a typical laboratory workflow in mind. You create a batch,

and the system injects samples into the instrument, runs the samples, analyzes the data, and

generates a report. You can set up a master method for specific compound groups or assays

that you expect to run in your laboratory. When you are ready to run a particular type of

sample, select the appropriate method and begin.

When using the application, follow these basic steps:

1. Create and save a master method in the Method Development mode.

A master method combines the instrument method and processing method that define

the following:

• How the raw data is acquired and processed

• How the error checking information evaluates the results

• How the results appear in reports

2. Create and submit a batch using the Acquisition wizard.

A batch lists samples for processing and reporting using a specified method. Each row of a

batch represents a unique sample.

3. Monitor the status of the batch in the Real Time Status view.

The real-time display is visible from all the TraceFinder modes. You can begin another

batch while you watch the real-time display of the currently acquiring batch.

4. Evaluate the data in the Analysis mode.

The Analysis mode includes views where you can review batches, batch data, reports, and

local methods.

5. View and print reports in the Report View of the Analysis mode.

Use the Report View to view or print the reports for the current batch.

Note At any time, you can quickly view the system status by looking in the upper

right corner of the TraceFinder window. This area displays a green, yellow, or red

status light and a description of any activity in the queues, as in this example:

The status light (in any color) might include an exclamation mark.

• An exclamation mark on a green status light, , might indicate that the

instrument method contains the wrong source (for example, APCI instead of

HESI).

• An exclamation mark on a red status light, , might indicate that a vial is

missing and the batch was forced to stop.

Click the status light to display details of the error.

1 Introduction

Reporting Features

6TraceFinder User Guide Thermo Scientific

Reporting Features

The report engine can generate several different types of reports designed to meet the needs of

the laboratory, the laboratory's customers, and key regulatory agencies that might review the

results. The following types of reports meet the requirements of various methods and global

regulatory agencies, helping to track the performance of LC and GC systems and methods.

Standard Report Types

•Ad Hoc Tune Report

•Batch Report

•Blank Report

• Breakdown Report

•Calibration Report

•Check Standard Report

• Chromatogram Report

• Compound Calibration Report

• Compound Calibration Report - Alternate

•Confirmation Report

•Confirmation Report 2

• High Density Calibration Report

• High Density Internal Standard Report Long

• High Density Sample Report 1 Long

• Intelligent Sequencing

• Internal Standard Summary Report

• Ion Ratio Failure Report

•LCSLCSD Report

• Manual Integration Report

•Method Detection Limit Report

•Method Report

• Method Validation Report

•MSMSD Report

• Quantitation Report

1 Introduction

Reporting Features

Thermo Scientific TraceFinder User Guide 7

• Quantitation Report - 2

• Sample Report

•Solvent Blank Report

• Standard Addition Report

• Surrogate Recovery Report

• Target Screening Height Density Sample Report

• Target Screening Height Density Sample Report 2

• Target Screening Summary Report

•TIC Report

• TIC Summary Report

•Tune Report

• Unknown Screening High Density Report

• Unknown Screening Long Report

• Unknown Screening Summary Report

Use the features in the Report Designer to create custom report types. See Chapter 7, “Using

the Report Designer.”

Thermo Scientific TraceFinder User Guide 9

Getting Started

This chapter includes the procedures for getting started with the TraceFinder application.

Installing the TraceFinder Application

To initially install the TraceFinder 4.1 application, follow the instructions in the TraceFin der

Installation Guide. Later, you might need to reinstall the application or other features using

the InstallShield Wizard.

Follow these instructions to reinstall, start, and log in to the application.

To reinstall the TraceFinder application

1. From the Thermo Foundation Instrument Configuration window, remove all

instruments.

2. From the Windows Control Panel, uninstall the application and then uninstall all

Thermo instrument drivers.

3. Insert the TraceFinder DVD, and install both the TraceFinder 4.1 application and the

NIST™ library as follows:

a. Open the TraceFinder launcher and click Next.

Contents

•Installing the TraceFinder Application

•Installing the NIST and QED Libraries

•Launching the NIST Library Browser

•Launching a Qualitative Explorer

•Converting Legacy Data

•Choosing a Mode or Console

2 Getting Started

Installing the TraceFinder Application

10 TraceFinder User Guide Thermo Scientific

The InstallShield Wizard opens.

b. Click Tr a ce Fi n der 4.1 , and follow the instructions in the InstallShield Wizard.

The installer verifies that you have the appropriate versions of the Thermo

Foundation™ platform and Xcalibur data system and updates them if necessary.

c. At the prompt, click Yes to completely remove any previously installed applications.

d. Open the TraceFinder launcher again and click Next.

e. Click TraceFinde r 4. 1, and follow the instructions in the InstallShield Wizard.

f. When prompted, choose to install either the GC or LC version of the software.

g. When the installation is complete, open the TraceFinder launcher again and click

Next.

h. When prompted to restart your computer, select the Yes option and click Finish.

IMPORTANT For the application to properly install, you might be prompted to

uninstall Foundation platform. Do the following:

1. Click Yes, and then when prompted to restart your computer, click OK.

The wizard continues the TraceFinder installation.

2. When prompted to install Thermo Foundation, click Yes, and then when

prompted to restart your computer, click OK.

The wizard continues the installation.

2 Getting Started

Installing the TraceFinder Application

Thermo Scientific TraceFinder User Guide 11

3. (Optional) After your system restarts, open the TraceFinder launcher again, click Next,

and install any of the following:

a. Click NIST Library and follow the instructions to install it.

b. Click Example Data.

The application installs example compound databases, instrument methods, and

batch data.

c. Click mzVault 1.0 SP1 and follow the instructions to install the Thermo mzVault

application.

4. Install the appropriate device drivers, and configure the instruments in the Thermo

Foundation Instrument Configuration window.

You can now start the TraceFinder application.

To start the TraceFinder application

1. Configure your instruments.

You must close the TraceFinder application before you can configure your instruments.

2. Double-click the TraceFind e r icon on your desktop, or choose Start > All Programs >

Thermo TraceFinder 4.1 > TraceFinder 4.1 General Quan.

By default, user security is not activated and the application does not require a password.

To activate user security, refer to the TraceFinder Administrator Console User Guide.

To log in to the TraceFinder application (when user security is activated)

1. Enter your user name in the TraceFinder login window.

2. Enter your password.

If your user name or password does not match, the system reports this error:

Correct the user name or password, or contact your system administrator.

3. Click Login.

The TraceFinder main window opens.

Note Before you can log in to the application when user security is activated, a system

administrator must set up a user account for you.

2 Getting Started

Installing the TraceFinder Application

12 TraceFinder User Guide Thermo Scientific

Figure 2. TraceFinder main window, showing the Analysis mode for a quantitation batch

Table 1. TraceFinder main window features (Sheet 1 of 2)

Parameter Description

Modes

Acquisition See Chapter 3, “Using the Acquisition Mode.”

Analysis See Chapter 4, “Using the Analysis Mode for Quantitation Batches.”

See Chapter 5, “Using the Analysis Mode for Target Screening Batches.”

See Chapter 6, “Using the Analysis Mode for Unknown Screening Batches.”

Method Development Refer to the TraceFinder Lab Director User Guide.

2 Getting Started

Installing the TraceFinder Application

Thermo Scientific TraceFinder User Guide 13

Figure 3. TraceFinder login window

Additional Features

A TraceFinder window with user security for a user in the default LabDirector role has

these functions.

Real Time Status Opens the Real Time Status pane for the current acquisition. The acquisition progress is

displayed within the current mode window.

User Displays the name of the current user.

Log Off Logs off the current user and displays the login screen. This function is available only

when user security is activated.

Help Opens the TraceFinder Help.

Application Configuration Opens the Configuration console where you can configure several options for using the

application. Refer to Chapter 1, “Using the Configuration Console,” in the Trac eFi nd er

Lab Director User Guide.

Table 1. TraceFinder main window features (Sheet 2 of 2)

Parameter Description

Table 2. Login window parameters

Parameter Description

Domain The authentication method.

Username The user’s assigned user name.

Password The assigned password for the user name.

Exit Closes the TraceFinder login window.

2 Getting Started

Installing the NIST and QED Libraries

14 TraceFinder User Guide Thermo Scientific

Installing the NIST and QED Libraries

When you are using triple quadrupole instruments, such as the TSQ Quantum XLS, follow

these instructions to install the NIST and QED libraries.

To install the NIST library

1. Open the TraceFinder launcher, and click Next.

2. Click NIST Library.

The NIST 08 MS Search and AMDIS Setup wizard opens.

3. Follow the instructions in the setup wizard.

4. When the wizard prompts you to select a destination folder, select

C:\Program Files\NISTMS.

5. Continue to follow the instructions in the wizard until the setup is complete.

To install the QED library

1. On your desktop, double-click the Xcalibur icon, .

The Thermo Xcalibur Roadmap opens.

Note The application installs the NIST 2008 library; however, it also supports the

NIST 2011 and NIST 2014 libraries.

2 Getting Started

Installing the NIST and QED Libraries

Thermo Scientific TraceFinder User Guide 15

2. Choose To ol s > Li b r a r y M a n a g e r from the main menu.

The Thermo Library Manager dialog box opens, showing the NIST Libraries list.

3. Click Add.

The Add Library dialog box opens.

4. Click Browse, and locate your QED library in the C:\Thermo folder.

5. Click OK.

The Xcalibur data system reports that it has added the library to the NIST application.

6. Click Dismiss to close the message box.

The Xcalibur data system adds the QED library to the NIST Libraries list in the Library

Manager dialog box.

2 Getting Started

Installing the NIST and QED Libraries

16 TraceFinder User Guide Thermo Scientific

7. Click Exit in the Thermo Library Manager dialog box.

8. To confirm the library installation, do the following:

a. Start the application.

b. Click Method Development in the navigation pane.

c. Click Method View in the Method Development navigation pane.

d. Choose File > New > Method Template from the main menu.

The Method Template Editor displays the QED NIST Library in the Use These

Libraries list.

2 Getting Started

Launching the NIST Library Browser

Thermo Scientific TraceFinder User Guide 17

Launching the NIST Library Browser

Use the NIST MS Search tool to search the NIST library.

To open the NIST library browser

Choose Tools > Launch Library Browser from the TraceFinder main menu.

The NIST MS Search window opens.

For detailed instructions about using the library browser, refer to the Help in the NIST MS

Search window.

2 Getting Started

Launching a Qualitative Explorer

18 TraceFinder User Guide Thermo Scientific

Launching a Qualitative Explorer

Use a qualitative explorer application to display chromatograms and spectra, detect

chromatogram peaks, search libraries, simulate spectra, subtract background spectra, apply

filters, add text and graphics, create and save layouts, and view instrument parameters as they

changed during the acquisition.

Your TraceFinder application is configured to use one of the following applications:

•Thermo Scientific FreeStyle

•Thermo Xcalibur Qual Browser

Thermo Scientific FreeStyle

To open the FreeStyle window

Choose To ol s > La u n ch Q ua l E xp l o rer from the TraceFinder main menu.

The FreeStyle application opens.

Figure 4. FreeStyle main window

For detailed instructions about using the FreeStyle application, click the Help icon, , in

the FreeStyle window.

IMPORTANT The Thermo Scientific FreeStyle™ application is available only when you

configure it as your default qualitative explorer in the Configuration console. Refer to

Chapter 1, “Using the Configuration Console,” in the Trace Fi n der Lab D irecto r Us e r

Guide.

2 Getting Started

Launching a Qualitative Explorer

Thermo Scientific TraceFinder User Guide 19

Thermo Xcalibur Qual Browser

To open the Qual Browser window

Choose To ol s > La u n ch Q ua l E xp l o rer from the TraceFinder main menu.

The Thermo Xcalibur Qual Browser application opens.

Figure 5. Qual Browser main window

For detailed instructions about using the Qual Browser application, refer to the Help in the

Qual Browser window.

IMPORTANT The Qual Browser application is available only when you configure it as

your default qualitative explorer in the Configuration console. Refer to Chapter 1, “Using

the Configuration Console,” in the TraceFinder Lab Director User Guide.

2 Getting Started

Converting Legacy Data

20 TraceFinder User Guide Thermo Scientific

Converting Legacy Data

Use the TraceFinder Legacy Data Converter to convert methods, batches, method templates,

batch templates, or compound databases (CDBs) from the source versions to compatible

TraceFinder 4.0/4.1 target configurations.

• You can convert legacy methods, batches, or method templates from TraceFinder versions

2.0, 2.1, 3.0, 3.1, 3.2, or 3.3.

• You can convert legacy batch templates from TraceFinder versions 3.0, 3.1, 3.2, or 3.3.

• You can convert legacy compound databases from TraceFinder versions 3.0, 3.1, 3.2, or

3.3.

• You can convert data from TraceFinder version 4.0/4.1 for general quantitation to

another installed configuration of TraceFinder 4.0/4.1.

Version Compatibility

This table shows which source versions of methods, batches, method templates, batch

templates, or compound databases are compatible with TraceFinder 4.0/4.1 target

configurations.

IMPORTANT TraceFinder 4.1 uses the same data configuration as TraceFinder 4.0. You

do not need to convert your data from 4.0 to 4.1. Data for the 4.1 release is stored in the

TraceFinderData/4.0 folder.

Table 3. Version compatibility (Sheet 1 of 2)

Source TraceFinder 4.0/4.1 target

General EFSa Clinical

Research

Forensic

Toxicology

TraceFinder 4.0/4.1 General 

TraceFinder 3.3 General 

Tr a c e Fi n d e r 3 . 3 E F S 

TraceFinder 3.3 Clinical Research 

TraceFinder 3.3 Forensic Toxicology 

TraceFinder 3.2 General 

Tr a c e Fi n d e r 3 . 2 E F S 

TraceFinder 3.2 Clinical Research 

TraceFinder 3.2 Forensic Toxicology 

TraceFinder 3.1 General 

Tr a c e Fi n d e r 3 . 1 E F S 

TraceFinder 3.1 Clinical Research 

TraceFinder 3.1 Forensic Toxicology 

TraceFinder 3.0 General 



2 Getting Started

Converting Legacy Data

Thermo Scientific TraceFinder User Guide 21

See the following topics:

•Converting Methods

•Converting Batches

•Converting Method Templates

•Converting Batch Templates

•Converting Compound Databases

To open the TraceFinder Legacy Data Converter

Choose Tools > Launch Legacy Data Converter from the TraceFinder main menu.

The TraceFinder Legacy Data Converter window opens.

Tr a c e Fi n d e r 3 . 0 E F S 

TraceFinder 3.0 Clinical Research 

TraceFinder 3.0 Forensic Toxicology 

TraceFinder 2.1 General 



Tr a c e Fi n d e r 2 . 1 E F S 

TraceFinder 2.1 Clinical Research 

TraceFinder 2.1 Forensic Toxicology 

TraceFinder 2.0 General 



Tr a c e Fi n d e r 2 . 0 E F S 

TraceFinder 2.0 Clinical Research 

aEnvironmental and Food Safety

Table 3. Version compatibility (Sheet 2 of 2)

Source TraceFinder 4.0/4.1 target

General EFSa Clinical

Research

Forensic

Toxicology

Note When you open the application, the system checks for any legacy data and

prompts you to open the Legacy Data Converter.

2 Getting Started

Converting Legacy Data

22 TraceFinder User Guide Thermo Scientific

Converting Methods

Use the data converter to convert legacy methods to TraceFinder 4.1 methods.

To convert a method

1. In the Data Type list, select Method.

The TraceFinder Legacy Data Converter displays the interface for converting methods.

The following example shows that you can convert methods from the TraceFinder 3.3

General configuration to the current General configuration. For a complete list of version

compatibilities, see Version Compatibility.

2. In the Source Version list, select the version of the method that you will convert.

The conversion table displays the methods in the Methods folder for the selected source

version. The application verifies that the method file is in the .mmx file format.

3. To convert a method that is not in the default list, do the following:

a. Click Browse and locate a different source method folder.

You can select a specific method folder or a folder that contains multiple methods.

b. Click OK in the Browse for Folder dialog box.

The application displays the selected method folder in the conversion table.

When you select a folder that contains multiple method folders, the application displays

all the methods.

4. In the Target Version list, select the version that you are converting to.

The list displays only TraceFinder configurations with compatible data. See Version

Compatibility.

5. (Optional) In the Target Name column, change the default new name for each method

that you want converted.

Note When you select Any Legacy, the Legacy Data Converter examines all possible

methods in the source folder, regardless of version.

2 Getting Started

Converting Legacy Data

Thermo Scientific TraceFinder User Guide 23

When you populate the conversion table, the application checks each method to see if a

method with this name exists in the target repository.

• If the method name already exists in the target repository, the default new name

appends “_1” to the original name.

• If the method name does not exist in the target repository, the application keeps the

original method name.

6. Select the Convert check box for each method that you will convert, and click

The application confirms that all methods to be converted use the .mmx file format.

When the conversion process begins, the application displays a status bar and a Cancel

button. You can cancel pending conversions, but not the method that is currently

converting.

When the Status column reports that a method is successfully converted, the application

writes the converted file to the specified target repository.

7. To view a log of the conversion, click View Log.

The application opens a cumulative log file for the session in a Microsoft Notepad text

editor window.

IMPORTANT The conversion cannot overwrite an existing file name. If the new name

is identical to an existing method file, the conversion will not work. When you

manually enter a new name, you must verify that the name does not already exist.

Note If a method conversion is unsuccessful, the Status column displays “Conversion

failed.” The log file contains details about the failed conversion.

2 Getting Started

Converting Legacy Data

24 TraceFinder User Guide Thermo Scientific

Converting Batches

Use the data converter to convert legacy batches to TraceFinder 4.1 batches.

To convert a batch

1. In the Data Type list, select Batch.

The following example shows that you can convert batches from the TraceFinder 3.3

General configuration to the current General configuration. For a complete list of version

compatibilities, see Version Compatibility.

2. In the Source Version list, select the version of the batch that you will convert.

The conversion table displays all batches in the Projects folder for the selected source

version.

3. In the Target Version list, select the version that you are converting to.

The list displays only TraceFinder configurations with compatible data. See Version

Compatibility.

4. In the Target Default Project and Subproject boxes, type the name of a project and

subproject, or select the Replicate Original Project/Subproject check box.

5. (Optional) In the New Name column, change the default new name for each batch that

you want converted.

When you populate the conversion table, the application checks each batch to see if a

batch with this name exists in the target repository.

• If the batch name already exists in the target repository, the default new name

appends “_1” to the original name.

• If the batch name does not exist in the target repository, the application keeps the

original batch name.

Note When you select Any Legacy, the Legacy Data Converter examines all possible

batches in the source folder, regardless of version.

2 Getting Started

Converting Legacy Data

Thermo Scientific TraceFinder User Guide 25

6. Select the Convert check box for each batch that you will convert, and click

The application confirms that all batches to be converted use the .btx file format.

When the conversion process begins, the application displays a status bar and a Cancel

button. You can cancel pending conversions, but not the batch that is currently

converting.

When the Status column reports that a batch is successfully converted, the application

writes the converted batch to the …\TraceFinderData\4.0\Projects folder and uses either

the original project and subproject names or the new names that you entered.

7. To view a log of the conversion, click View Log.

IMPORTANT The conversion cannot overwrite an existing file name. If the new name

is identical to an existing batch folder, the conversion will not work. When you

manually enter a new name, you must verify that the name does not already exist.

Note If a batch conversion is unsuccessful, the Status column displays “Conversion

failed.” The log file contains details about the failed conversion.

2 Getting Started

Converting Legacy Data

26 TraceFinder User Guide Thermo Scientific

Converting Method Templates

Use the data converter to convert legacy method templates to TraceFinder 4.1 method

templates.

To convert a method template

1. In the Data Type list, select Method Template.

The following example shows that you can convert method templates from the

TraceFinder 3.3 General configuration to the current General configuration. For a

complete list of version compatibilities, see Version Compatibility.

2. In the Source Version list, select the version of the method template that you will convert.

The conversion table displays the method templates in the Templates folder for the

selected source version. The application verifies that the method template file is in

the .pmtx file format.

3. To convert a method template that is not in the default list, do the following:

a. Click Browse and locate a template folder.

You can select a specific template folder or a folder that contains multiple templates.

b. Click OK in the Browse for Folder dialog box.

The application displays the selected folder in the conversion table.

When you select a folder that contains multiple method template folders, the application

displays all the method templates.

4. In the Target Version list, select the version that you are converting to.

The list displays only TraceFinder configurations with compatible data. See Version

Compatibility.

5. (Optional) In the Target Name column, change the default name for each method

template that you want converted.

Note When you select Any Legacy, the Legacy Data Converter examines all possible

method templates in the source folder, regardless of version.

2 Getting Started

Converting Legacy Data

Thermo Scientific TraceFinder User Guide 27

When you populate the conversion table, the application checks each method template to

see if a method template with this name exists in the target repository.

• If the method template name already exists in the target repository, the default new

name appends “_1” to the original name.

• If the method template name does not exist in the target repository, the application

keeps the original method template name.

6. Select the Convert check box for each method template that you will convert, and click

The application confirms that all method templates to be converted use the .pmtx file

format.

When the conversion process begins, the application displays a status bar and a Cancel

button. You can cancel pending conversions, but not the template that is currently

converting.

When the Status column reports that the template is successfully converted, the

application writes the converted template to the specified target repository.

7. To view a log of the conversion, click View Log.

The application opens a cumulative log file for the session in a Notepad text editor

window.

IMPORTANT The conversion cannot overwrite an existing file name. If the new name

is identical to an existing method template file, the conversion will fail. When you

manually enter a new name, you must verify that the name does not already exist.

Note If a template conversion fails, the Status column displays “Conversion failed.”

The log file contains details about the failed conversion.

2 Getting Started

Converting Legacy Data

28 TraceFinder User Guide Thermo Scientific

Converting Batch Templates

Use the data converter to convert legacy batch templates to TraceFinder 4.1 batch templates.

To convert a batch template

1. In the Data Type list, select Batch Template.

The following example shows that you can convert batch templates from the TraceFinder

3.3 General configuration to the current General configuration. For a complete list of

version compatibilities, see Version Compatibility.

2. In the Source Version list, select the version of the batch template that you will convert.

The conversion table displays the batch templates in the Templates folder for the selected

source version.

3. To convert a batch template that is not in the default list, do the following:

a. Click Browse and locate a template folder.

You can select a specific batch template folder or a folder that contains multiple batch

templates.

b. Click OK in the Browse for Folder dialog box.

The application displays the selected folder in the conversion table.

When you select a folder that contains multiple batch template folders, the application

displays all the batch templates.

4. In the Target Version list, select the version that you are converting to.

The list displays only TraceFinder configurations with compatible data. See Version

Compatibility.

5. (Optional) In the New Name column, change the default new name for each batch

template that you want converted.

When you populate the conversion table, the application checks each batch template to

see if a batch template with this name exists in the target repository.

• If the batch template name already exists in the target repository, the default new

name appends “_1” to the original name.

Note When you select Any Legacy, the Legacy Data Converter examines all possible

batch templates in the source folder, regardless of version.

2 Getting Started

Converting Legacy Data

Thermo Scientific TraceFinder User Guide 29

• If the batch template name does not exist in the target repository, the application

keeps the original batch template name.

6. Select the Convert check box for each batch template that you will convert, and click

The application confirms that all batch templates to be converted use the .btx file format.

When the conversion process begins, the application displays a status bar and a Cancel

button. You can cancel pending conversions, but not the template that is currently

converting.

When the Status column reports that the template is successfully converted,

the application writes the converted template folder to the

…\TraceFinderData\4.0\Templates\Batches folder.

7. To view a log of the conversion, click View Log.

The application opens a cumulative log file for the session in a Notepad text editor

window.

IMPORTANT The conversion cannot overwrite an existing file name. If the new name

is identical to an existing batch template file, the conversion will fail. When you

manually enter a new name, you must verify that the name does not already exist.

Note If a template conversion fails, the Status column displays “Conversion failed.”

The log file contains details about the failed conversion.

2 Getting Started

Converting Legacy Data

30 TraceFinder User Guide Thermo Scientific

Converting Compound Databases

Use the data converter to convert legacy compound databases to TraceFinder 4.1 compound

databases.

To convert compound databases

1. Click Convert CDBs (in the upper right corner of the window).

The Confirm dialog box lists all databases that will be converted to TraceFinder 4.1.

2. Click Yes.

The Confirm dialog box lists all databases that are converted to TraceFinder 4.1.

3. Click OK.

The converted compound databases are now available in the TraceFinder 4.1 application.

Note If your window is too narrow, you might not see the Convert CDBs button.

Widen the window to expose the button in the upper right corner.

2 Getting Started

Choosing a Mode or Console

Thermo Scientific TraceFinder User Guide 31

Choosing a Mode or Console

When user security is activated, the navigation pane displays the modes and consoles available

to the current user’s assigned roles and permissions. The following table shows the available

modes and consoles for each user role.

Follow these procedures:

•To choose a mode

•To open the Configuration console

•To open the Administrator console

•To display a log of instrument errors

•To monitor instrument status

•To watch acquisition and processing in real time

Table 4. User roles and default access

User role Method

Development Acquisition Analysis Configuration

console

Administrator

Console

Security Security only

LabDirector  

ITAdmin 

Supervisor  

Technician 

QAQC 

Note When user security is not activated, all modes and consoles are available to all users.

2 Getting Started

Choosing a Mode or Console

32 TraceFinder User Guide Thermo Scientific

To choose a mode

In the navigation pane, click the mode where you want to work.

The navigation pane shows only the modes that you have permission to use.

To open the Configuration console

Click the Application Configuration icon, , in the upper right corner of the

Tr a c e Fi n d e r w i n d o w.

When user security is activated, you must have Configuration permissions to access the

Configuration console. Refer to Chapter 1, “Using the Configuration Console,” in the

TraceFinder Lab Director User Guide.

To open the Administrator console

Choose Tools > Administrator Console from the TraceFinder main menu.

When user security is activated, you must have Administrator permissions to access the

Administrator Console. Refer to the TraceFinder Administrator Console User Guide.

Mode Description

Acquisition Opens the Acquisition mode where you can create and review batches,

batch data, reports, and local methods.

See Chapter 3, “Using the Acquisition Mode.”

Analysis Opens the Analysis mode where you can review batches, batch data,

reports, and local methods.

See Chapter 4, “Using the Analysis Mode for Quantitation Batches.”

See Chapter 5, “Using the Analysis Mode for Target Screening

Batches.”

See Chapter 6, “Using the Analysis Mode for Unknown Screening

Batches.”

Method

Development

Opens the Method Development mode where you can create a master

method or an instrument method.

Refer to the TraceFinder Lab Director User Guide.

2 Getting Started

Choosing a Mode or Console

Thermo Scientific TraceFinder User Guide 33

To display a log of instrument errors

1. Click the status light in the upper right corner of the TraceFinder window.

The Instrument Log dialog box opens.

The Instrument Log displays all instrument errors that have occurred since the

application started or since the last time that you cleared the message log.

2. Do any of the following:

• Click Refresh to display errors that occur after you open the Instrument Log dialog

box.

• Click Clear Messages to remove messages from the Instrument Log display.

The application clears messages only from the Instrument Log display. These

messages remain in the following log file:

C:\Thermo\TraceFinder\4.0\General\Logs\TraceFinder.log

• Click OK to dismiss the Instrument Log dialog box.

To monitor instrument status

Look at the status light in the upper right corner of the TraceFinder window.

Green indicates that the instrument is ready.

Yellow indicates that the instrument is in standby mode, waiting for contact

closure, or warming up the lamp.

Red indicates that the instrument is not ready because it is turned off, not

configured or connected, currently initializing, or otherwise busy.

Status light

2 Getting Started

Choosing a Mode or Console

34 TraceFinder User Guide Thermo Scientific

The status light (in any color) might include an exclamation mark.

• An exclamation mark on a green status light, , might indicate that the

instrument method contains the wrong source (for example, APCI instead of HESI).

• An exclamation mark on a red status light, , might indicate that a vial is missing

and the batch was forced to stop.

Click the status light to display details of the error.

To watch acquisition and processing in real time

Click Real Time Status in the upper right corner of the TraceFinder window.

The application displays the Real Time Status pane at the bottom of the window.

For descriptions of all the features of the Real Time Status pane, see Real Time Status

Pane in Chapter 3, “Using the Acquisition Mode.”

Thermo Scientific TraceFinder User Guide 35

Using the Acquisition Mode

This chapter describes the tasks associated with the Acquisition mode.

When you plan to work with multiple samples or use similarly designed batches, use the

Acquisition mode to reduce the amount of data you must enter.

Because the nature and types of batches are often similar (in some cases specified by laboratory

standard practices), you can define a batch template that supplies the basic structure of a

batch.

Using a master method, you can create a batch and run the samples. A batch represents one or

more samples that are to be acquired, processed, reviewed, and reported as a set. After you

create a batch of samples, you can submit the batch and review the results in Data Review or

you can go directly to viewing and printing reports.

You can set up a calibration batch with known concentrations of the target compounds and

compare the calibration values against samples in future batches.

You can also use the Quick Acquisition feature to quickly submit samples from any page in

the Acquisition mode. See Appendix A, “Using Quick Acquisition.”

Contents

•Working with Batches

•Real Time Status Pane

•Sample Types

IMPORTANT When user security is activated, you must have Acquisition Wizard –

Template Editing permission to create a batch template.

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36 TraceFinder User Guide Thermo Scientific

Working with Batches

See the instructions for the following tasks:

•Opening and Navigating the Acquisition Mode

•Creating and Submitting Batches

Opening and Navigating the Acquisition Mode

To access the Acquisition mode

Click Acquisition in the navigation pane.

The navigation pane for the Acquisition mode opens.

As you progress through the Acquisition mode using any of these methods for creating a

batch, the task pane at the top of the view tracks your progress. As you complete each

stage, you can hold your cursor over the view name in the task pane to display the

parameters that you specified for the batch. See Example task pane when you have

completed the Acquisition mode.

IMPORTANT TraceFinder 4.1 uses the same data as TraceFinder 4.0. By default, the application

stores the batch data for the 4.1 release in the TraceFinderData\4.0\Projects folder.

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Thermo Scientific TraceFinder User Guide 37

Figure 6. Example task pane when you have completed the Acquisition mode

Categories in the Sample Definition list:

QC Samples: QC Std

Calibration Samples: Cal Std

Blank Samples: Matrix Blank

Unknown Samples: All other samples

Hold your cursor over Batch Selection, Sample Definition,

or Report Selection to view the parameters for your batch.

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Creating and Submitting Batches

To create and submit a batch, the Acquisition mode uses a wizard-style interface to guide you

through these major steps:

1. Selecting a Batch

2. Defining a Sample List

3. Selecting and Reviewing Reports

4. Submitting a Batch in the Acquisition Wizard

The Acquisition mode provides multiple techniques for creating either a batch or a batch

template. Each batch creation technique has an associated workflow, as shown in the

following flowcharts. Each workflow uses a different combination of Acquisition mode pages.

Workflow for Creating an Original Batch

To create an original batch, start with any of these instructions: To start a new quantitation

batch, or To start a new target screening batch, or To start a new unknown screening batch.

To see how to acquire a new batch

1. Choose Help > Animations.

2. From the list of animation topics, click Acquiring a New Batch.

Workflow for Acquiring a Prepared Batch

To acquire a prepared batch, start with the instructions To select a prepared batch.

Batch and

Method

Finish

Reports

Samples

Batch

Finish Samples

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Thermo Scientific TraceFinder User Guide 39

To see how to acquire a prepared batch

1. Choose Help > Animations.

2. From the list of animation topics, click Acquiring a Prepared Batch.

Workflow for Reinjecting a Previously Acquired Batch

To process a previously acquired batch, start with the instructions To reinject samples in a

previously acquired batch.

To see how to reinject samples in a previously acquired batch

1. Choose Help > Animations.

2. From the list of animation topics, click Reinjecting Samples.

Workflow for Creating or Editing a Batch Template

To create a batch template, start with any of these instructions: To create a quantitation batch

template, To create a target screening batch template, or To c r ea t e an u n k n ow n s c re e n i n g

batch template.

To see how to create a batch template

1. Choose Help > Animations.

2. From the list of animation topics, click Creating a Batch Template.

IMPORTANT When user security is activated, you must have Acquisition Wizard –

Template Editing permission to create a batch template.

Batch

Finish

Samples

Finish

Samples

Template and

Method

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Selecting a Batch

On the Batch Selection page of the Acquisition mode, you can create a new quantitative,

target screening, or unknown screening batch in any of your current projects/subprojects. Or,

you can submit a batch that you previously prepared and saved, reinject the samples in a batch

that you previously acquired, or create a batch template to use for future batches.

Follow these procedures:

•To start a new quantitation batch

•To start a new target screening batch

•To start a new unknown screening batch

•To start a new batch from a template

•To select a prepared batch

•To reinject samples in a previously acquired batch

•To create a quantitation batch template

•To create a target screening batch template

•To create an unknown screening batch template

To start a new quantitation batch

1. Click Create a New Batch in the navigation pane.

2. Select the Quantitation option.

3. Select the batch folder where you want to create the new batch.

4. Type a unique name for the new batch in the Batch Name box.

If the name you enter is not unique, a red warning flashes.

5. Select a method from the Method Selection list.

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The Method Compound Data pane displays the compounds in the method. You cannot

edit the compounds list from the Acquisition mode.

6. To continue to the next page, click Next.

The Sample Definition page opens. See Defining a Sample List.

To start a new target screening batch

1. Click Create a New Batch in the navigation pane.

2. Select the Target Screening option.

3. Select the batch folder where you want to create the new batch.

4. Type a name for the new batch in the Batch Name box.

If the name you enter is not unique, a red warning flashes.

5. Select a method from the Method Selection list.

The Method Compound Databases pane displays the compound databases in the

method. The application uses these databases to identify the compounds in the samples.

You cannot edit the compound database list from the Acquisition mode.

6. To continue to the next page, click Next.

The Sample Definition page opens. See Defining a Sample List.

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To start a new unknown screening batch

1. Click Create a New Batch in the navigation pane.

2. Select the Unknown Screening option.

3. Select the batch folder where you want to create the new batch.

4. Type a name for the new batch in the Batch Name box.

5. Select a method from the Method Selection list.

The Method Search Databases pane displays the databases that you selected in the

method. The application uses these databases to identify the compounds in the samples.

You cannot edit the database list from the Acquisition mode.

6. To continue to the next page, click Next.

The Sample Definition page opens. See Defining a Sample List.

To start a new batch from a template

1. Click Create a New Batch in the navigation pane.

2. Select either the Quantitation, Target Screening, or Unknown Screening option.

The Available Templates pane displays only batch templates for the selected option.

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Thermo Scientific TraceFinder User Guide 43

3. In the Available Templates pane, select the template and method combination that you

want to use.

The system creates a batch name with the selected template name and appends the date

and time stamp. You can change the batch name, the default batch folder, or the method

associated with this template.

4. (Optional) Click and select a different batch folder where you want to create the

new batch.

5. (Optional) Select a different method to use for the new batch.

6. To continue to the next page, click Next.

The Sample Definition page of the Acquisition mode opens. See Defining a Sample List.

To select a prepared batch

1. Click Submit a Prepared Batch in the navigation pane.

The application displays all your unacquired, saved batches. The application stores all

unacquired batches in the …\TraceFinderData\4.0\Projects\… folder.

2. Select the batch that you want to acquire.

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3. To continue to the next page, click Next.

The Finish page of the Acquisition mode opens. From the Finish page, you can save the

batch, submit the batch for acquisition, or go to the Sample Definition page to edit the

sample list for this batch.

• If the batch is unreadable, the application reports that the batch file is not valid and

cannot be opened.

• If a sample in the batch is unreadable, the application cannot open the sample. The

application creates a new sample with the same name and flags the sample. You must

complete the missing information such as Sample Type, Level, and so forth, and then

save the batch before you submit it for acquisition. Or, you can browse in a new raw

data file to replace the corrupt file.

4. Do one of the following:

• To edit the sample list, click Previous.

For detailed instructions, see Defining a Sample List.

–or–

• To prepare the batch for acquisition, click Submit, .

For detailed instructions, see Submitting a Batch in the Acquisition Wizard.

–or–

• To save the batch to be acquired later, click Save, .

The application saves your batch in the following folder:

…\TraceFinderData\4.0\Projects\....

The application closes the Acquisition mode and returns you to the mode you were

last using.

To reinject samples in a previously acquired batch

1. Click Reinject Samples in the navigation pane.

2. On the Batch page, select the batch that you want to reacquire.

The Batch page displays all previously acquired quantitation, target screening, and

unknown screening batches.

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Thermo Scientific TraceFinder User Guide 45

3. To continue to the next page, click Next.

The Sample Definition page of the Acquisition mode opens. See Defining a Sample List.

• If the batch is unreadable, the application reports that the batch file is not valid and

cannot be opened.

• If a sample in the batch is unreadable, the application creates a new sample with the

same name and flags the sample. You must complete the missing information, such as

Sample Type, Level, and so forth, and then save the batch before you submit it for

acquisition. Or, you can browse in a new raw data file to replace the corrupt file.

To create a quantitation batch template

1. Click Create or Edit a Template in the navigation pane.

2. Select the Quantitation option.

3. Click and select the folder where you want to create the new batch template.

4. Type a name for the new batch template in the Template Name box.

5. Select a method from the Method Selection list.

The Method Compound Data pane displays the compounds in the method. You cannot

edit the compounds list from the Acquisition mode.

6. To continue to the next page, click Next.

The Sample Definition page of the Acquisition mode opens. See Defining a Sample List.

Note When user security is activated, you must have Acquisition Wizard – Template

Editing permission to create a batch template.

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To create a target screening batch template

1. Click Create or Edit a Template in the navigation pane.

2. Select the Target Screening option.

3. Click and select the folder where you want to create the new batch template.

4. Type a name for the new batch template in the Template Name box.

5. Select a method from the Method Selection list.

The Method Compound Databases pane displays the screening databases available for the

selected method.

6. Select the check box for each database that you want to use for screening.

7. To continue to the next page, click Next.

The Sample Definition page of the Acquisition mode opens. See Defining a Sample List.

Note When user security is activated, you must have Acquisition Wizard – Template

Editing permission to create a batch template.

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Thermo Scientific TraceFinder User Guide 47

To create an unknown screening batch template

1. Click Create or Edit a Template in the navigation pane.

2. Select the Unknown Screening option.

3. Click and select the folder where you want to create the new batch template.

4. Type a name for the new batch template in the Template Name box.

5. Select a method from the Method Selection list.

The Method Compound Databases pane displays the unknown screening databases

available for the selected method.

6. Select the check box for each database that you want to use for unknown screening.

7. To continue to the next page, click Next.

The Sample Definition page of the Acquisition mode opens. See Defining a Sample List.

Note When user security is activated, you must have Acquisition Wizard – Template

Editing permission to create a batch template.

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Defining a Sample List

Use the Samples page on the Sample Definition page of the Acquisition mode to create a list

of samples for the batch. You can add samples, insert samples, import a sample list, or remove

samples from the list. You can use the Reference Sample page to select a reference sample to

use as a reference peak in the Data Review.

To create the sample list, you can use either of two sets of function buttons (described in the

following graphic) or you can use commands in the shortcut menu (see the Shortcut menu

commands area of the Samples page parameters).

As you enter sample values, you can use the Copy Down and Fill Down commands to quickly

enter column values. For detailed instructions on using Copy Down and Fill Down to enter

column values, see Appendix B, “Using Copy Down and Fill Down.”

Use any of the following procedures to create a sample list. When you finish defining the list

of samples, click Next.

• When you create a batch from scratch and click Next, the Report Selection page opens.

See Selecting and Reviewing Reports.

• When you edit a prepared batch, reinject samples, create a batch from a template, or edit

a batch template and then click Next, the Finish Selection page opens. See Submitting a

Batch in the Acquisition Wizard.

Icons in the toolbar

Buttons at the bottom of the sample definition page

Add samples

Insert samples

Remove samples

Import samples

Add samples Insert samples Import samples

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Thermo Scientific TraceFinder User Guide 49

Follow these procedures:

•To add samples to the list

•To insert samples into the list

•To import samples into the list

•To remove samples from the list

•To reinject a sample from a previously acquired batch

•To select channels for the batch

•To assign a specific channel to a sample

•To select a reference sample

•To add an auto sample type

•To specify different instrument methods for samples

To add samples to the list

1. Select the number of sample rows to add and then click the Add icon, or

2. Type a file name in the Filename column for each sample.

Each file name must be unique.

3. Select a sample type from the Sample Type list for each sample.

For a detailed description of each sample type, see Sample Types.

4. For each Cal Std or QC Std sample, select a level from the Level list.

The master method defines the sample levels. If there are no levels to select in the Level

list, ask a user with Method Development permission to edit the method and specify the

levels. Then return to the Acquisition mode, and begin the batch again. The application

does not save a batch when you leave the Acquisition mode.

If you have Method Development permission, do the following:

a. Return to the Method Development mode.

b. Open the method.

c. Click the Compounds tab.

d. Click the Calibration Levels tab.

e. Add the levels.

f. Save the method.

For detailed instructions, refer to Chapter 4, “Using the Method Development Mode for

Quantitation Methods,” in the TraceFinder Lab Director User Guide.

Available sample types

Matrix Blank Solvent QC Std Unknown

Cal Std

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5. (Optional) To assign samples to a group, do the following:

a. For each sample, type a group name in the Groups column.

Repeat this for each sample that you want to include in a group.

b. Create as many groups as you want.

• For quantitation experiments, after creating groups, you can choose one of the

samples as a threshold sample for the group and then compare all of the samples in

the Comparative View in Data Review.

For information about specifying a threshold sample for a group of samples, see

Threshold Samples Page for Quantitation Batches. For information about viewing

grouped samples in Data Review, see Comparative View for Quantitation Batches.

For information about Group Averages, see Group Averages.

• For unknown screening experiments, you can create a control group (specify the

group name as Control) to use for group averages in Data Review. For information

about Group Averages, see Group Averages Pane.

6. For each sample, type a vial position in the Vial Position column.

7. For each sample, type a volume in the Injection Volume column.

The minimum injection volume value allowed is 0.1 μL; the maximum injection volume

value allowed is 5000 μL.

8. (Optional) Type or edit the values for the remaining columns.

To automatically copy or fill values in these columns, see Appendix B, “Using Copy

Down and Fill Down.”

Note To assign a sample to multiple groups, separate the groups with a comma.

The application uses only the first group listed for calculating the Maximum Fold

and Group Averages.

For information about Maximum Fold analysis in unknown screening analysis,

see Cross Sample Peak List Pane.

Tip Use the Fill Down command to make entering vial positions easier.

Note When you use the scroll bar at the bottom of the sample list, the following

columns remain fixed: Status, Filename, Sample Type, Groups, Qual Processing

(quantitation) or Blank Subtraction (target screening), Level, Sample ID, and Sample

Name, while the other columns scroll right and left.

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To insert samples into the list

1. Select the sample above which you want to insert new Unknown samples.

You cannot use the Insert command to create the first sample row.

2. Select the number of samples to insert and then click the Insert icon, or

The application inserts the Unknown samples above the selected sample.

3. For each sample, type a file name in the Filename column.

Each file name must be unique.

4. For each sample, select a sample type from the Sample Type list.

5. For each Cal Std or QC Std sample, click the Level cell and select a level from the list.

The master method defines the sample levels. If there are no levels to select from the Level

list, ask a user with Method Development permission to edit the method and specify the

levels. Then return to the Acquisition mode, and begin the batch again. The application

does not save a batch when you leave the Acquisition mode.

If you have Method Development permission, follow the instructions in step 4 of the

procedure To add samples to the list.

6. (Optional) To assign samples to a group, do the following:

a. For each sample, type the group name in the Groups column.

Repeat this for each sample that you want to include in a group.

b. Create as many groups as you want.

Available sample types

Matrix Blank Solvent QC Std Unknown

Cal Std

Inserted

samples

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• For quantitation experiments, after creating groups, you can choose one of the

samples as a threshold sample for the group and then compare all of the samples in

the Comparative View in the Analysis mode.

For information about specifying a threshold sample for a group of samples, see

Threshold Samples Page for Quantitation Batches. For information about viewing

grouped samples in Data Review, see Comparative View for Quantitation Batches.

For information about Group Averages, see Group Averages.

• For unknown screening experiments, you can create a control group (specify the

group name as Control) to use for group averages in Data Review. For information

about group averages, see Group Averages Pane.

7. Type a vial position in the Vial Position column for each sample.

8. For each sample, type a volume in the Injection Volume column.

The minimum injection volume allowed is 0.1 μL; the maximum injection volume

allowed is 5000 μL.

9. (Optional) Type or edit the values for the remaining columns.

Note To assign a sample to multiple groups, separate the groups with a comma.

The application uses only the first group listed for calculating the Maximum Fold

and Group Averages.

For information about Maximum Fold analysis in unknown screening analysis,

see Cross Sample Peak List Pane.

Tip Use the Fill Down command to make entering vial positions easier.

Note When you use the scroll bar at the bottom of the sample list, the following

columns remain fixed: Status, Filename, Sample Type, Groups, Qual Processing

(quantitation) or Blank Subtraction (target screening), Level, Sample ID, and Sample

Name, while the other columns scroll right and left.

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To import samples into the list

1. Click Import, .

The Sample Import Tool dialog box opens.

Use this dialog box to import a sample list from a CSV, an XML, or an SLD file.

2. Click Browse and select a CSV, an XML, or an SLD file with the sample definitions that

you want to import.

3. From the Imported Samples Will Be list, select either Appended to the End of the List

or Inserted at the Selected Row.

4. Click Import.

The Sample Import Tool dialog box closes, and the application adds the specified samples

to the sample list.

When you import samples from an Xcalibur sequence file (.sld), the application makes

the following column name substitutions.

When you import samples from an Xcalibur sequence file (.sld), the application makes

the following sample type substitutions.

For each imported sample, the application uses the Instrument Method specified in the

local method.

Note The .csv, .xml, or .sld data format must match the TraceFinder data format.

Xcalibur column TraceFinder column

Position Vial position

Inj Vol Injection volume

Dil Factor Conversion Factor

Xcalibur sample type TraceFinder sample type

Blank Matrix Blank

QC QC Std

Std Bracket Cal Std

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5. For each Cal Std or QC Std sample, click the Level cell and select a level from the list.

The master method defines the sample levels. If there are no levels to select from the Level

list, ask a user with Method Development permission to edit the method and specify the

levels. Then return to the Acquisition mode, and begin the batch again. The application

does not save a batch when you leave the Acquisition mode.

If you have Method Development permission, follow the instructions in step 4 of the

procedure To add samples to the list.

For detailed instructions about defining calibration levels, refer to Chapter 4, “Using the

Method Development Mode for Quantitation Methods,” in the Trac eFi nd er L a b D ire c t or

User Guide.

6. Type a vial position in the Vial Position column for each sample.

7. Type a volume in the Injection Volume column for each sample.

The minimum injection volume value allowed is 0.1 μL; the maximum injection volume

value allowed is 5000 μL.

8. (Optional) Type or edit the values for the remaining columns.

9. (Optional) When using multiplexing, select a channel for each imported sample.

Imported samples default to Auto.

To remove samples from the list

1. Select the samples that you want to remove.

2. Right-click and choose Remove Selected Samples.

To reinject a sample from a previously acquired batch

1. In the sample list, select the sample to reinject.

2. Right-click and choose Reinject Selected Samples.

The application creates a copy of the selected sample and appends INJ001 to the file

name. Additional reinjections of the same sample are numbered INJ002, INJ003, and so

forth.

The application copies all parameter values from the original sample.

Tip Use the Fill Down command to make entering vial positions easier.

Note When you use the scroll bar at the bottom of the sample list, the following

columns remain fixed: Status, Filename, Sample Type, Groups, Qual Processing

(quantitation) or Blank Subtraction (target screening), Level, Sample ID, and Sample

Name, while the other columns scroll right and left.

Tip Use the CTRL or SHIFT keys to select multiple samples.

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A green status icon indicates previously acquired samples (acquired and processed), and

the sample name is grayed out. A blue status icon indicates samples created for reinjection

(not acquired).

When you submit this batch, the application acquires only the reinjection samples.

To select channels for the batch

To disable a configured channel, clear the check box for the channel in the Multiplexing

Channels area at the bottom of the page.

By default, all configured channels are selected. The configured channels are determined

by the multiplexing settings in the Configuration console. Refer to Chapter 1, “Using the

Configuration Console,” in the TraceFinder Lab Director User Guide.

Clearing a channel in the Multiplexing Channels area does not remove this channel

selection from the Channels list for each sample. When you assign a channel to a sample,

be careful not to assign a channel that is not available.

To assign a specific channel to a sample

1. Scroll to the Channel column.

All samples default to Auto.

2. Select a channel from the Channel list.

Note These features are available only when you have activated multiplexing in the

Configuration console. Refer to Chapter 1, “Using the Configuration Console,” in

the TraceFinder Lab Director User Guide.

Note The Channel column is available only when you have activated multiplexing in

the Configuration console. Refer to Chapter 1, “Using the Configuration Console,”

in the TraceFinder Lab Director User Guide.

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When you submit the batch, samples that are set to Auto run on any of the available

channels and samples that are set to a specific channel run only on that channel.

If you select a channel that is not available for this batch, the application flags the sample

sequence on the Finish page of the Acquisition mode. See the previous procedure, To

select channels for the batch.

3. If you see this error, do the following:

a. Click Previous to return to the Sample Definition page.

The incorrect sample is marked with an error flag.

b. Correct the channel selection.

To select a reference sample

1. Click the Reference Sample tab.

The Reference Sample page on the Sample Definition page opens.

You can select one reference sample to use as a reference peak in the Data Review.

2. Right-click the Reference Sample page and choose Add Reference Sample.

The Open Chromatograph Reference Sample dialog box opens.

3. Select a batch from the list.

The application displays only batches that were created using the current master method.

Note If you are using a new method, you will not see any samples here. You must

create and save a batch using the current method to see available samples in this list.

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4. Select a sample from the list of processed samples on the right.

The application displays all the processed samples in the selected batch. To use a sample

as a reference sample, the sample must have been processed with the current master

method.

5. Click Open.

The application adds the reference sample to the Reference Sample page.

6. (Optional) Enter values for Sample ID, Sample Name, Comment, and Barcode Actual.

7. (Optional) Change the Vial Position for the sample.

The application uses the peak in this sample as a reference peak in Data Review. See Reference

Peak.

To add an auto sample type

1. Click the Auto Samples tab.

The Auto Samples page opens.

2. Right-click and choose Add Auto Sample, or click the Add New Auto Sample icon,

The application adds a Solvent sample to the sample list.

You can add, insert, or remove samples from this list as you would any sample list.

3. To change the sample type to a Matrix Blank, click the Sample Type column and select

Matrix Blank from the list.

4. In the Injection Volume column for the sample, type a volume.

The minimum injection volume value allowed is 0.1 μL; the maximum injection volume

value allowed is 5000 μL.

5. In the Number of Injections column, type the number of injections available in the

designated Solvent or Matrix Blank vial.

After auto sample injections have occurred, you can return to this page to view the

number of Injections Used in each vial.

6. In the Vial Position column, type the vial position for the Solvent or Matrix Blank

sample.

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To specify different instrument methods for samples

1. Display the Instrument Method column in the sample list:

a. Right-click the sample list and choose Modify Columns.

The Modify Columns dialog box opens.

b. In the Available Columns pane, select Instrument Method.

c. Click to move the Instrument Method column to the Displayed Columns

pane.

d. Click OK.

The application displays the Instrument Method column, defaulting to the instrument

method specified in the master method.

2. Click the Instrument Method column and select an instrument method from the list.

This list contains all the available instrument methods. The application prefixes

instrument methods from external sources with “Ext:”.

You can specify a different instrument method for each sample.

Figure 7. Instrument method column

When you submit the batch, the application saves a copy of the selected instrument

methods to the following folders:

External instrument methods:

…\TraceFinderData\4.0\Projects\…\batch\Methods\method\ExternalMethods

Local instrument methods:

…\TraceFinderData\4.0\Projects\…\batch\Methods\method

Note By default, the Instrument Method column is not displayed on the Sample

Definition page. See Instrument method column.

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Samples

Use the features on the Samples page to create a list of samples for the batch.

Figure 8. Samples page on the Sample Definition page

Table 5. Samples page parameters (Sheet 1 of 2)

Parameter Definition

Previous Returns you to the previous Acquisition page.

Next Takes you to the next Acquisition page.

Status Sample is not acquired.

Sample is acquired but not processed.

Sample is acquired and processed.

Sample is currently acquiring.

Sample Controls

Add Adds the specified number of empty rows to the sample grid.

Insert Inserts the specified number of empty rows above the selected row.

Import Opens the Sample Import Tool to import samples from a CSV, an XML, or an SLD file.

Multiplexing Channels

These features are available only when you have activated multiplexing in the

Configuration console. Refer to Chapter 1, “Using the Configuration Console,” in the

TraceFinder Lab Director User Guide.

All Channels Uses all configured channels to acquire this batch.

Channel 1-nUses only the selected channels to acquire this batch.

Shortcut menu commands

Add Sample Adds a single empty row to the sample grid.

Insert Sample Inserts a single empty row to the sample grid above the selected row.

Insert Copy Sample Copies the currently selected row and inserts a copy above the row.

Reinject Selected

Samples

Creates a copy of the selected sample and appends INJ001 to the file name. Additional

reinjections of the same sample are numbered INJ002, INJ003, and so forth.

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Remove Selected

Samples

Removes selected samples from the sample grid.

Import Samples Opens the Sample Import Tool. Follow the instructions To import samples into the list.

Copy Down Copies the value in the selected row to all rows below it. For detailed instructions about

using the Copy Down command, see Appendix B, “Using Copy Down and Fill Down.”

Fill Down Enters sequential values in the column starting with the value in the selected row and

ending with the last row in the column. For detailed instructions about using the Fill

Down command, see Appendix B, “Using Copy Down and Fill Down.”

Modify Columns Opens the Modify Columns dialog box. See Column Display.

Enable/Disable Sample

Weight Calculation

Displays or hides the Sample Volume, Dilution Factor, Sample Weight, Calculation Type,

and Final Units columns.

Copy Copies the data in the selected rows or columns to the Clipboard. Use this command to

copy sample information to a text editor or spreadsheet application. You cannot paste this

data back into the Acquisition mode sample list.

Copy with Headers Copies the data in the selected rows or columns and the associated column headers to the

Clipboard. Use this command to copy sample information to a text editor or spreadsheet

application. You cannot paste this data back into the Acquisition mode sample list.

Paste Pastes a single column of copied data from a text editor or spreadsheet application, into the

selected column.

Undo Last Paste Removes the last pasted item in the Acquisition mode sample list.

Export to CSV File Opens the Save As dialog box where you can save the current sample list to a CSV file.

Edit Instrument Method Opens the Instrument Setup window where you can edit the parameters of the instrument

method.

• When you edit an external method, the application updates the method in the

…\Xcalibur\methods folder.

• When you edit an internal method, the application updates the method in the

…\TraceFinderData\4.0\Projects\project\subproject\batch\Methods\method folder.

For detailed information about editing instrument methods, refer to Chapter 3, “Using

Instrument Methods in the Method Development Mode,” in the TraceFi nde r Lab D irecto r

User Guide.

Table 5. Samples page parameters (Sheet 2 of 2)

Parameter Definition

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Column Display

The Samples page contains many columns of information. You can scroll to see all the

columns, and you can customize which ones to display and their display order.

To scroll the sample list

Use the horizontal scroll bar at the bottom of the sample list to view all the information.

When you use the scroll bar at the bottom of the sample list, the following columns

remain fixed: Status, Filename, Sample Type, Groups, Qual Processing (quantitation) or

Blank Subtraction (target screening) Level, Sample ID, and Sample Name, while the

other columns scroll right and left.

To customize the column display

1. Right-click the sample list and choose Modify Columns.

The Modify Columns dialog box opens.

2. Use the arrow buttons to move all the columns that you want displayed to the Displayed

Columns pane.

These columns appear after the Status, Filename, Sample Type, Groups, Qual Processing

(quantitation) or Blank Subtraction (target screening), Level, Sample ID, and Sample

Name columns.

3. To arrange the order of the columns, do the following:

a. In the Displayed Columns pane, select a column name.

b. Use Up or Down to move the selected column up or down in the list.

The first column in the list represents the leftmost column in the Samples page

sample list, and the last column in the list represents the rightmost column in the

Samples page sample list.

4. To change the width of a column, do the following:

a. In the Displayed Columns pane, select the column width.

b. Type a new value for the width.

5. Repeat step 4 for all columns whose widths you want to change, and click OK.

The columns in the sample list immediately reflect your changes.

Note The following columns are fixed: Status, Filename, Sample Type, Groups,

Qual Processing (quantitation) or Blank Subtraction (target screening), Level,

Sample ID, and Sample Name.

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Figure 9. Modify Columns dialog box

Table 6. Button descriptions for the Modify Columns dialog box

Button Description

Moves all columns to the Displayed Columns pane.

Moves the selected column to the Displayed Columns pane.

The following buttons apply to all columns, except for those that are fixed: Status, Filename,

Sample Type, Groups, Qual Processing (quantitation) or Blank Subtraction (target

screening), Level, Sample ID, and Sample Name.

Moves the selected column to the Available Columns pane.

Moves all columns except fixed columns.

Moves the selected column name in the Displayed Columns pane one row

up in the column order.

Moves the selected column name in the Displayed Columns pane one row

down in the column order.

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Auto Samples

Use the features on the Auto Samples Sample page to identify the Solvent or Matrix Blank

samples to use for any Auto Sample or Auto Sample and Reinject failure actions as specified

on the Intelligent Sequencing page of the method. Refer to Chapter 4, “Using the Method

Development Mode for Quantitation Methods,” in the TraceFinder Lab Director User Guide.

Each sample type that you specify for a failure action on the Intelligent Sequencing page must

be defined in the samples list on the Auto Samples page.

Figure 10. Auto Samples page on the Sample Definition page

Table 7. Auto Samples page parameters

Column Description

Sample Type The sample type for the auto sample injection as specified on the Intelligent Sequencing page of

the method—either Solvent or Matrix Blank.

Default: Solvent

Injection Volume The injection volume used for the sample acquisition as specified on the Samples page.

Valid range: 0.1 through 5000 μL

Injections Used The number of times a vial has been used. The count is cumulative across all batches.

Number of

Injections

The number of injections available in the designated Solvent or Matrix Blank vial.

Vial Position Vial position for this sample type as specified on the Samples page.

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Reference Sample

Use the features on the Reference Sample page to select a sample to use as a reference peak in

Data Review.

Figure 11. Reference Sample page on the Sample Definition page

Table 8. Reference Sample page parameters

Parameter Description

Status Sample is not acquired.

Sample is acquired but not processed.

Sample is acquired and processed.

Sample is currently acquiring.

Filename Name of the raw data file that contains the sample data.

Sample ID A user-defined, alphanumeric string that identifies a sample.

Sample Name A user-defined name that identifies a sample.

Vial Position The tray vial number used for an autosampler acquisition.

Barcode Actual A user-entered barcode for the vial.

Shortcut menu commands

Add Reference Sample Opens the Open Chromatogram Reference Sample dialog box where you can select a

reference sample.

Delete Selected Deletes the reference sample.

Copy Copies the data in the selected rows or columns to the Clipboard. Use this command to

copy sample information to a text editor or spreadsheet application. You cannot paste this

data back into the reference sample list.

Copy with Headers Copies the data in the selected rows or columns and the associated column headers to the

Clipboard. Use this command to copy sample information to a text editor or spreadsheet

application. You cannot paste this data back into the reference sample list.

Paste Pastes a single column of copied data from a text editor or spreadsheet application, into the

selected column.

Export to CSV File Opens the Save As dialog box where you can save the current sample list to a CSV file.

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Selecting and Reviewing Reports

On the Report Selection page, you can specify the types of reports that you want to create. See

Report Selection. In addition to the report type, you can specify a report description for each

of your reports.

For each report that you generate, you can create a hard-copy printout, a PDF file, a CSV file,

or an Excel file.

Use any of the following procedures to create a reports list. When you finish specifying your

report options, click Next to go to the Finish page and submit your batch. See Submitting a

Batch in the Acquisition Wizard.

The application writes the resulting output files for your reports to the following folder:

…\TraceFinderData\4.0\Projects\…\batch\Reports

Follow these procedures:

•To edit a report title

•To specify a report in print format or as a PDF, a CSV, or an Excel file

To edit a report title

Select the Report Title column and edit the default title.

The default report title is the same as the report name.

To specify a report in print format or as a PDF, a CSV, or an Excel file

1. For each type of report that you want to create, select the corresponding check box in the

Print, Create PDF, Create CSV, or Create Excel column.

2. To duplicate the output type for all reports, right-click the cell and choose Copy Down.

All check boxes in the column below the selected cell duplicate the selected or cleared

state in the selected cell. This action applies only to report types that make this output

format available.

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Report Selection

Use the features on the Report Selection page to specify the types of reports that you want to

create.

Figure 12. Report Selection page

Table 9. Report Selection page parameters

Parameter Description

Report Name The name of a report.

Report Title User-editable description to be used on a report.

Print Reports to be sent to the printer.

Create PDF Reports to be saved as PDF files.

Create CSV Reports to be exported as CSV files.

Create Excel Reports to be exported as Excel files.

Shortcut menu:

Copy Down

Copies the selected or cleared state to all subsequent reports in the column.

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Submitting a Batch in the Acquisition Wizard

On the Finish page of the Acquisition mode, you can specify a startup method, a shutdown

method, or a calibration batch. You can save the batch to be acquired later, or you can acquire

and process data and optionally create reports.

Follow these procedures:

•To specify startup or shutdown methods

•To automatically update the timed SRM information

•To specify a calibration batch

•To specify device states

•To save a batch for later acquisition or processing

•To start acquisition or processing

•To view the output files

To specify startup or shutdown methods

1. Select a method from the System Startup Method list.

The application runs this method before running the batch. No autosampler injection

takes place. This feature is not available for all instruments.

2. Select a method from the System Shutdown Method list.

The application runs this method after running the batch. This feature is not available for

all instruments.

To automatically update the timed SRM information

Select the Auto TSRM Update check box.

When you submit the batch, the application updates the TSQ method with mass

transitions, collision energy, and other appropriate data for TSRM functionality.

Note If you are working with a batch template, the only available function is Save.

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To specify a calibration batch

1. In the Calibration area, select a calibration (.calx) file from the list.

2. To add calibration data from the current batch to the selected calibration file, select the

Extend Calibration option.

To specify device states

In the System Status area, select the name of the device, right-click, and then choose a

device state.

Note You must acquire at least one batch with the current method to create a

calibration (.calx) file.

Table 10. Instrument states (Sheet 1 of 2)

Instrument state Description

Turn Device On Keeps the system in the On state when the current run finishes,

so you can begin another run without waiting. All power and

flows are maintained at operational levels.

Default: On

Turn Device Standby Keeps the system in the Standby state when the current run

finishes, so you can begin another run with only a short delay

between runs.

Some devices do not have a Standby feature. For devices with

this feature, the device enters a power-saving or

consumable-saving mode, and you can switch the device back

on in approximately 15 minutes. Depending on the

instrument, this state turns liquid flows off but maintains

heaters and other subsystems in an On state so that there is no

warm-up time required when you change from Standby to On.

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To save a batch for later acquisition or processing

From the Finish page, click Save, .

The application saves your batch as a prepared file.

To start acquisition or processing

1. Click Submit, .

The Submit Options dialog box opens.

2. To acquire (or reacquire) the submitted samples, select the Acquire Data check box.

• When all submitted samples have been previously acquired, this option is (by default)

not selected.

• When one or more submitted samples have not been acquired, this option is (by

default) selected.

3. To process the submitted samples, select the Process Data check box.

The application displays options for each type of method that the batch uses:

Quantitation, Target Screening, Unknown Screening, or a combination of methods.

Turn Device Off Keeps the system in the Off state when the current run

finishes. The Off state indicates that all power to the

instrument, which the application can control, is turned off.

This includes power to all heaters and subassemblies, but in

some cases not all subassemblies.

Some devices do not have an Off feature. For devices that do

have this feature, the device enters a power-saving or

consumable-saving mode, and you can switch the device back

on. When several runs are queued, the application uses the

system power scheme of the last submitted run.

Instrument status indicators

Green indicates that the device is turned on or is running.

Yellow indicates that the device is in standby mode or is

waiting for contact closure.

Red indicates that the device is turned off or that there is an

error with the device.

Tip You can process the data with or without performing peak detection. For

example, you might want to turn off peak detection when reprocessing samples.

Table 10. Instrument states (Sheet 2 of 2)

Instrument state Description

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4. For each method type, select the check box for the options that you want to use.

Peak Detect: Performs peak detection for all method types. You can process the data with

or without performing peak detection. For example, you might want to turn off peak

detection when reprocessing samples.

Quantitate: Performs quantitation for quantitation methods.

Identify: Performs identification for unknown screening methods.

Identify and Confirm: Performs both identification and confirmation for target

screening methods.

With RT Alignment: Performs retention time alignment for unknown screening

methods. This produces the heat map and group averages data in the Unknown Screening

View. When you select this option, the application automatically selects the Peak Detect

option.

5. (Optional) Select the Create Reports check box.

6. (Optional with multiplexing activated) Select the Priority Sequence check box.

The application acquires the priority batch on the next available channel or the assigned

channel.

7. (Optional without multiplexing activated) Select the Priority Sequence check box and

then select one of the following priority options to place the batch in the queue:

•Next Available Batch places the batch immediately after the currently acquiring

batch.

•Next Available Sample places the batch immediately after the currently acquiring

sample.

8. To specify the following optional parameters, click Show Details.

a. Select the Use check box for the device that you want to use for this acquisition.

b. Select the Start Device check box to indicate the device that will initiate

communication with the other instruments.

This is usually the autosampler.

c. Select the Start When Ready check box, which starts all instruments together when

they are all ready.

When you clear this check box, individual instruments can start at different times

and then must wait for the last instrument to be ready.

d. Select the system state after it acquires the last batch: On, Standby, or Off.

Note When you select Full Sequence Submission in the Configuration console, these

options are unavailable because the current batch and the current sample are, in effect,

the same thing.

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9. To start the selected processes, click OK.

The selected processes begin, and the application shows the real-time display at the

bottom of the current window. You can begin another batch in the Acquisition mode

while you watch the real-time display of the currently acquiring batch.

IMPORTANT When your batch uses unknown screening features, after the first

processing, you might see an error message stating that the total number of results is too

large for a single batch (more than 500 000). Return to the Processing pages for the

unknown screening features (refer to Chapter 6, “Using the Method Development Mode

for Unknown Screening Methods,” in the TraceFinder Lab Director User Guide) and make

one or more of these parameter adjustments:

• Limit the RT range.

• Shorten the signal range.

• Specify a lower value for the Number of Top Matches.

• Specify a Simple Search instead of an Exhaustive Search.

• Specify Top Peaks instead of All Peaks.

• Limit the number of search types.

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Figure 13. Submit Options dialog box

Table 11. Submit Options dialog box parameters (Sheet 1 of 3)

Parameter Description

User Name Name of the current user.

Samples Number of samples to be submitted for acquisition, upload,

processing, or reporting.

Method Types Lists the types of methods (quantitation, target screening, or unknown

screening) used in the submitted batches.

Workflow Steps to Perform

Acquire Data Submits the current batch to acquisition.

• When all submitted samples have been previously acquired, this

option is (by default) not selected.

• When one or more samples in the batch have not been acquired,

this option is (by default) selected.

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Process Data Processes the data for the current batch using any of the following

options:

Peak Detect: Performs peak detection for all method types. You can

process the data with or without performing peak detection. For

example, you might want to turn off peak detection when reprocessing

samples.

Quantitate: Performs quantitation for quantitation methods.

Identify: Performs identification for unknown screening methods.

Identify and Confirm: Performs both identification and confirmation

for target screening methods.

With RT Alignment: Performs retention time alignment for unknown

screening methods. This produces the heat map and group averages

data in the Unknown Screening View. When you select this option, the

application automatically selects the Peak Detect option.

Create Reports Creates reports for the current batch.

Submit as a Priority Sequence?

Priority Sequence With multiplexing activated, places the batch immediately after the

currently acquiring batch.

Without multiplexing activated, specifies one of the following priority

options to place the batch in the queue:

Next Available Batch: Places the batch immediately after the currently

acquiring batch.

Next Available Sample: Places the batch immediately after the

currently acquiring sample.

Note When you select Full Sequence Submission in the

Configuration console, these options are unavailable because the

current batch and the current sample are, in effect, the same thing.

Acquisition pane

Device Name Lists all configured instruments.

If the instrument that you want to use is not configured, close the

TraceFinder application, configure the instrument, and then reopen

the application. You cannot configure an instrument while the

TraceFinder application is running.

Available only when you select the Acquire Data check box.

Table 11. Submit Options dialog box parameters (Sheet 2 of 3)

Parameter Description

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To view the output files

Locate the files to view from the following directories:

The application writes saved batches to the project folder:

…\TraceFinderData\4.0\Projects\…

For each acquired sample, the application writes an RSX file to the batch Data folder:

…\TraceFinderData\4.0\Projects\…\Data

The application saves method information to the batch Methods folder:

…\TraceFinderData\4.0\Projects\…\Methods

The application writes the reports to the batch Reports folder:

…\TraceFinderData\4.0\Projects\…\batch\Reports

Use Specifies the instruments used for this acquisition.

Available only when you select the Acquire Data check box.

Start Device Specifies the instrument that initiates the communication with the

other instruments. This is usually the autosampler.

Available only when you select the Acquire Data check box.

Start When Ready Starts the specified device when all the instruments are ready to acquire

data. When this is cleared, individual instruments can start at different

times and then must wait for the last instrument to be ready.

Post-run System

State

Specifies the system state after it acquires the last batch: On (default),

Standby, or Off.

Buttons

Hide/Show

Details

Collapses or expands the acquisition details of the Submit Options

dialog box.

OK Begins the selected processes.

Cancel Closes the Submit Options dialog box without submitting any tasks.

Table 11. Submit Options dialog box parameters (Sheet 3 of 3)

Parameter Description

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Finish

Use the features on the Finish page to save the batch to be acquired later or acquire and

process data and optionally create reports.

Figure 14. Finish page

Table 12. Finish page parameters

Parameter Description

System Status The System Status pane displays the following:

• Devices used for the acquisition

• Project, subproject, and name of the batch

• Number of acquired and unacquired samples in the batch

• Number of reports to be printed and saved as PDF, CSV, or Excel files

• Local method and instrument method used for the batch

• Number of compounds in the method

System Startup Method

System Shutdown Method

The instrument methods that run before and after the batch. No autosampler injection

takes place. These features are not available for all instruments.

Auto TSRM Update Updates the TSQ method with mass transitions, collision energy, and other appropriate

data for TSRM functionality.

Calibration • Use calibration: Uses the selected calibration file to process the current data.

• Extend calibration: Adds calibration data from the current batch to the selected

calibration file.

Save Saves the current batch as a prepared batch.

Submit Opens the Submit Options dialog box.

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Real Time Status Pane

You can access the Real Time Status pane from any mode in the application.

To access the Real Time Status Pane from any mode

Click Real Time Status in the upper right corner of the TraceFinder window.

The Real Time Status pane opens at the bottom of the current view.

Figure 15. Real Time Status pane

The Real Time Status pane has four pages of information and a real-time trace pane:

•Real Time Status – Acquisition Page

•Real Time Status – Instrument Page

•Real Time Status – Queues Page

•Instrument Controls Page

•Real-Time Trace Display

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Real Time Status – Acquisition Page

Use the Acquisition page to monitor the progress as the application acquires the samples.

To display the last acquired raw data file in a qualitative browser

On the Acquisition page of the real-time status pane, right-click and choose View Last

File in Qual Explorer.

The last acquired file opens in either the FreeStyle or Qual Browser application.

Use the Start, , Stop, , or Pause, , icons

to control batches in the Acquisition queue.

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To open the Instrument Setup window

Right-click anywhere in the Acquisition page and choose Open Instrument Method

Editor.

The Thermo Instrument Setup window opens, displaying the currently running

instrument method.

For detailed information about editing instrument methods, refer to Chapter 3, “Using

Instrument Methods in the Method Development Mode,” in the Trace Finde r La b Direct o r

User Guide.

Real Time Status – Instrument Page

Use the Instrument page to monitor the currently acquiring sample.

To view the last acquired file in a qualitative browser

Right-click anywhere in the top pane of the Instrument page and choose View Last File

in Qual Explorer.

The last acquired file opens in either the FreeStyle or Qual Browser application.

Note Changes you make and save to the instrument method do not affect the

currently running batch.

When you run single sample

submission, this displays the

sample name instead of the

batch name.

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To open the Instrument Setup window

Right-click anywhere in the top pane of the Instrument page and choose Open

Instrument Method Editor.

The Thermo Instrument Setup window opens, displaying the currently running

instrument method.

For detailed information about editing instrument methods, refer to Chapter 3, “Using

Instrument Methods in the Method Development Mode,” in the Trace Finde r La b Direct o r

User Guide.

Real Time Status – Queues Page

Use the Queues page to monitor and control the Acquisition, Upload, Processing, and

Reporting queues.

•Queue-Level Commands: Pause or remove batches in any of the queues.

•Batch-Level Commands: Pause or remove entire batches or samples within batches from

any of the queues.

•Additional Commands: Open the FreeStyle application or the Instrument Setup window.

Queue-Level Commands

Use the queue-level commands to pause or remove batches in any of the queues on the

Queues page. See Queue-Level Shortcut Menu.

Follow these procedures:

•To pause all batches in a queue

•To remove a single batch from a queue

•To remove all batches in a queue

•To re m ove a l l p e n d i n g b a t c h e s

Note Changes you make and save to the instrument method do not affect the

currently running batch.

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To pause all batches in a queue

1. Select a queue (Acquisition, Upload, Processing, or Reporting).

2. Right-click and choose Pause Queue.

After the current sample is complete, the application pauses all batches and samples in the

specified queue. Only the selected queue is affected.

3. To restart a paused queue, select the queue, right-click, and choose Resume Queue.

To remove a single batch from a queue

1. Select a queue (Acquisition, Upload, Processing, or Reporting).

2. Right-click and choose Stop Active Batch.

The application confirms that you want to remove the active batch from the selected

queue. After the current sample is complete, the application removes the batch and all

pending samples from the queue. Only the selected queue is affected.

To remove all batches in a queue

1. Select a queue (Acquisition, Upload, Processing, or Reporting).

2. Right-click and choose Stop All Batches.

The application removes all batches with pending samples from the selected queue. The

current sample continues to acquire. Only the selected queue is affected.

To remove all pending batches

1. Select a queue (Acquisition, Upload, Processing, or Reporting).

2. Right-click and choose Remove Pending Batches.

The application removes all batches that contain only pending samples. Only the selected

queue is affected.

Note When multiplexing is activated, you can have as many as four samples acquiring

at once. Pausing the Acquisition queue does not affect any acquiring samples.

Note This command is available only when there are active batches in the queue.

Paused batches and batches that contain only pending samples are not “active.”

Note A pending batch is a batch in which all samples are pending. If any sample in

the batch is active, the batch is not affected by this command.

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Queue-Level Shortcut Menu

Use the commands in the shortcut menu to pause or remove batches in any of the queues on

the Queues page.

Figure 16. Queue-level shortcut menu

Batch-Level Commands

Use the batch-level commands to pause or remove entire batches or samples within batches

from any of the queues on the Queues page. See Batch-level shortcut menu.

Follow these procedures:

•To remove a single pending sample from a batch

•To remove all pending samples from a batch

•To s t op a b a t ch

•To re m ove a pe n d i n g ba t c h

Table 13. Queue-level shortcut menu commands

Command Description

Pause Queue

Resume Queue

After the current sample is complete, the application pauses the

specified queue. Only the selected queue is affected.

Returns the paused queue to active status.

Stop Active Batch Removes all pending samples from the specified queue. The active

sample is not affected.

Stop All Batches Removes all pending samples and batches from the specified

queue. The active sample is not affected.

Reactivate All Batches Returns all paused batches to active status.

Remove Pending

Batches

Removes all pending batches from the specified queue. The active

batch is not affected.

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To remove a single pending sample from a batch

1. Select a pending sample.

2. Right-click the sample and choose Remove Sample.

The application confirms that you want to remove the selected sample from the batch and

then removes the sample.

To remove all pending samples from a batch

1. Select a batch in any of the queues (Acquisition, Upload, Processing, or Reporting).

The batch must have at least one pending sample.

2. Right-click and choose Remove Pending Samples.

The application confirms that you want to remove all pending samples from the batch

and then removes the samples. If the batch includes only pending samples, the

application removes the batch from the queue.

To stop a batch

1. Select an active batch in any of the queues (Acquisition, Upload, Processing, or

Reporting).

2. Right-click and choose Stop Batch.

The application confirms that you want to remove the selected batch from the queue.

After the current sample is complete, the application removes the batch and all pending

samples from the queue.

To remove a pending batch

1. Select a pending batch in any of the queues (Acquisition, Upload, Processing, or

Reporting).

Note The batch must have at least one active sample and one pending sample.

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Thermo Scientific TraceFinder User Guide 83

2. Right-click and choose Remove Pending Batch.

The application confirms that you want to remove the selected batch from the queue and

then removes the batch from the queue.

Figure 17. Batch-level shortcut menu

Additional Commands

You can open the FreeStyle application or the Instrument Setup window using additional

commands that you access from the Queues page.

To access the shortcut menu with these commands, you must click in the white space below

the list of queues. If you click on the name of or to the right of the queues, the application

displays queue-, batch-, or sample-level shortcut menus.

Note A pending batch is a batch in which all samples are pending. If any sample in

the batch is active, this command is not available.

Table 14. Batch-level shortcut menu commands

Command Description

Stop Batch After the current sample is complete, the application removes all

samples in the selected batch.

Remove Pending Batch Removes all samples from the selected pending batch.

Remove Pending

Samples

Removes all pending samples from the selected batch.

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84 TraceFinder User Guide Thermo Scientific

To view the last acquired file in a qualitative browser

Right-click below the queues list on the Queues page and choose View Last File in Qual

Explorer.

The last acquired file opens in either the FreeStyle or Qual Browser application.

To open the Instrument Setup window

Right-click below the queues list on the Queues page and choose Open Instrument

Method Editor.

The Thermo Instrument Setup window opens, displaying the currently running

instrument method.

For detailed information about editing instrument methods, refer to Chapter 3, “Using

Instrument Methods in the Method Development Mode,” in the Trace Finde r La b Direct o r

User Guide.

Instrument Controls Page

Use the Instrument Controls page to monitor the status of the instrument. The feedback you

see on the Instrument Controls page depends on the instrument you are using. The following

examples show an Accela™ autosampler and an Aria™ multiplexing device.

Note Changes you make and save to the instrument method do not affect the

currently running batch.

Right-click below the

list of queues.

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Thermo Scientific TraceFinder User Guide 85

Accela Autosampler Feedback

Aria Multiplexing Feedback

Follow these procedures:

•To pause the autosampler

•To control the channels

•To open the Instrument Setup window

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86 TraceFinder User Guide Thermo Scientific

•To view the pressure trace

•To access the Aria multiplexing controls

•To view the last acquired file in a qualitative browser

To pause the autosampler

1. Click Hold Autosampler.

The autosampler finishes the current autosampler step and then pauses. The autosampler

and LC pumps continue to run.

2. To restart the autosampler, click Hold Autosampler again.

To control the channels

Right-click the channel name and choose a command from the shortcut menu.

Table 15. Autosampler shortcut menu commands

Command Description

On Turns on a stopped pump and continues acquiring the sample

list assigned to that channel.

Off After the current sample is complete, the application stops

acquiring and the pump shuts down.

Standby After the current sample is complete, the application stops

acquiring. The pump continues to run.

Disable/Enable Disable: Prevents the channel from receiving samples. When

you choose Disable during a run, the application finishes the

current sample on the channel and then stops.

Enable: Allows the channel to receive samples.

When you disable a channel that is set to On, the channel is

highlighted in green and the status is READY. You can turn

the channel to Off or Standby.

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Thermo Scientific TraceFinder User Guide 87

To open the Instrument Setup window

Right-click in the header of the Instrument Controls page and choose Open Instrument

Method Editor.

The Thermo Instrument Setup window opens, displaying the currently running

instrument method.

For detailed information about editing instrument methods, refer to Chapter 3, “Using

Instrument Methods in the Method Development Mode,” in the Trace Finde r La b Direct o r

User Guide.

To view the pressure trace

1. Click the Pres tab.

The Pressure page displays a pump pressure graph for each sample in the batch. A

fluctuation or change in the pump pressure could indicate a change in the

chromatography conditions.

2. To view the pressure for a specific pump, select the Pres 1 or Pres 2 option.

By default, the pressures for all pumps are displayed.

3. To view the pressure for a specific channel, select the corresponding channel number.

By default, the pressures for all channels are displayed.

Note Changes you make and save to the instrument method do not affect the

currently running batch.

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To access the Aria multiplexing controls

Click Direct Control.

The Aria MX Direct Control window opens.

For detailed descriptions of the features in this window, refer to the Transcend Systems with

Xcalibur Software User Guide.

To view the last acquired file in a qualitative browser

Right-click in the header of the Instrument Controls page and choose View Last File in

Qual Explorer.

The last acquired file opens in either the FreeStyle or Qual Browser application.

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Thermo Scientific TraceFinder User Guide 89

Real-Time Trace Display

As each sample is acquired, the real-time chromatogram pane shows the retention time and

intensity of the TIC trace.

By default, the Real Time Status pane shows only the TIC trace as each sample is acquired. To

observe specific traces, such as the internal standard, use the RTV Display Traces function to

display multiple traces.

When you create your method, you can specify additional traces to display in the real-time

viewer and in which order the traces are displayed. The application always displays the TIC

trace in the top pane. See Real Time Status Pane.

To display multiple traces

Right-click the chromatogram pane and choose the number of traces to display.

The chromatogram pane displays real-time chromatograms for the selected number of

traces.

The TIC is always displayed at the top. When there are more traces than can fit in the

pane, you can scroll through the traces.

For each trace, the application displays the mass or precursor mass. See Real-time trace

display with multiple traces.

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Figure 18. Real-time trace display with multiple traces

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Sample Types

Thermo Scientific TraceFinder User Guide 91

Sample Types

The TraceFinder application uses the following sample types in all sample definitions and

reports.

Table 16. Sample type definitions

Sample type Definition

Matrix Blank Contains no target compounds but might contain an ISTD when you

use the internal standard quantitative analysis technique. By analyzing a

blank sample, you can confirm that there are no residual compounds in

the solvent system that can cause erroneous results.

Cal Std (Calibration standard) Contains known amounts of all target

compounds. The purpose of a standard is to measure the response of the

instrument to the target compounds so that the processing application

can generate a calibration curve for each compound.

QC Std (Quality Check standard) Contains a known amount of one or more

specific target compounds. The application places check standard

samples in the sequence so that it can test quantitative analysis results

for quality assurance purposes. After the application analyzes the QC

Std sample, it compares the measured quantity with the expected value

and an acceptability range. The quantitative analysis of a QC Std sample

is classified as passed if the difference between the observed and expected

quantities is within the user-defined tolerance. A QC Std sample is

classified as failed if the difference between the observed and expected

quantities is outside the user-defined tolerance.

Solvent Contains only solvent.

Unknown Used for quantitative analysis of samples.

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Thermo Scientific TraceFinder User Guide 93

Using the Analysis Mode for Quantitation Batches

Use the features of the Analysis mode to do the following:

• Create quantitation batches.

• Submit quantitation batches for acquisition, processing, or report generation.

• Review quantitation batches, batch data, reports, and local methods.

To access the Analysis mode

Click Analysis in the navigation pane.

The Analysis navigation pane opens.

IMPORTANT TraceFinder 4.1 uses the same data as TraceFinder 4.0. By default, the application

stores the method, project, template, and compound database data for the 4.1 release in the

TraceFinderData\4.0 folder.

Contents

•Working in the Batch View for Quantitation Batches

•Working in Data Review for Quantitation Batches

•Working in the Report View for Quantitation Batches

•Working in the Local Method View for Quantitation Batches

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Working in the Batch View for Quantitation Batches

In the Batch View, you can manually create and edit a new quantitation batch or open and

edit a previously saved batch. When you submit a batch, you can acquire and process data and

optionally create reports for the submitted samples.

The Analysis mode includes a toolbar:

Use the Toolbar or the equivalent commands in the Batch View Shortcut Menu to create the

sample list and submit samples for acquisition.

See the following topics:

•Samples Page for Quantitation Batches

•Auto Samples Page for Quantitation Batches

•Reference Sample Page for Quantitation Batches

•Threshold Samples Page for Quantitation Batches

To open the Batch View

1. Click Analysis in the navigation pane of the current mode.

2. Click Batch View.

The Batch View navigation pane opens.

Samples Page for Quantitation Batches

To open the Samples page, click Samples in the Batch View navigation pane.

For details about the Samples page, see the following topics:

•Samples Page Features

•Creating a New Quantitation Batch

•Editing a Quantitation Batch

•Submitting a Quantitation Batch

Available only when you activate Intelligent

Sequencing in the Configuration console

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Samples Page Features

The Samples page is divided into two panes:

• Samples pane

Use the Samples Pane to create a batch.

• Compound Active Status pane

Use the Compound Active Status Pane to make specific compounds active or inactive.

Samples Pane

The samples pane includes the following features:

•Column Display

•Status Indicators

•Groups

•Qual Processing

•Sample Weight Calculation

•Instrument Methods

•Toolbar

•Batch View Sample List

•Batch View Shortcut Menu

Samples pane

Compound Active Status pane

Tip To resize the panes, drag the separator that divides the panes.

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Column Display

The sample list contains many columns of information. You can scroll to see all the columns,

and you can customize which ones to display and their display order.

To scroll the sample list

Use the horizontal scroll bar at the bottom of the sample list to view all the information.

When you use the scroll bar at the bottom of the sample list, the following columns

remain fixed: Status, Filename, Sample Type, Groups, Qual Processing, Level, Sample ID,

and Sample Name, while the other columns scroll right and left.

To customize the column display

1. Right-click the sample list and choose Modify Columns.

The Modify Columns dialog box opens.

2. Use the arrow buttons to move all the columns that you want displayed to the Displayed

Columns pane.

These columns appear to the right of the sample list’s fixed columns: Status, Filename,

Sample Type, Groups, Qual Processing, Level, Sample ID, and Sample Name.

3. To arrange the order of the columns, do the following:

a. In the Displayed Columns pane, select a column name.

b. Use Up or Down to move the selected column up or down in the list.

The first column in the list represents the leftmost column in the Batch View sample

list, and the last column in the list represents the rightmost column in the Batch View

sample list.

4. To change the width of a column, do the following:

a. In the Displayed Columns pane, select the column width.

b. Type a new value for the width.

5. Repeat step 4 for all columns whose widths you want to change, and click OK.

The columns in the sample list immediately reflect your changes. The application uses

these settings for all sample lists in the Batch View.

Note The following columns are fixed: Status, Filename, Sample Type, Groups,

Qual Processing, Level, Sample ID, and Sample Name.

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Figure 19. Modify Columns dialog box

Table 17. Button descriptions for the Modify Columns dialog box

Button Description

Moves all columns to the Displayed Columns pane.

Moves the selected column to the Displayed Columns pane.

The following buttons apply to all columns, except for those that are fixed: Status, Filename,

Sample Type, Groups, Qual Processing, Level, Sample ID, and Sample Name.

Moves the selected column to the Available Columns pane.

Moves all columns except fixed columns.

Moves the selected column name in the Displayed Columns pane one row

up in the column order.

Moves the selected column name in the Displayed Columns pane one row

down in the column order.

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Status Indicators

Status indicators show the current status of each sample during the acquisition and

processing.

Sample is not acquired.

Sample is acquired but not processed.

Sample is acquired and processed.

Sample is currently acquiring.

Groups

Use the Groups feature to assign samples to a group.

To create a group

1. For each sample, type the name of a group in the Groups column.

Repeat this for each sample that you want to include in a group.

2. Create as many groups as you want.

Note To assign a sample to multiple groups, separate the groups with a comma.

Status indicators

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Qual Processing

Use the Qual Processing feature to indicate samples to be processed with the qualitative peak

processing criteria specified in the method.

The Qualitative View displays processed data for the selected samples. See Qualitative View

for Quantitation Batches.

Sample Weight Calculation

Use the sample weight features to calculate the conversion factor for a sample. The application

uses different methods to calculate the conversion factor for liquid or solid calculation types.

Liquid: SampleVolume DilutionFactor

Solid: (SampleVolume × DilutionFactor) SampleWeight

Manual: The application does not calculate the Conversion Factor. Instead, you can enter the

Conversion Factor value.

Follow these procedures:

•To display the features for calculating sample weight

•To calculate the conversion factor for a liquid sample

•To calculate the conversion factor for a solid sample

•To manually specify the conversion factor for a sample

To display the features for calculating sample weight

If the Conversion Factor, Sample Volume, Dilution Factor, Sample Weight, Calculation

Type, and Final Units columns are not visible, right-click and choose Enable Sample

Weight Calculation.

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To calculate the conversion factor for a liquid sample

1. From the Calculation Type list, select Liquid.

For a liquid sample, the Sample Weight value is not editable.

2. In the Sample Volume column, type the volume in ng/mL for your sample.

3. In the Dilution Factor column, type the value for the dilution.

For example, if you have 1000 ng/mL of a substance that is too concentrated for the mass

spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion

factor is 1000, and your sample amount is 1000.

4. In the Final Units column, type the units that you want to use for the calculated amount

in the Data Review view or in reports.

To calculate the conversion factor for a solid sample

1. From the Calculation Type list, select Solid.

2. In the Sample Weight column, type the weight in ng for your sample.

3. In the Sample Volume column, type the volume in ng/ml for your sample.

4. In the Dilution Factor column, type the value for the dilution.

For example, if you have 1000 ng/ml of a substance that is too concentrated for the mass

spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion

factor is 1000, and your sample amount is 1000.

5. In the Final Units column, type the units that you want to use for the calculated amount

in the Data Review view or in reports.

To manually specify the conversion factor for a sample

1. From the Calculation Type list, select Manual.

For a manually calculated sample, the only available columns are the Conversion Factor

and the Final Units.

2. In the Conversion Factor column, type the conversion factor to use for your sample.

3. In the Final Units column, type the units that you want to use for the calculated amount

in the Data Review view or in reports.

Note The application uses the following formula to calculate the Conversion Factor:

SampleVolume DilutionFactor

Note The application uses the following formula to calculate the Conversion Factor:

(SampleVolume × DilutionFactor) SampleWeight

Note The application uses the specified conversion factor when it calculates the

amount for the sample.

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Instrument Methods

Use the Instrument Methods column to specify instrument methods for the samples.

To specify instrument methods for samples

1. Display the Instrument Method column in the sample list:

a. Right-click the sample list and choose Modify Columns.

The Modify Columns dialog box opens.

b. In the Available Columns pane, select Instrument Method.

c. Click to move the Instrument Method column to the Displayed Columns

pane.

d. Click OK.

The application displays the Instrument Method column, defaulting to the instrument

method specified in the master method.

2. Click the Instrument Method column and select an instrument method from the list.

This list contains all the available instrument methods. Instrument methods from

external sources are prefixed with “Ext:”.

You can specify a different instrument method for each sample.

When you submit the batch for acquisition, the application saves a copy of the selected

instrument methods to the following folders:

External instrument methods:

…\TraceFinderData\4.0\Projects\…\batch\Methods\method\ExternalMethods

Local instrument methods:

…\TraceFinderData\4.0\Projects\…\batch\Methods\method

Note By default, the Instrument Method column is not displayed in the Batch View

sample list.

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Toolbar

The Analysis mode includes this toolbar for creating and submitting a batch.

Table 18. Toolbar icons

Icon Description

Adds the specified number of new, empty samples to the end of the

sample list. See the instructions To add samples to the list.

Inserts a new, empty sample or samples above the selected sample. See

the instructions To insert samples into the list.

Removes the selected samples from the sample list. See the

instructions To remove samples from the list.

Adds imported samples from a CSV, an XML, or an SLD file to the

sample list. See the instructions To import samples into the list.

Submits only the selected samples for acquisition, processing, or

report generation. See the instructions To submit samples in the

batch.

Submits the batch for acquisition, processing, or report generation.

See the instructions To submit samples in the batch.

Submits only the selected peaks for processing. See the instructions To

submit selected peaks for processing.

Opens the Acquisition mode where you can use a batch template to

define a standard sequence composed of various sample types to be

assembled into a batch of samples. See Working in Data Review for

Quantitation Batches.

Opens the Acquisition mode where you can create a batch template

that contains the basic settings and sample types for your batches. See

Using the Acquisition Mode.

Opens the Quick Acquisition window where you can quickly submit a

single sample. See Appendix A, “Using Quick Acquisition.”

Opens the Audit Viewer where you can view audit logs. See

Chapter 8, “Using the Audit Viewer.” Available only when you enable

Auditing in the Administrator Console. Refer to the instructions in

the TraceFinder Administrator Console User Guide.

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Batch View Sample List

The sample list displays all the quantitative data for the samples of a batch.

Status indicators for each sample indicate if the sample is currently acquiring, not acquired,

acquired, or processed.

The sample list includes the following columns of information:

Figure 20. Batch View sample list

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Table 19. Batch View sample list columns (Sheet 1 of 2)

Column Description

Status Sample is not acquired.

Sample is acquired but not processed.

Sample is acquired and processed.

Sample is currently acquiring.

Note When you include unknown screening features in the quantitation method and you

choose to process with only the quantitation criteria, the Sample View shows the Status for

the samples as acquired and processed ( ), and the Unknown Screening View shows the

Status for the samples as acquired but not processed ( ).

Note When you include unknown screening features in the quantitation method and you

choose to process with only the unknown screening criteria, both the Sample View and the

Unknown Screening View show the Status for the samples as acquired and processed ( ).

Groups Threshold group to which a sample belongs. Samples can be viewed by group in the

Comparative View of Data Review.

Filename Name of the raw data file that contains the sample data.

Sample Type Defines how the application processes the sample data. Each sample is classified as one of the

following sample types: Matrix Blank, Solvent, Cal Std, QC Std, or Unknown.

Default: Unknown

Qual Processing Indicates samples to be processed with the qualitative peak processing criteria specified in the

method. The Qualitative View displays processed data for the selected samples.

Level The level defined for a calibration sample or quality control sample.

Sample ID A user-defined, alphanumeric string that identifies a sample.

Sample Name A user-defined name that identifies a sample.

Vial Position The tray vial number used for an autosampler acquisition.

Injection Volume The injection volume (in microliters) of the injected sample.

When you are using an autosampler, you can set the default injection volume in the

Autosampler dialog box in the Instrument View. The minimum and maximum injection

volumes that you can use depend on the autosampler you configure. The usable range depends

on the injection mode and might be smaller than the displayed range.

The Injection Volume value set in the master method overwrites the value in the instrument

method.

Valid range: 0.1 through 5000 μL

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Calculation Type Liquid: The application calculates the Conversion Factor as

SampleVolume DilutionFactor

Solid: The application calculates the Conversion Factor as

(SampleVolume × DilutionFactor) SampleWeight

Manual: Sample Volume, Dilution Factor, Sample Weight, and Final Units columns are not

available, and the Conversion Factor value is editable.

Conversion Factor Editable only when Calculation Type is Manual.

Default: 1

Sample Volume Default: 1

Dilution Factor Default: 1

Sample Weight Available only when Calculation Type is Solid.

Default: 1

Final Units Specifies the calculated amount in the Data Review view or in reports.

Default: 1

Instrument Method Specifies the instrument to use for the acquisition. This column is hidden by default. To display

this column, see To customize the column display.

Channel Specifies the channel on which the sample was run. If the sample is not acquired, the value is

Pending. The Channel column is available only when you have activated multiplexing in the

Configuration console. Refer to Chapter 1, “Using the Configuration Console,” in the

TraceFinder Lab Director User Guide.

Barcode Expected A user-entered barcode for the vial.

Barcode Actual An actual barcode for the vial. This value is not editable.

Comment A user-defined comment for the sample.

Table 19. Batch View sample list columns (Sheet 2 of 2)

Column Description

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Batch View Shortcut Menu

The Batch View includes a shortcut menu for creating a batch.

Table 20. Batch View shortcut menu commands (Sheet 1 of 2)

Command Description

Add Sample Adds a single empty row to the sample grid.

Insert Sample Inserts a single empty row to the sample grid above the selected

row.

Insert Copy Sample Copies the currently selected row and inserts a copy above the

row.

Reinject Selected

Samples

Creates a copy of the selected sample and appends INJ001 to the

file name. Additional reinjections of the same sample are

numbered INJ002, INJ003, and so forth.

Remove Selected

Samples

Removes selected samples from the sample grid.

Import Samples Opens the Sample Import Tool. See To import samples into the

list.

Browse in Raw File

(Move)

Opens a dialog box where you can select a raw data file to use for

the selected sample row. The application removes the raw data

file from the source location.

Browse in Raw File

(Copy)

Opens a dialog box where you can select a raw data file to use for

the selected sample row. The application copies the raw data file

from the source location.

Map Raw Files to

Samples

Opens a dialog box where you can select multiple raw data files

to use for the selected sample rows.

Copy Down Copies the value in the selected row to all rows below it. This

command is available only when you have selected a value that

can be copied down.

Fill Down Enters sequential values in the column starting with the value in

the selected row and ending with the last row in the column.

This command is available only when you have selected a value

that can be filled down.

Modify Columns Opens the Modify Columns Dialog Box.

Hide Sample Weight

Calculation

Displays or hides the Sample Volume, Dilution Factor, Sample

Weight, Calculation Type, and Final Units columns.

Copy Copies the data in the selected rows or columns to the Clipboard.

Use this command to copy sample information into a text editor

or spreadsheet application. You cannot paste this data back into

the Batch View sample list.

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Copy with Headers Copies the data in the selected rows or columns and the

associated column headers to the Clipboard. Use this command

to copy sample information into another text editor or

spreadsheet application. You cannot paste this data back into the

sample list.

For example

Paste Pastes a single column of copied data from another text editor or

spreadsheet application into the selected column.

Undo Last Paste Removes the last pasted item in the Batch View.

Export to CSV File Opens the Save As dialog box where you can save the current

sample list to a CSV file.

Edit Instrument Method Opens the Instrument Setup window where you can edit the

parameters of the instrument method.

• When you edit an external method, the application updates

the method in the …\Xcalibur\methods folder.

• When you edit an internal method, the application updates

the method in the

…\TraceFinderData\4.0\Projects\…\batch\Methods\method

folder.

For detailed information about editing instrument methods,

refer to Chapter 3, “Using Instrument Methods in the Method

Development Mode,” in the TraceFinder Lab Director User

Guide.

View Sample in Qual

Explorer

Displays the selected sample in the qualitative explorer

application that you configured as your default in the

Configuration console. Refer to Chapter 1, “Using the

Configuration Console,” in the Tra ceFin der L ab D irector Use r

Guide.

Table 20. Batch View shortcut menu commands (Sheet 2 of 2)

Command Description

Copy with Headers

from TraceFinder Paste into an Excel spreadsheet.

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Compound Active Status Pane

In the Compound Active Status pane, you can choose specific compounds to be active or

inactive.

To set a compound as active or inactive

1. In the sample list, select a sample.

All compounds in the selected sample are listed in the Compound Active Status pane.

The default active/inactive status is determined by the identification settings in the local

method. For information about setting the identification parameters, refer to Chapter 4,

“Using the Method Development Mode for Quantitation Methods,” in the Tra ce Fi nder

Lab Director User Guide.

• To display compounds alphabetically, right-click and choose Sort by Compound

Name.

• To display compounds from shorter to longer retention time, right-click and choose

Sort by Retention Time.

2. Select or clear the Active check box for the compound.

To change the active/inactive status in the Data Review view, see Inactive and Excluded

Compounds.

Compound Active Status

You can specify which compounds are active or inactive in the Local Method View or the

Batch View.

Figure 21. Active and inactive compounds in the Local Method View

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For details about setting the status on the Identification page, refer to Chapter 4, “Using the

Method Development Mode for Quantitation Methods,” in the TraceFin d er L ab D irecto r Use r

Guide.

Figure 22. Active and inactive compounds in the Batch View

For details about setting the status in the Batch View, see Compound Active Status Pane.

Creating a New Quantitation Batch

In the Batch View, you can create a new batch.

Follow these procedures:

•To c re a t e a ne w b a t c h

•To add samples to the list

•To insert samples into the list

•To import samples into the list

•To remove samples from the list

•To c o py a sa m pl e

•To reinject a sample

•To edit sample values

•To browse in raw data files

•To customize the column display

To create a new batch

1. Choose File > New > Batch from the main menu.

The Create New Batch Dialog Box opens, displaying all drives that contain projects.

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2. Select a drive from the list.

3. Select the folder where you want to store your batch.

To create a new folder for the storage location, see Editing Folders for Batches.

4. Select Quan from the Type list.

The batch list displays all batches in the selected folder. The Method list displays all

methods for the quantitation type.

5. Select a master method from the Master Method list.

6. Click Create.

A new batch opens with one Unknown sample.

The batch name in the title bar indicates that you are creating a quantitation batch.

When you create a batch using a quantitation method that includes unknown screening

features, the title bar indicates that the method includes unknown screening.

To add samples to the list

1. To add a single sample row, right-click the sample list and choose Add Sample.

2. To add multiple sample rows, select the number of rows and then click the Add Sample

icon, .

The application adds the specified number of new, empty samples to the end of the

sample list.

Tip The application displays all configured and enabled repositories.

Tip To activate the Create button, you must enter a unique batch name. If the Create

button is not activated, you have entered a batch name that is already used.

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To insert samples into the list

Select the sample above which you will insert new, Unknown samples, and then do one of

the following:

• To insert a single sample row, right-click and choose Insert Sample.

• To insert multiple sample rows, select the number of rows and then click the Insert

Sample icon .

The application inserts the Unknown samples above the selected sample.

To import samples into the list

1. Choose Batch > Import Samples from the main menu, or click the Import Samples

icon, .

The Sample Import Tool dialog box opens.

From this dialog box, you can import samples from a CSV, an XML, or an SLD file.

2. Click Browse and select a CSV, an XML, or an SLD file that contains the samples to

import.

3. From the Imported Samples Will Be list, select Appended to the End of the List or

Inserted at the Selected Row.

4. Click Import.

The Sample Import Tool dialog box closes, and the application adds the specified samples

to the sample list.

Inserted samples

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When you import samples from an Xcalibur sequence file (.sld), the application makes

the following column name substitutions.

When you import samples from an Xcalibur sequence file (.sld), the application makes

the following sample type substitutions.

5. (Optional) When using multiplexing, select a channel for each imported sample.

Imported samples default to Auto.

To remove samples from the list

1. Select the samples that you want to remove.

2. Right-click and choose Remove Selected Samples.

To copy a sample

1. Select the sample that you want to copy.

2. Right-click and choose Insert Copy Sample.

The application inserts the copy above the selected sample.

To reinject a sample

1. In the sample list, select the sample that you want to reinject.

2. Right-click and choose Reinject This Sample.

The application creates a copy of the selected sample and appends INJ001 to the file

name. Additional reinjections of the sample are numbered INJ002, INJ003, and so forth.

The application copies all parameter values from the original sample.

Xcalibur column TraceFinder column

Position Vial Position

Inj Vol Injection Volume

Dil Factor Conversion Factor

Xcalibur sample type TraceFinder sample type

Blank Matrix Blank

QC QC Std

Std Bracket Cal Std

Note The Channel column is available only when you have activated multiplexing in

the Configuration console. Refer to Chapter 1, “Using the Configuration Console,”

in the TraceFinder Lab Director User Guide.

Tip Use the CTRL or SHIFT keys to select multiple samples.

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To edit sample values

1. For each sample, do one of the following:

Type a new file name over the current filename.

–or–

Double-click the Filename column and locate a raw data file to use for the sample.

–or–

Right-click and choose Browse in Raw File, and then locate a raw data file to use for the

sample.

By default, the application sets the Sample Type to Unknown.

2. For each sample, click the Sample Type column and select a sample type from the list.

3. For each Cal Std or QC Std sample, select a level from the Level list.

The sample levels are defined in the master method. If there are no levels to select in the

Level list, do the following:

a. Return to the Method Development mode.

b. Open the method.

c. Click Compounds in the navigation pane.

d. Click the Calibration Levels tab.

e. Add the levels.

f. Save the method.

g. Return to the Batch View in the Analysis mode, and then click Update.

The application updates the local method with the new sample levels.

For detailed instructions about specifying calibration levels, refer to Chapter 4, “Using the

Method Development Mode for Quantitation Methods,” in the Trac eFi nd er L a b D ire c t or

User Guide.

4. Type a vial position in the Vial Position column for each sample.

5. Type a volume in the Injection Volume column for each sample.

The minimum injection volume value allowed is 0.1 μL; the maximum injection volume

value allowed is 5000 μL.

Available sample types

Matrix Blank Solvent QC Std Unknown

Cal Std

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6. (Optional) Type or edit the values for the remaining columns.

To automatically copy or fill values in these columns, see Appendix B, “Using Copy

Down and Fill Down.”

To browse in raw data files

1. Do one of the following:

Double-click the Filename column.

–or–

Right-click and choose Browse in Raw File.

The What Raw File Would You Like to Use dialog box opens.

2. Select a raw data file to use for the sample or use the CTRL key to select multiple files,

and then click Open.

The application overwrites the selected, unacquired sample in the batch with the first

“browsed in” file and adds any additional browsed in files below the selected sample.

For all browsed-in raw data files, the application sets the Status to Acquired, , and sets

the Sample Type to Unknown.

To customize the column display

1. Right-click the Batch View sample list and choose Modify Columns.

The Modify Columns dialog box opens.

2. Use the arrow buttons to move all the columns that you want displayed to the Displayed

Columns pane.

All the columns you select appear after the Status, Filename, Sample Type, Groups, Qual

Processing, Level, Sample ID, and Sample Name columns.

3. To arrange the order of the columns, do the following:

a. In the Displayed Columns pane, select a column name.

b. Use Up or Down to move the selected column up or down in the list.

The first column in the list represents the leftmost column in the Batch View sample

list, and the last column in the list represents the rightmost column in the Batch View

sample list.

Note When you use the scroll bar at the bottom of the sample list, the following

columns remain fixed: Status, Filename, Sample Type, Groups, Qual Processing,

Level, Sample ID, and Sample Name, while the other columns scroll right and left.

Note You cannot overwrite an acquired sample. When you select a sample that is

acquired, the application adds all browsed in files below the selected sample.

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4. To change the width of a column, do the following:

a. In the Displayed Columns pane, select the column width.

b. Type a new value for the width.

5. When you have completed your changes, click OK.

The columns in the sample list immediately reflect your changes. The application uses

these settings for all sample lists in the Batch View.

Modify Columns Dialog Box

Use the Modify Columns dialog box to select the columns that you want to display.

Figure 23. Modify Columns dialog box

Note The following columns are fixed: Status, Filename, Sample Type, Groups,

Qual Processing, Level, Sample ID, and Sample Name.

Table 21. Button descriptions for the Modify Columns dialog box (Sheet 1 of 2)

Button Description

Moves all columns to the Displayed Columns pane.

Moves the selected column to the Displayed Columns pane.

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Create New Batch Dialog Box

Use the Create New Batch dialog box to select a folder and method for your batch and to

name the new batch.

Figure 24. Create New Batch dialog box

The following buttons apply to all columns, except for those that are fixed: Status, Filename,

Sample Type, Groups, Qual Processing, Level, Sample ID, and Sample Name.

Moves the selected column to the Available Columns pane.

Moves all columns except those that are fixed.

Moves the selected column name in the Displayed Columns pane one row

up in the column order.

Moves the selected column name in the Displayed Columns pane one row

down in the column order.

Table 21. Button descriptions for the Modify Columns dialog box (Sheet 2 of 2)

Button Description

Table 22. Create New Batch dialog box parameters (Sheet 1 of 2)

Parameter Description

Create New Folder

Adds one of the following:

• When a drive is selected, adds a new project-level folder to the drive.

• When a project folder is selected, adds a subproject-level folder to the selected project.

• When a subproject folder is selected, adds a lower-level folder to the subproject.

Or, you can right-click and choose Create Folder.

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Editing Folders for Batches

From the Create New Batch dialog box, you can create new folders for your batches. You can

also delete or rename folders.

Use these procedures:

•To create new project folders

•To delete project folders

•To rename project folders

Delete Folder

With no confirmation prompt, immediately removes the selected folder.

You cannot delete a folder that contains lower-level folders; you must delete the lower-level

folders first.

Or, you can right-click and choose Delete.

Rename Folder

Renames the selected folder.

Or, you can right-click and choose Rename.

Batch table

Batch Name of batches in the selected project.

Type Type of batch: Quan, Screening, or Unknown Only.

Date Changed Date that the batch was last updated.

Samples Number of samples in the batch.

Method Name of the method used to create the batch.

Size Size of the batch in megabytes.

Domain TraceFinder domain in which the batch was created.

New batch parameters

New Batch Name of the new batch to create.

Note If the Create button is not activated, you have entered a name that is already used or

you have not selected a method.

Type Type of batch to create: Quan, Screening, or Unknown Only.

Method Method used to create the new batch.

Path Path to the project in the TraceFinderData\4.0\Projects folder where the batch is created.

Buttons

Create Creates the specified batch and opens the Batch View for the new batch.

Cancel Closes the Create New Batch dialog box without creating a batch.

Table 22. Create New Batch dialog box parameters (Sheet 2 of 2)

Parameter Description

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To create new project folders

1. In the Create New Batch dialog box, select the folder for which you will create a new

lower-level folder.

• You can select the main TraceFinderData\4.0\Projects folder and create a new folder

under it.

• You can select one of the existing folders and create a lower-level folder under it.

2. Click the Create Folder icon, .

The application adds a new lower-level folder to the selected folder.

3. Select the new folder name and type a name for the folder.

Folder names are limited to 30 characters and can contain spaces and special characters,

except for the following special characters: \ / : + ? ” < >

To delete project folders

1. In the Create New Batch dialog box, select the folder to delete.

2. Click the Delete Folder icon, .

With no confirmation prompt, the application immediately removes the selected folder.

To rename project folders

1. In the Create New Batch dialog box, select the folder to rename.

2. Click the Rename Folder icon, .

3. Type a new name for the folder and press ENTER.

The application saves the new folder name.

Editing a Quantitation Batch

In the Batch View, you can open a saved batch and edit the sample list. You can add samples,

edit samples, or remove samples. If the batch has already been acquired, you can select specific

samples for reinjection. If the batch has unacquired samples when you complete your edits,

you can save it as a “ready to acquire” batch.

Note After you add a lower-level folder, you cannot rename the parent folder.

Note You cannot delete folders that contains lower-level folders; you must delete the

lower-level folders first.

Note You cannot rename folders that contain lower-level folders.

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Follow these procedures:

•To o p e n a sa v e d b at c h

•To open a recent batch

•To edit samples in a batch

•To reinject a sample from a previously acquired batch

To open a saved batch

1. Choose File > Open > Batch from the main menu.

The Open Batch dialog box opens.

2. Select a project and a subproject.

3. Select Quan or Any from the Type list.

The batch list displays all batches created with quantitation methods (or all methods of all

types when you select Any).

4. Select a batch from the list.

5. Click Open.

The selected batch opens in the Batch View.

Open Batch Dialog Box

Use the Open Batch dialog box to select a batch to open.

Figure 25. Open Batch dialog box

Table 23. Open Batch dialog box parameters (Sheet 1 of 2)

Parameter Description

Batch Name of batches in the selected project.

Type Type of batch: Quan, Screening, or Unknown Only.

Date Changed Date the batch was last updated.

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To open a recent batch

Choose File > Recent Files > batch from the main menu.

The selected batch opens in the Batch View.

To edit samples in a batch

Use the commands described in Working in the Batch View for Quantitation Batches.

You can add new samples, edit samples, or delete samples.

To reinject a sample from a previously acquired batch

1. In the sample list, select the sample that you want to reinject.

2. Right-click and choose Reinject This Sample.

The application creates a copy of the selected sample and appends INJ001 to the file

name. Additional reinjections of the sample are numbered INJ002, INJ003, and so forth.

The application copies all parameter values from the original sample.

Samples Number of samples in the batch.

Method Name of the method used to create the batch.

Size Size of the batch in megabytes.

Domain TraceFinder domain in which the batch was created.

Path Path to the project in the TraceFinderData\4.0\Projects folder

where the batch is stored.

Buttons

Type Type of batch to display in the Batch list: Quan, Screening,

Unknown Only, or Any.

Open Opens the Batch View for the selected batch.

Cancel Closes the Open Batch dialog box without opening a batch.

Table 23. Open Batch dialog box parameters (Sheet 2 of 2)

Parameter Description

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A green status icon indicates previously acquired samples (acquired and processed), and

the sample name is grayed out. A blue status icon indicates samples created for reinjection

(not acquired).

When you submit all samples in this batch, the application acquires all samples (including

previously acquired samples).

3. To save this batch with the new samples for reinjection, choose File > Save > Batch from

the main menu.

The batch is saved as a prepared batch that is ready to submit. You can open this batch

from the Reinject Samples page in the Acquisition mode and submit the batch. The

application acquires only the samples that have not been previously acquired.

Submitting a Quantitation Batch

In the Batch View, you can submit an entire batch or only selected samples in the batch.

When you submit a batch for acquisition and processing, you can choose to create reports for

the submitted samples. See Submit Options dialog box.

For a description of commands in the shortcut menu, see Batch View shortcut menu

commands.

Follow these procedures:

•To submit selected peaks for processing

•To submit samples in the batch

•To view the output files

To submit selected peaks for processing

1. In the Peak List, select the Selected check box for the peaks that you want to process.

2. Click the Submit … for Processing icon, .

The application processes the selected peaks and updates the data in the Data Review

panes.

To submit samples in the batch

1. Do one of the following:

• To submit all samples in the batch, click the Submit Batch icon, .

• To submit specific samples, select the samples and click the Submit Selected

Samples icon, .

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The Submit Options dialog box opens.

2. To acquire (or reacquire) the submitted samples, select the Acquire Data check box.

• When all submitted samples have been previously acquired, this option is (by default)

not selected.

• When one or more samples in the batch have not been acquired, this option is (by

default) selected.

3. To process the submitted samples, select the Process Data check box.

The application displays processing options for the method.

If the quantitation method includes unknown screening features, the application also

displays unknown screening options. For specifying processing data for batches that also

use unknown screening features, see To submit samples in the batch of Chapter 6, “Using

the Analysis Mode for Unknown Screening Batches.”

4. Select the check box for the quantitation options that you want to use.

Peak Detect: Performs peak detection. You can process the data with or without

performing peak detection. For example, you might want to turn off peak detection when

reprocessing samples.

Quantitate: Performs quantitation.

5. (Optional) Select the Create Reports check box.

6. (Optional with multiplexing activated) Select the Priority Sequence check box.

The application acquires the priority batch on the next available channel or the assigned

channel.

7. (Optional without multiplexing activated) Select the Priority Sequence check box and

then select one of the following priority options to place the batch in the queue:

•Next Available Batch places the batch immediately after the currently acquiring

batch.

•Next Available Sample places the batch immediately after the currently acquiring

sample.

Note You can also submit only selected peaks for processing. See To submit selected

peaks for processing.

Tip You can process the data with or without performing peak detection. For

example, you might want to turn off peak detection when reprocessing samples.

Note When you select Full Sequence Submission in the Configuration console, these

options are unavailable because the current batch and the current sample are, in effect,

the same thing.

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8. To specify the following optional parameters, click Show Details.

a. Select the Use check box for the device that you want to use for this acquisition.

b. Select the Start Device check box to indicate the device that will initiate

communication with the other instruments.

This is usually the autosampler.

c. Select the Start When Ready check box, which starts all instruments together when

they are all ready.

When this is cleared, individual instruments can start at different times and then have

to wait for the last instrument to be ready.

d. Select the system state after it acquires the last batch: On, Standby, or Off.

9. To start the selected processes, click OK.

The selected processes begin, and the application shows the real-time display at the

bottom of the current window. You can begin another batch in the Analysis mode while

you watch the real-time display of the currently acquiring batch.

IMPORTANT When your batch also uses unknown screening features, after the first

processing, you might see an error message stating that the total number of results is too

large for a single batch (more than 500 000). Return to the Processing pages for the

unknown screening features (refer to Chapter 6, “Using the Method Development Mode

for Unknown Screening Methods,” in the TraceFinder Lab Director User Guide) and make

one or more of these parameter adjustments:

• Limit the RT range.

• Shorten the signal range.

• Specify a lower value for the Number of Top Matches.

• Specify a Simple Search instead of an Exhaustive Search.

• Specify Top Peaks instead of All Peaks.

• Limit the number of search types.

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Submit Options Dialog Box

Use the Submit Options dialog box to submit a batch for acquisition, processing, or

reporting.

Figure 26. Submit Options dialog box

Table 24. Submit Options dialog box parameters (Sheet 1 of 3)

Parameter Description

User Name Name of the current user.

Samples Number of samples to be submitted for acquisition, processing, or

reporting.

Workflow Steps to Perform

Acquire Data Submits the current batch to acquisition.

• When all submitted samples have been previously acquired, this

option is (by default) not selected.

• When one or more samples in the batch have not been

acquired, this option is (by default) selected.

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Process Data Processes the data for the current batch using any of the following

options:

Peak Detect: Performs peak detection. You can process the data

with or without performing peak detection. For example, you

might want to turn off peak detection when reprocessing samples.

Quantitate: Performs quantitation.

Note Quantitation methods can include unknown screening

features. For specifying processing data for batches that also use

unknown screening features, see To submit samples in the batch.

Create Reports Creates reports for the current batch.

Submit as a Priority Sequence?

Priority Sequence With multiplexing activated, places the batch immediately after the

currently acquiring batch.

Without multiplexing activated, specifies one of the following

priority options to place the batch in the queue:

Next Available Batch: Places the batch immediately after the

currently acquiring batch.

Next Available Sample: Places the batch immediately after the

currently acquiring sample.

Note When you select Full Sequence Submission in the

Configuration console, these options are unavailable because the

current batch and the current sample are, in effect, the same

thing.

Acquisition pane

Device Name Lists all configured instruments.

If the instrument that you want to use is not configured, close the

TraceFinder application, configure the instrument, and then reopen

the application. You cannot configure an instrument while the

TraceFinder application is running.

Available only when you select the Acquire Data check box.

Use Specifies the instruments used for this acquisition.

Available only when you select the Acquire Data check box.

Start Device Specifies the instrument that initiates the communication with the

other instruments. This is usually the autosampler.

Available only when you select the Acquire Data check box.

Table 24. Submit Options dialog box parameters (Sheet 2 of 3)

Parameter Description

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To view the output files

Locate the files to view from the following directories:

The application writes saved batches to the project folder:

…\TraceFinderData\4.0\Projects\…

For each acquired sample, the application writes an RSX file to the batch Data folder:

…\TraceFinderData\4.0\Projects\…\Data

The application saves method information to the batch Methods folder:

…\TraceFinderData\4.0\Projects\…\Methods

The application writes the reports to the batch Reports folder:

…\TraceFinderData\4.0\Projects\…\batch\Reports

Start When Ready Starts the specified device when all the instruments are ready to

acquire data. When this is cleared, individual instruments can start

at different times and then must wait for the last instrument to be

ready.

Post-run System State Specifies the system state after it acquires the last batch: On

(default), Standby, or Off.

Buttons

Hide/Show Details Collapses or expands the acquisition details of the Submit Options

dialog box.

OK Begins the selected processes.

Cancel Closes the Submit Options dialog box without submitting any

tasks.

Table 24. Submit Options dialog box parameters (Sheet 3 of 3)

Parameter Description

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Saving a Batch to a New Location

You can move the current batch to a different project folder, or you can make a copy of the

current batch and save the copy to a different project folder.

Follow these procedures:

•To save a batch to another project folder

•To move a batch to another folder

•To create a new project folder

•To delete project folders

•To rename project folders

To save a batch to another project folder

1. Choose File > Save > Save Batch As from the Batch View main menu in the Analysis

mode.

The Save Batch As Dialog Box opens.

2. Select a storage location.

The default storage location is C:\TraceFinderData\4.0\Projects.

3. Select or create a project folder.

4. Type a name for the new batch.

If you are saving the batch to a different folder, you must give it a unique name. You

cannot overwrite an existing batch in a folder.

5. Click Save.

When you save the batch to a different folder, the reports reflect the original project

folders and the application does not save the calibration history.

To move a batch to another folder

1. Choose File > Save > Move Batch from the Batch View main menu in the Analysis

mode.

The Save Batch As Dialog Box opens.

2. Select a storage location.

The default storage location is C:\TraceFinderData\4.0\Projects.

3. Select or create a project folder.

4. Type a name for the new batch.

You must give the batch a unique name in the new subproject folder. You cannot

overwrite an existing batch.

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5. Click Save.

When you move the batch, the reports reflect the original project and subproject folders

and the application does not save the calibration history.

To create a new project folder

1. In the Save Batch As dialog box, select the folder for which you will create a new

lower-level folder.

• You can select the main TraceFinderData\4.0\Projects folder and create a new folder

under it.

• You can select one of the existing folders and create a lower-level folder under it.

2. Click the Create Folder icon, .

The application adds a new lower-level folder to the selected folder.

3. Select the new folder name and type a name for the folder.

Folder names can contain spaces and special characters, except for the following special

characters: \ / : + ? ” < >

To delete project folders

1. In the Save Batch As dialog box, select the folder to delete.

2. Click the Delete Folder icon, .

With no confirmation prompt, the application immediately removes the selected folder.

To rename project folders

1. In the Save Batch As dialog box, select the folder to rename.

2. Click the Rename Folder icon, .

3. Type a new name for the folder and press ENTER.

The application saves the new folder name.

Note After you add a lower-level folder, you cannot rename the parent folder.

Note This feature is not available for folders that contain lower-level project or batch

folders; you must first delete the lower-level project or batch folders.

Note This feature is not available for folders that contain lower-level project or batch

folders; you must first delete the lower-level project or batch folders.

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Save Batch As Dialog Box

Use the features in the Save Batch As dialog box to save a batch to a new name or to move a

batch to a different project folder.

Figure 27. Save Batch As dialog box

Table 25. Save Batch As dialog box parameters (Sheet 1 of 2)

Parameter Description

Create New Folder

Adds one of the following:

• When a drive is selected, adds a new project-level folder to the drive.

• When a project folder is selected, adds a subproject-level folder to the selected project.

• When a subproject folder is selected, adds a lower-level folder to the subproject.

Or, you can right-click and choose Create Folder.

Delete Folder

With no confirmation prompt, immediately removes the selected folder.

You cannot delete a folder that contains lower-level project or batch folders; you must first

delete the lower-level project or batch folders.

Or, you can right-click and choose Delete.

Rename Folder

Renames the selected folder.

You cannot rename a folder that contains lower-level project or batch folders; you must first

delete the lower-level project or batch folders.

Or, you can right-click and choose Rename.

Batch table

Batch Name of batches in the selected project.

Type Type of batch: Quan, Screening, or Unknown Only.

Date Changed Date that the batch was last updated.

Samples Number of samples in the batch.

Method Name of the method used to create the batch.

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Size Size of the batch in megabytes.

Domain TraceFinder domain in which the batch was created.

New batch parameters

New Batch Name of the new batch to create.

Note If the Create button is not activated, you have entered a name that is already used or

you have not selected a method.

Path Path to the project in the TraceFinderData\4.0\Projects folder where the batch is created.

Buttons

Save Saves the batch to the specified name and folder and opens the Batch View for the new

batch.

Cancel Closes the Save Batch As dialog box without saving the batch.

Shortcut menu commands

Create Folder Adds one of the following:

• When a drive is selected, adds a new project-level folder to the drive.

• When a project folder is selected, adds a subproject-level folder to the selected project.

• When a subproject folder is selected, adds a lower-level folder to the subproject.

Delete Folder Immediately removes the selected folder. There is no prompt to confirm that you want to

delete the selected folder.

You cannot delete a folder that contains lower-level project or batch folders; you must first

delete the lower-level project or batch folders.

Rename Folder Renames the selected folder.

You cannot rename a folder that contains lower-level project or batch folders; you must first

delete the lower-level project or batch folders.

Expand Child Nodes Expands all project and subproject folders in the Project tree.

Collapse Child Nodes Collapses all project and subproject folders in the Project tree.

Table 25. Save Batch As dialog box parameters (Sheet 2 of 2)

Parameter Description

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Auto Samples Page for Quantitation Batches

The Auto Samples page identifies the Solvent or Matrix Blank samples to use for any Auto

Sample or Auto Sample and Reinject failure actions as specified on the Intelligent Sequencing

page of the method. Refer to Chapter 4, “Using the Method Development Mode for

Quantitation Methods,” in the TraceFinder Lab Director User Guide.

Each sample type that you specify for a failure action on the Intelligent Sequencing page must

be defined in the samples list on the Auto Samples page.

To add an auto sample type

1. Click Auto Samples in the Batch View navigation pane.

The Auto Samples page opens.

2. Right-click and choose Add Auto Sample, or in the toolbar click the Add New Auto

Sample icon, .

The application adds a Solvent sample to the sample list.

You can add, insert, or remove samples from this list as you would any sample list. See

Samples Page for Quantitation Batches.

3. To change the sample type to a Matrix Blank, click the Sample Type column and select

Matrix Blank from the list.

4. In the Injection Volume column for the sample, type a volume.

The minimum injection volume value allowed is 0.1 μL; the maximum injection volume

value allowed is 5000 μL.

5. In the Number of Injections column, type the number of injections available in the

designated Solvent or Matrix Blank vial.

After auto sample injections have occurred, you can return to this page to view the

number of Injections Used in each vial.

6. In the Vial Position column, type the vial position for the Solvent or Matrix Blank

sample.

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Auto Samples Page

Use the Auto Samples page to specify the sample types to use with Intelligent Sequencing.

Figure 28. Auto Samples page

Table 26. Auto Samples page parameters

Column Description

Sample Type The sample type for the auto sample injection as specified on the

Intelligent Sequencing page—either Solvent or Matrix Blank.

Default: Solvent

Injection Volume The injection volume used for the sample acquisition as specified on

the Samples page.

Valid range: 0.1 through 5000 μL

Injections Used The number of times a vial has been used. The count is cumulative

across all batches.

Number of

Injections

The number of injections available in the designated Solvent or Matrix

Blank vial.

Vial Position Vial position for this sample type as specified on the Samples page.

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Reference Sample Page for Quantitation Batches

The Reference Sample page displays the reference samples that you selected for this batch.

To specify a chromatogram reference sample

1. In the Batch View, click Reference Sample.

An empty reference sample table opens.

2. Click the Add Reference Sample icon, , in the toolbar, or right-click and choose

Add Reference Sample.

The Open Chromatogram Reference Sample dialog box opens.

3. Select a project from the list of projects.

4. Select a subproject from the list of subprojects.

5. Select a batch from the list of batches.

The application displays only batches that were created using the current master method.

6. Select a sample from the list of processed samples.

The application displays all the processed samples in the selected batch. Before using a

sample as a reference sample, you must have processed the sample with the current master

method.

7. Click Open.

Note If you are using a new method, no reference samples appear here. You must first

process a batch using the current method to see the reference samples in this list.

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Threshold Samples Page for Quantitation Batches

For each group in a batch, you can specify a sample in the group as the threshold sample to

use in the Comparative View.

To specify a threshold sample

1. In the Batch View, click Threshold Samples.

2. Click the Sample list for each group and select a sample in the group to be the threshold

sample.

The Comparative View uses the threshold method and amount you specified in the method,

the group you created on the Samples page, and the threshold sample you selected on this

page to define the threshold guide that it displays in the sample peak plots.

To specify the method for creating a threshold guide, refer to Chapter 4, “Using the Method

Development Mode for Quantitation Methods,” in the TraceFinder Lab Director User Guide.

For information about creating groups, see Groups.

For information about using the threshold guide in the Comparative View, see Comparative

View for Quantitation Batches.

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Working in Data Review for Quantitation Batches

In the Data Review view, you can view the data generated by the master method. Use Data

Review to verify the data for a compound before you generate reports.

Follow these procedures:

•To open the Data Review view

•To move, dock, or float Data Review panes

•To restore the default layout

To open the Data Review view

1. Click Analysis in the navigation pane.

The Analysis navigation pane opens.

2. Click Data Review.

The Data Review navigation pane opens.

Choose from a Sample View, Compound View, Comparative View, or Qualitative View to

analyze the data generated by the master method.

In addition to these views, see the following topics:

•Compound Details for Quantitation Batches

•Column Parameters for Compound Results and Sample Results

To move, dock, or float Data Review panes

Follow the instructions in Appendix C, “Moving Data Review Panes.”

To restore the default layout

Choose View > Restore Default Layout.

The Sample View, Compound View, Comparative View, and Qualitative View have their

own defaults for which panes are displayed and in which location.

Displays the Comparative View for Quantitation Batches.

Displays the Compound View for Quantitation Batches.

Displays the Sample View for Quantitation Batches.

Displays the Qualitative View for Quantitation Batches.

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Sample View for Quantitation Batches

The Sample View displays a list of all samples in the current batch and the compound results

for all compounds in the method.

To display or hide a pane on the Sample View page

From the View menu, choose to display or hide any of the following panes.

A check mark indicates a displayed pane.

The Sample View display includes the following features:

•Samples Pane

•Compound Results Pane

•Sample-centric Plot Pane

•XIC Overlay

Samples Pane

Use the Samples pane in the Sample View to select a specific sample. The associated

Compound Results Pane displays all compounds in the method and flags any compound with

errors in the selected sample.

To hide or display columns in the Samples pane

1. Click the Field Chooser icon, , in the upper left corner of the pane.

Note The Samples pane is required for the Sample View display. You cannot hide the

Samples pane.

Displays the XIC Overlay.

Displays the Sample-centric Plot Pane.

Displays the Compound Results Pane.

Displays the Compound Details for Quantitation Batches.

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The Field Chooser displays all available columns of data for the Samples pane.

2. Select the check box for each column that you want to display, or clear the check box for

each column that you want to hide.

The application immediately displays or hides the column in the Samples pane.

3. When you are finished modifying the column display, click to close the Field

Chooser.

Figure 29. Samples pane

Note The Field Chooser also lists any custom columns that you defined in the

Configuration console. Refer to Chapter 1, “Using the Configuration Console,” in

the TraceFinder Lab Director User Guide.

Table 27. Samples pane columns (Sheet 1 of 2)

Column Description

Batch Order Sequentially numbers the samples.

Comments User-defined comments for the sample.

No compound error in the selected sample

Compound error in the selected sample

Selected sample

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Excluded Turns a compound on or off in the calibration curve in the Compound

Details pane.

Filename A user-defined name that identifies a sample.

Flags Caution flag displayed when a compound in the sample has an error. See

Caution Flags.

Group Threshold group to which a sample belongs. Samples can be viewed by

group in the Comparative View of Data Review.

Level The level defined for a calibration sample or quality control sample.

Sample ID A user-defined, alphanumeric string that identifies a sample.

Sample Name A user-defined name that identifies a sample.

Sample Type Defines how the application processes the sample data. Each sample is

classified as one of the following sample types: Matrix Blank, Solvent, Cal

Std, QC Std, or Unknown.

Status Sample is not acquired.

Sample is acquired but not processed.

Sample is acquired and processed.

Sample is currently acquiring.

Note When you include unknown screening features in the

quantitation method and you choose to process with only the

quantitation criteria, the Sample View shows the Status for the samples

as acquired and processed ( ), and the Unknown Screening View shows

the Status for the samples as acquired but not processed ( ).

Note When you include unknown screening features in the quantitation

method and you choose to process with only the unknown screening

criteria, both the Sample View and the Unknown Screening View show

the Status for the samples as acquired and processed ( ).

Table 27. Samples pane columns (Sheet 2 of 2)

Column Description

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Compound Results Pane

Use the Compound Results pane in the Sample View to select a specific compound in the

selected sample. The associated Sample-centric Plot Pane highlights the selected compound.

To hide or display columns in the Compound Results pane

1. Click the Field Chooser icon, , in the upper left corner of the pane.

The Field Chooser displays all available columns of data for the Compound Results pane.

2. Select the check box for each column that you want to display, or clear the check box for

each column that you want to hide.

The application displays or hides the column in the Compound Results pane.

3. When you are finished modifying the column display, click to close the Field

Chooser.

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Figure 30. Compound Results pane

For descriptions of the column parameters in the Compound Results pane, see Common

Column Parameters.

Sample-centric Plot Pane

The Sample-centric Plot pane in the Sample View displays the chromatogram, retention time,

area, height, and signal-to-noise ratio for each compound in the Compound Results pane.

The application highlights the chromatogram for the compound that is currently selected in

the Compound Results pane.

You can use the Sample-centric Plot pane to view an overlay of the quantitation and

confirming peaks for each sample in the batch.

Follow these procedures:

•To select a sample to view

•To display details for a compound

•To change the number of rows and columns in the display

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•To change the target and confirming peaks that are displayed

•To zoom in on a peak

•To copy a plot to another format

To select a sample to view

1. In the Samples pane, select the sample that you want to view.

The Sample-centric Plot pane displays the compound chromatograms for all compounds

in the selected sample. A blue border indicates the compound in the sample that is

currently selected in the Compound Results pane.

Figure 31. Sample-centric Plot pane

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To display details for a compound

Double-click the chromatogram in the Sample-centric Plot pane.

The Compound Details pane opens.

The Compound Details pane displays information about the quantitative peak,

calibration curve, confirming ion, internal standard, reference peak, ion overlay, and

spectra for the compound.

For a detailed description of the available information in the Compound Details pane, see

Compound Details for Quantitation Batches.

To change the number of rows and columns in the display

1. Right-click and choose Display Settings.

The Batch Overview Settings dialog box opens.

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2. To change the number of rows or columns to fit in the Sample-centric Plot pane, type

new values in the Number of Columns or Number of Rows boxes.

These values do not change the number of rows (compounds) and columns (samples) that

are available in the Sample-centric Plot pane. They determine how many rows and

columns you want to view at one time in the display. The default is two rows and three

columns. Use the scroll bar to view all compound chromatograms.

3. Click OK.

To change the target and confirming peaks that are displayed

1. Right-click and choose Display Settings.

The Batch Overview Settings dialog box opens.

2. Select any of the following display options:

• First Quan Peak Only

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•Quan Peaks Overlay

• First Quan and Confirming Peaks Overlay

• All Quan and Confirming Peaks Overlay

3. Click OK.

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To zoom in on a peak

1. In any of the chromatogram cells, drag your cursor to delineate a rectangle around the

peak.

The delineated area expands to fill the chromatogram area.

2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling.

To copy a plot to another format

1. Right-click the plot that you want to copy and choose Copy to Clipboard.

The application copies the plot graphic to the Clipboard.

2. In the source format (for example, an Excel spreadsheet or email window), right-click and

choose Paste.

The application pastes the graphic into the new format.

XIC Overlay

Use the XIC Overlay pane to view specific groups of peaks. You can choose to view all peaks,

selected peaks only, or the top 20 most intense peaks (by area). The XIC Overlay plot is a

collection of overlaid, extracted m/z ion plots that use a different color for each peak.

Follow these procedures:

•To display all peaks in a sample

•To display only selected peaks in a sample

•To display the top 20 peaks in a sample

•To focus on a specific peak

To display all peaks in a sample

1. In the Samples pane, select the sample whose peaks you want to view.

2. In the XIC Overlay pane, select the All check box.

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The application displays all the peaks in the selected sample.

Figure 32. XIC Overlay pane showing all peaks

To display only selected peaks in a sample

1. In the Samples pane, select the sample whose peaks you want to view.

2. In the Compound Results pane, select the check box for each peak that you want to view.

3. In the XIC Overlay pane, choose the Selected option.

Note If there are more than 1000 peaks in the sample, performance might be slow.

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The application displays only the selected peaks.

Figure 33. XIC Overlay pane showing selected peaks

To display the top 20 peaks in a sample

1. In the Samples pane, select the sample whose peaks you want to view.

2. In the XIC Overlay pane, select the Top 20 option.

The application displays the top 20 peaks in the selected sample.

Figure 34. XIC Overlay pane showing the top 20 peaks

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To focus on a specific peak

In the XIC Overlay pane, click any displayed peak.

The application indicates the selected peak with a red, vertical marker and updates the

focus in the other Data Review panes with data for that peak.

Caution Flags

In the Sample View, the application displays caution flags in both the Samples pane and the

Compound Results pane.

See the following topics:

•Flags in the Samples Pane

•Flags in the Compound Results Pane

•Error Indicators in the Sample-centric Plot Pane

Flags in the Samples Pane

The Flags column in the Samples pane displays a caution flag if any compound in the sample

is not in compliance with the method criteria.

Click the caution flag icon, , to display the details. Information in the pop-up box shows

the compound that is in error and describes the exact error condition.

Error condition

Compound name

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Flags in the Compound Results Pane

The Flags column in the Compound Results pane displays a flag if the compound in the

selected sample is not in compliance with the method criteria.

Hold your cursor over the flag icon, , to display details for the compound in the selected

sample.

Colored flags in the Compound Results pane have the following meaning:

Red for compounds that have violated (or are activated by) any of the values set in

the method. Refer to Chapter 4, “Using the Method Development Mode for

Quantitation Methods,” in the TraceFinder Lab Director User Guide.

Red for compounds that are outside the specified ion ratio range. See Ion ratio

failure flag.

Orange for compounds that are below the limit of quantitation (LOQ), below the

limit of detection (LOD), or between the LOD and LOQ values specified in the

method. For descriptions of these limits, refer to Chapter 4, “Using the Method

Development Mode for Quantitation Methods,” in the Trace Finde r Lab Direct o r

User Guide.

Green for “found” compounds that are over the limit of reporting (LOR) amount

specified in the method. For a description of the LOR limit, refer to Chapter 4,

“Using the Method Development Mode for Quantitation Methods,” in the

TraceFinder Lab Director User Guide.

Yellow for compounds that are equal to or below the LOR amount specified in the

method.

Yellow for compounds that are not found in Calibrator or QC sample types.

The Compound Results pane does not flag compounds that are not found in

Specimen sample types.

No flag for compounds that have no errors or where no report options are selected.

Note These criteria for flag states do not apply to Matrix Blank sample types when the

compound is an internal standard.

Error condition of the Sulfisomidine

compound in the selected sample

Selected sample

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Error Indicators in the Sample-centric Plot Pane

In the Sample-centric Plot pane, peak plots are outlined with the color of their associated

error flag. In the following example, the FENTHION peak plot is highlighted in blue to

indicate that FENTHION is the selected compound, and the Sulfisomidine peak plot is

outlined in red to indicate that the Sulfisomidine compound in the selected sample is outside

the specified ion ratio range.

Figure 35. Ion ratio failure flag

Red flag indicating ion ratio failure

Peak with ion ratio failure outlined in red

Selected peak

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Compound View for Quantitation Batches

The Compound View displays a list of all compounds available in the method, all samples in

the current batch, and the peak plots for all found compounds.

To display or hide a pane on the Compound View page

From the View menu, choose to display or hide any of the following panes.

A check mark indicates a displayed pane.

The Compound View includes the following features:

•Compounds Pane

•Sample Results Pane

•Compound-centric Plot

•Group Averages

•Retention Time Summary

•Caution Flags

Compounds Pane

Use the Compounds pane in the Compound View to select a specific compound. The Sample

Results Pane displays all samples in the batch and flags any sample that contains errors

associated with the selected compound.

To hide or display columns in the Compounds pane

1. Click the Field Chooser icon, , in the upper left corner of the pane.

Note The Compounds pane is required for the Compound View display. You cannot

hide the Compounds pane.

Displays the Compound-centric Plot.

Displays the Sample Results Pane.

Displays the Compound Details for Quantitation Batches.

Displays the Group Averages.

Displays the Retention Time Summary.

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The Field Chooser displays all available columns of data for the Compounds pane.

2. Select the check box for each column that you want to display, or clear the check box for

each column that you want to hide.

The application immediately displays or hides the column in the Compounds pane.

3. When you are finished modifying the column display, click to close the Field

Chooser.

Figure 36. Compounds pane

Table 28. Compounds pane columns

Column Description

Flags Caution flag displayed when a compound has an error in any of the samples.

Compound Compound names as identified in the library. If there is no library selected in

the method template, the compound name is identified as peak@RT.

RT Expected retention time for the compound.

Type Specified compound type: Target Compound or Internal Standard.

Selected compound No error associated with

the selected compound in

this sample

Error associated with

the selected compound

in this sample

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Sample Results Pane

Use the Sample Results pane in the Compound View to select a specific compound in a

specific sample. The Compound-centric Plot pane highlights the selected sample/compound

and displays the following information about the compound: chromatogram, retention time,

area, height, and signal-to-noise ratio.

To hide or display columns in the Sample Results pane

1. Click the Field Chooser icon, , in the upper left corner of the pane.

The Field Chooser displays all default columns of data for the Sample Results pane.

2. Select the check box for each column that you want to display, or clear the check box for

each column that you want to hide.

The application immediately displays or hides the column in the Sample Results pane.

3. When you are finished modifying the column display, click to close the Field

Chooser.

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Figure 37. Sample Results pane

Table 29. Sample Results pane columns (Sheet 1 of 2)

Column Description

Displays the selected samples in the other Data Review panes.

Flags Displays a caution flag when a compound within the sample has an error.

Flag Details Indicates the type of error:

• I: Confirming ion coelution failure or Ion ratio failure

• A: Amount error

• B: Matrix blank error

• H: Peak not found

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Compound-centric Plot Pane

The Compound-centric Plot pane in the Compound View displays the compound

chromatogram, retention time, area, height, and signal-to-noise ratio associated with the

selected compound in each of the samples in the batch. The application highlights the

compound chromatogram for the sample that is currently selected in the Sample Results pane.

Status Sample is not acquired.

Sample is acquired but not processed.

Sample is acquired and processed.

Sample is currently acquiring.

Note When you include unknown screening features in the quantitation method and you choose to

process with only the quantitation criteria, the Sample View shows the Status for the samples as

acquired and processed ( ), and the Unknown Screening View shows the Status for the samples as

acquired but not processed ( ).

Note When you include unknown screening features in the quantitation method and you choose to

process with only the unknown screening criteria, both the Sample View and the Unknown

Screening View show the Status for the samples as acquired and processed ( ).

Filename Specifies a user-defined name that identifies a sample.

Group Specifies the threshold group to which a sample belongs. Samples can be viewed by group in the

Comparative View of Data Review.

Sample Type Defines how the application processes the sample data. Each sample is classified as one of the

following sample types: Matrix Blank, Solvent, Cal Std, QC Std, or Unknown.

The remainder of the columns in the Sample Results pane are common to both the Sample View and the Compound

View displays. See Common Column Parameters.

Table 29. Sample Results pane columns (Sheet 2 of 2)

Column Description

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To display details for a compound

Double-click the chromatogram in the Compound-centric Plot pane.

The application adds the Compound Details pane to the window.

The Compound Details pane displays information about the quantitative peak, calibration

curve, confirming ion, internal standard, reference peak, ion overlay, and spectra for the

compound.

For details about the available information in the Compound Details pane, see Compound

Details for Quantitation Batches.

Compound-centric Plot

Use the Compound-centric Plot pane to view an overlay of the quantitation and confirming

peaks for each sample in the batch.

Follow these procedures:

•To select a sample to view

•To change the target and confirming peaks that are displayed

•To change the number of rows and columns in the display

•To copy a plot to another format

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To select a sample to view

In the Compounds pane, select the compound that you want to view.

The Compound-centric Plot pane displays the compound chromatograms for the

selected compound in each sample in the batch. A blue border indicates the compound in

the sample that is currently selected in the Sample Results pane.

Figure 38. Compound-centric Plot pane

To change the number of rows and columns in the display

1. Right-click and choose Display Settings.

The Batch Overview Settings dialog box opens.

2. To change the number of rows or columns to fit in the Compound-centric Plot pane,

type new values in the Number of Columns or Number of Rows boxes.

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These values do not change the number of rows (compounds) and columns (samples) that

are available in the Compound-centric Plot pane. They determine how many rows and

columns you want to view at one time in the display. The default is two rows and three

columns.

3. Click OK.

To change the target and confirming peaks that are displayed

1. Right-click and choose Display Settings.

The Batch Overview Settings dialog box opens.

2. Select any of the following display options:

• First Quan Peak Only

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•Quan Peaks Overlay

• First Quan and Confirming Peaks Overlay

• All Quan and Confirming Peaks Overlay

3. Click OK.

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To zoom in on a peak

1. In any of the chromatogram cells, drag your cursor to delineate a rectangle around the

peak.

The delineated area expands to fill the chromatogram area.

2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling.

To copy a plot to another format

1. Right-click the plot that you want to copy and choose Copy to Clipboard.

The application copies the plot graphic to the Clipboard.

2. In the source format (for example, an Excel spreadsheet or email window), right-click and

choose Paste.

The application pastes the graphic into the new format.

Group Averages

Use the Group Averages pane to compare the peak areas of different samples to a control

group of samples. You must have at least two groups defined, and one group must be a control

group.

The control group is displayed to the left, and other samples and groups are listed in the order

in which they appear in the Batch View. To specify a group as the control group, see Groups.

Each group displays a colored bar that indicates the average response of the group.

Figure 39. Group Averages pane

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To display areas for each sample in the batch

Hold the cursor over an indicator icon ( , ).

The application displays the area for the selected compound in each represented sample.

Retention Time Summary

Use the Retention Time Summary pane to view variations of the retention times for a

compound across all samples in a batch. The Retention Time Summary pane displays each

color-coded compound for each sample in the batch.

Figure 40. Retention Time Summary pane

End RT specified in the method

Start RT specified in the method

Deviation

Actual RT

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Caution Flags

In the Compound View, the application displays caution flags in both the Compounds pane

and in the Sample Results pane.

See the following topics:

•Flags in the Compounds Pane

•Flags in the Sample Results Pane

•Error Indicators in the Compound-centric Plot pane

Flags in the Compounds Pane

The Flags column in the Compounds pane displays a caution flag if the compound in any of

the samples is not in compliance with the method criteria.

Click the caution flag icon, , to display the details. Information in the pop-up box shows

the sample where the compound is in error and describes the exact error condition.

Flags for the Sulfisomidine compound

in each sample

Selected Sulfisomidine compound

Error condition

Sample name

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Flags in the Sample Results Pane

The Flags column in the Sample Results pane displays a flag if the selected compound in the

sample is not in compliance with the method criteria.

Hold your cursor over the flag icon, , to display the details for the selected compound in

the sample.

Colored flags in the Sample Results pane have the following meaning.

Flag Description

Green for compounds that are over the LOR amount specified in the method.

Red for compounds that have violated (or are activated by) any of the values set

in the method. Refer to Chapter 4, “Using the Method Development Mode for

Quantitation Methods,” in the TraceFinder Lab Director User Guide.

Red for compounds that are outside the specified ion ratio range. See Ion ratio

failure flag.

Orange for compounds that are not found in Cal Std or QC Std sample types.

“Not found” compounds are below the LOQ, below the LOD, or between the

LOD and LOQ values specified in the method. The Sample Results pane does

not flag compounds that are not found in Unknown sample types.

No flag for compounds that have no errors or where no report options are

selected.

Note These criteria for flag states do not apply to Matrix Blank sample types when the

compound is an internal standard.

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Error Indicators in the Compound-centric Plot pane

In the Compound-centric Plot pane, peak plots are outlined with the color of their associated

error flag. In the following example, the peak plot is highlighted in blue to indicate that

Benzo_25557 is the selected sample and outlined in red to indicate that the FENTHION

compound in the selected sample is outside the specified ion ratio range.

Figure 41. Ion ratio failure flag

Compound Details for Quantitation Batches

The Compound Details pane is identical for Sample View and Compound View. Use the

Compounds Details pane to display any of the following types of data:

•Quan Peak

•Confirming Ions

•Calibration Curve

•Ion Overlay

•ISTD

•Reference Peak

•Spectra

•Library Match

Red flag indicating ion ratio failure

Peak with ion ratio failure

Selected peak

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•Isotope

•Fragments

•Quan Peaks Overlay

•Caution Flags

To open the Compound Details pane

1. Double-click the chromatogram in the Sample-centric plot or the Compound-centric

plot.

The Compound Details pane opens.

By default, the first display pane shows the quantitative peak for the selected compound.

2. In the second pane, select the additional type of data that you want to display.

Follow these procedures to change the display of the peak data in either of the panes:

•To change the peak panes

•To zoom in on a peak

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To change the peak panes

In any of the peak panes, click to view a list of commands.

To zoom in on a peak

1. In any of the views, drag your cursor to delineate a rectangle around the peak or

spectrum.

The delineated area expands to fill the view.

2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling.

Command Description

Make All Panels

the Same Size

Evenly divides the area to make all panes the same width. This

command does not change the pane height.

Move Panel Left Moves the current pane one space to the left. This command is

not available when the current pane is the leftmost pane.

Move Panel Right Moves the current pane one space to the right. This command is

not available when the current pane is the rightmost pane.

Add a Panel Adds an empty peak pane to the display. You can display a

maximum of four peak panes.

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Quan Peak

A compound can have multiple quantitative peaks. You can switch between quantitative

peaks, but you cannot view multiple quantitative peaks at the same time. The Quan Peak

pane uses a unique shortcut menu. See Quan Peak pane shortcut menu commands.

Figure 42. Quantitative peak pane with multiple quantitative peaks

Follow these procedures to modify the quantitative peak data:

•To manually integrate a peak by swiping the peak

•To manually integrate a peak by moving the peak delimiters

•To remove a manually created peak

•To switch between Method, Manual, and User integration modes

•To customize the labels in the display

•To modify the peak detection settings

To manually integrate a peak by swiping the peak

1. Right-click anywhere in the quantitative peak pane and then choose Swipe Manual

Integration, or click the icon in the upper right corner, .

2. Click the left base of the peak that you want to identify.

3. Drag to the right base and release the mouse.

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The application places the peak delimiter tags at these locations and automatically

updates the peak values (area, height, and so forth) in the result set.

To manually integrate a peak by moving the peak delimiters

1. Hold your cursor over one of the two peak delimiter tags in the peak pane.

When the tag can be selected, the cursor changes to a crosshair-style cursor. You can zoom

in on the baseline to make it easier to select the tag.

2. Drag the peak delimiter tag to another location and automatically update the peak values

(area, height, and so forth) into the result set.

The generated reports for the data identify the manual modifications.

You can store two peak value sets (method and manual integration settings) with each

compound in each file. These settings can result in a different set of stored values. The

application originally calculates the method values based on the processing method

parameters. The manual values are a result of what you edited.

To remove a manually created peak

Right-click the pane and then choose Delete Peak, or click the icon in the upper right

corner, .

The application removes the manual integration from the selected peak.

To switch between Method, Manual, and User integration modes

Right-click the chromatogram pane and choose Integration Settings.

Initially, the method, manual, and user integration settings that are stored for a

compound and file are identical. When you switch modes, the saved result set does not

change. However, when either manual or user data are available, both the chromatogram

plots and the result set update as you switch between modes.

As you switch between modes, each pane in Data Review reflects the changes. The

generated reports for the data identify the manual or user modifications.

Manually added right

and left base points

Crosshair cursor

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To customize the labels in the display

1. Right-click and choose Peak Display Settings.

The Peak Display Settings dialog box opens.

2. To display labels for the peak retention time (RT), area (AA), height (AH), or

signal-to-noise (SN), select the appropriate check box.

3. Click OK in the Peak Display Settings dialog box.

Figure 43. Example of displayed labels

To modify the peak detection settings

1. Right-click the chromatogram view and choose one of the following:

•Peak Detection Settings > Edit Local Method Peak Detection Settings: Makes

changes to the selected compound for all samples in this batch. The application

identifies these settings as “Manual.”

•Peak Detection Settings > Edit User Peak Detection Settings: Makes changes to

the selected compound for only the selected sample. The application saves these

changes with the batch and stops applying the local method detection settings to the

compound for this sample only. The application identifies these settings as “User.”

The Peak Detection Settings dialog box opens where you can adjust detection settings

that were specified in the method. The title bar of the dialog box lists the selected

compound and indicates whether you are making changes to only the selected sample or

to the local method.

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Figure 44. Peak Detection Settings dialog box

2. Edit any of the detection settings.

For detailed descriptions of all detection settings, refer to Chapter 4, “Using the Method

Development Mode for Quantitation Methods,” in the TraceFinder Lab Director User

Guide.

3. To save your changes to this compound, click Apply.

• When you are editing a single sample, the application makes changes to the selected

compound for this sample. If the sample is a calibration sample type, this update

changes the calibration curve which, in turn, affects all calculated amounts.

• When you are editing the local method, the application makes changes to the selected

compound for all samples in this batch.

Editing all samples in the batch

Editing only the selected sample

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Table 30. Quan Peak pane shortcut menu commands

Command Description

Reset Scaling Resets the original scaling after a zoom operation.

Copy to Clipboard Copies the graphic display to the Clipboard.

Send RT to Method Sets the current retention time as the expected retention time for the compound in the

local method.

Swipe Manual Integration Switches to manual integration mode, where you can manually define the peak.

Also available from the icon in the upper right corner, .

Integration Settings

(Method, Manual, User)

Switches the display between Method, Manual, or User integration modes.

Method (default): The settings defined in the master method.

Manual: Modifications made using the Peak Detection Settings > Edit Local Method

Peak Detection Settings command. The application applies the modified peak

detection settings to all samples in the batch.

User: Modifications made using the Peak Detection Settings > Edit User Peak

Detection Settings command. The application applies the modified peak detection

settings to only the selected sample.

Clear User Peak Detection

Settings

Resets modified peak detection settings to the settings in the master method, and

identifies the integration mode as Method.

Delete Peak Removes the peak and all data for this peak from all Compound View panes.

Also available from the icon in the upper right corner, .

Peak Display Settings Opens the Peak Display Settings dialog box.

Peak Detection Settings Edit Local Method Peak Detection Settings: Edits the peak detection settings for all

samples in the batch. The application identifies these settings as “Manual.”

Edit User Peak Detection Settings: Edits the peak detection settings for only the

selected sample. The application identifies these settings as “User.”

After you apply either of these updates, the application does not retain the modified

integration settings.

The changes that you make on the Signal page in the Peak Detection Settings dialog

box can affect all quantification and ion ratio calculations and are not auto-reversible.

These changes can also create a mismatch with calibration files that are not fully

defined in the batch.

Note The Peak Detection Settings commands are also available in the Confirming

Ions pane.

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Confirming Ions

The Confirming Ions pane displays a list of peaks, a graphical view of all

qualifying/confirming ions for the selected compound, and calculated ion ratios and ion ratio

acceptance windows. A red border indicates that an ion ratio is outside of its window. See

Quantitative peak with multiple confirming ions. The Confirming Ions pane uses a unique

shortcut menu. See Confirming Ions pane shortcut menu commands.

In the peaks list, the application displays the mass of each confirming ion peak. When a peak

is within the tolerance set, the peak status is green. When a peak is not within the tolerance

set, the peak status is red.

Follow these procedures:

•To remove a peak

•To customize the labels in the display

•To display surrounding apex times

•To manually integrate a peak

•To switch between Method, Manual, and User integration modes

To remove a peak

Right-click the Confirming Ions pane, and choose Delete Peak.

The application removes the peak displayed in the Confirming Ions pane. All data for this

peak are removed from the Compound View panes.

To customize the labels in the display

1. Right-click and choose Peak Display Settings.

The Peak Display Settings Dialog Box opens.

2. To display labels for the peak retention time (RT), mass area (MA), mass height (MH), or

signal-to-noise (SN), select the appropriate check box. See Example of displayed labels.

3. Click OK in the Peak Display Settings dialog box.

Note For compounds with an analog detection type, the application displays “No

Confirming Ions are Enabled” in the Confirming Ions pane.

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Figure 45. Example of displayed labels

To display surrounding apex times

1. Right-click and choose Peak Display Settings.

The Peak Display Settings dialog box opens.

2. Select the Show All Apex Times check box.

3. Click OK in the Peak Settings dialog box.

Figure 46. Example of displayed apex times

To manually integrate a peak

1. Right-click and then choose Swipe Manual Integration, or click the Swipe Manual

Integration icon, .

The cursor changes to indicate the manual integration mode.

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2. Drag the cursor to define the beginning and ending base points for the new peak.

The application updates the area of the peak to the baseline that you have just added.

When you regenerate the reports, they display the manually modified data.

You can store three peak value sets (method, manual, and user integration settings) with

each compound in each file. These settings can result in a different set of stored values.

The application originally calculates the method values based on the processing method

parameters. The manual or user values are a result of what you edited.

To switch between Method, Manual, and User integration modes

Right-click the Confirming Ions pane and choose Integration Settings.

Initially, the method, manual, and user integration settings that are stored for a

compound and file are identical. When you switch modes, the saved result set does not

change. However, when either manual or user data are available, both the chromatogram

plots and the result set update as you switch between modes.

As you switch between modes, each pane in Data Review reflects the changes. The

generated reports for the data identify the manual or user modifications.

Note You must drag the cursor inside the x axis and y axis.

Note Because a Blank Report displays only the quantitation mass, when you manually

integrate a confirming ion, the manual integration flag in the report is displayed on

the quantitation mass.

Drag the cursor across

the peak at the base

points for the new peak.

The application identifies the peak

and indicates the manual

integration in the labels.

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Figure 47. Quantitative peak with multiple confirming ions

Figure 48. Confirming ion with coelution failure

Table 31. Confirming Ions pane shortcut menu commands (Sheet 1 of 2)

Command Description

Reset Scaling Resets the original scaling after a zoom operation.

Copy to Clipboard Copies the graphic display to the Clipboard.

Swipe Manual

Integration

Switches to manual integration mode, where you can manually

define the peak.

Also available from the icon in the upper right corner, .

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Integration Settings

(Method, Manual,

User)

Switches the display between Method, Manual, or User

integration modes.

Method (default): The settings defined in the master method.

Manual: Modifications made using the Peak Detection Settings >

Edit Local Method Peak Detection Settings command. The

application applies the modified peak detection settings to all

samples in the batch.

User: Modifications made using the Peak Detection Settings >

Edit User Peak Detection Settings command. The application

applies the modified peak detection settings to only the selected

sample.

Clear User Peak

Detection Settings

Resets modified peak detection settings to the settings in the

master method, and identifies the integration mode as Method.

Delete Peak Removes the peak and all data for this peak from all Compound

View panes.

Also available from the icon in the upper right corner, .

Peak Display Settings Opens the Peak Display Settings dialog box.

Peak Detection

Settings

Edit Local Method Peak Detection Settings: Edits the peak

detection settings for all samples in the batch. The application

identifies these settings as “Manual.”

Edit User Peak Detection Settings: Edits the peak detection

settings for only the selected sample. The application identifies

these settings as “User.”

After you apply either of these updates, the application does not

retain the modified integration settings.

The changes that you make on the Signal page in the Peak

Detection Settings dialog box can affect all quantification and ion

ratio calculations and are not auto-reversible. These changes can

also create a mismatch with calibration files that are not fully

defined in the batch.

Note The Peak Detection Settings commands are also available

in the Confirming Ions pane.

Table 31. Confirming Ions pane shortcut menu commands (Sheet 2 of 2)

Command Description

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Peak Display Settings Dialog Box

Use the features in the Peak Display Setting dialog box to change the labels in the Confirming

Ions pane display.

Figure 49. Peak Display Settings dialog box

Table 32. Peak Display Settings dialog box parameters (Sheet 1 of 2)

Command Description

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the most

intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Peak Labels

RT Displays the retention time (RT) label in the peak chromatogram

pane.

Height Displays the peak height (AH) label in the peak chromatogram pane.

Area Displays the peak area (AA) label in the peak chromatogram pane.

Signal to Noise Displays the signal-to-noise (SN) label in the peak chromatogram

pane.

Plot Header

Sample ID Displays a user-defined, alphanumeric string that identifies a sample.

Threshold Displays the peak threshold.

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m/z Displays the mass-to-charge ratio found in the spectrum for the

peak. Assumes the charge is 1.

Sample Filename Displays the name of the current, selected sample where the peak

was found.

Compound Name Displays the matched compound name found in the library or

compound database.

Filter String Displays the filter used to identify the peak. Specified in the raw data

file or the master method.

Plot Style

Point To Point Displays chromatograms in the following format:

Stick Displays chromatograms in the following format:

Chromatogram

Show All Apex Times Displays all surrounding apex times in the plot.

Table 32. Peak Display Settings dialog box parameters (Sheet 2 of 2)

Command Description

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Calibration Curve

The Calibration Curve pane displays a graphical view of the calibration curve for the selected

compound and key statistical values for evaluating the quality of the calibration. The

Calibration Curve pane uses a unique shortcut menu. See Calibration Curve pane shortcut

menu commands.

Figure 50. Quantitative peak with a calibration curve plot

To manually exclude a calibration point

In the Sample Results pane, select the Excluded check box for the sample.

You might need to use the horizontal scroll bar at the bottom of the table to scroll to the

Excluded column. See Inactive and Excluded Compounds.

When the application no longer uses a calibration point, its value appears as an empty box

in the graphical view of the calibration curve.

Excluded

calibration

point

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Table 33. Calibration Curve pane shortcut menu commands

Command Description

Standard Type Sets the standard type to External or Internal.

Calibration Curve Type Sets the calibration curve type to one of the following:

• Linear: Uses all settings with this exception: When Origin is

set to Include, all Weighting values are grayed out and

Weighting is set to Equal.

• Quadratic: Uses all settings with this exception: When

Origin is set to Include, all Weighting values are grayed out

and Weighting is set to Equal.

• Average RF: Uses no Weighting or Origin selections. All

Weighting and Origin values are grayed out. Weighting is set

to Equal, and Origin is set to Ignore.

Response Via Sets the response to Area or to Height.

Weighting Sets the weighting to equal, 1/X, 1/X^2, 1/Y, or 1/Y^2.

Origin Sets the origin to Ignore, Force, or Include.

Units Sets the units.

Done with Settings Saves the calibration curve settings.

Reset Scaling Resets the original scale in the calibration curve pane.

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Ion Overlay

The Ion Overlay pane represents an overlay of the entire ion set—target and confirming—for

the selected compound. Use this pane to graphically review the peak apex alignment and

coeluting peak profiles.

Figure 51. Target peak with a confirming ion overlay

Note For compounds with an analog detection type, the application displays “No Data”

in the Ion Overlay pane.

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ISTD

The ISTD pane displays the internal standard specified for the compound in the method.

Refer to the instructions “To specify an internal standard type for a compound” in Chapter 4,

“Using the Method Development Mode for Quantitation Methods,” in the Tra c eFind er L ab

Director User Guide.

Figure 52. Quantitative peak with an internal standard

Reference Peak

The Reference Peak pane displays the reference peak as specified in the method.

Figure 53. Quantitative peak with a reference peak

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To specify a chromatogram reference peak

1. In the Batch View task pane, click Reference Sample.

An empty reference sample table opens.

2. Right-click and choose Add Reference Sample.

The Open Chromatogram Reference Sample dialog box opens.

3. Select a project from the list of projects.

4. Select a subproject from the list of subprojects.

5. Select a batch from the list of batches.

The application displays only batches that were created using the current master method.

6. Select a sample from the list of processed samples.

The application displays all the processed samples in the selected batch. To use a sample

as a reference sample, the sample must have been processed with the current master

method.

7. Click Open.

The selected sample is displayed as the chromatogram reference sample in the Method

View in the Method Development mode.

Note If you are creating a new method, you will not see any reference samples here.

You must create and save a batch using the current method to see the reference

samples in this list.

Tip To clear the reference sample from the master method, right-click and choose

Delete Selected.

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Spectra

The Spectra pane displays a comparison of the spectra found in the data and the method

reference.

Follow these procedures:

•To zoom in on a peak

•To copy a plot to another format

•To display the MS reference

•To customize the labels in a small molecule or peptide spectrum

To zoom in on a peak

1. In the Spectra pane, drag the cursor to delineate a rectangle around the peak.

The delineated area expands to fill the view.

2. To restore the default view, right-click the Spectra pane and choose Reset Scaling.

To copy a plot to another format

1. In the data spectrum or the reference spectrum, right-click and choose Copy to

Clipboard.

The application copies the specified plot graphic to the Clipboard.

2. In the source format (for example, an Excel spreadsheet or email window), right-click and

choose Paste.

The application pastes the graphic into the new format.

To display the MS reference

Right-click the Spectra pane and choose Show MS-Reference.

The application displays or hides the reference spectrum in the Spectra pane.

Note For compounds with an analog detection type, the application displays “Not

Available” in the Spectra pane.

Note The application copies only the indicated data spectrum or the reference

spectrum. It does not copy the entire Spectra pane.

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To customize the labels in a small molecule or peptide spectrum

1. Right-click the Spectra pane and choose Display Settings.

The Spectrum Plot Display Settings dialog box opens.

2. Select the check box for each label that you want to display and click OK.

Figure 54. Quantitative peak with data and reference spectra

Additional options

for a peptide spectrum

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Library Match

The Library Match pane displays all library matches for the selected compound.

Figure 55. Library Match for the selected compound

If you have no matches for any of your compounds, make sure you have completed all of the

following:

• Installed a library.

• Selected screening libraries in the Configuration console. Refer to Chapter 1, “Using the

Configuration Console,” in the TraceFinder Lab Director User Guide.

• Enabled Library Matching in the method. Refer to Chapter 4, “Using the Method

Development Mode for Quantitation Methods,” in the TraceFinder Lab Director User

Guide.

Isotope

The Isotope pane displays all isotopes for the selected compound. The Isotope pane includes a

shortcut menu. See Isotope pane shortcut menu commands.

The isotopes pane displays isotopic pattern results for all adducts of a compound according to

the threshold and deviation parameters defined in the method.

Note When you select different samples, the current compound remains selected (as long

as that compound is found in the sample).

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To identify or confirm the presence of a compound, the resulting score percentage from

isotopic pattern matching must be higher than the specified fit threshold percentage.

• An isotope peak is not found if its intensity, relative to the monoisotopic ion’s intensity, is

more than the specified intensity deviation percentage away from the theoretical relative

intensity of the isotope ion.

• An isotope peak is found if its measured m/z is less than the specified mass deviation

amount away from its expected m/z.

To specify isotopic criteria in a method, refer to Chapter 4, “Using the Method Development

Mode for Quantitation Methods,” in the TraceFinder Lab Director User Guide.

Figure 56. Isotope pane

Table 34. Isotope pane shortcut menu commands

Command Description

Reset Scaling Resets the original scaling after a zoom operation.

Copy to Clipboard Copies the graphic display to the Clipboard.

Display Overlay Spectra

Display Stack Spectra

Overlays the two spectrum displays, or stacks the peak apex spectrum over the

simulated spectrum.

Show/Hide Noise Label Adds a noise label to each peak. Expected isotope peaks (displayed in blue) do not

display a noise label.

Show/Hide Resolution Label Adds a resolution label to each peak. Expected isotope peaks (displayed in blue) do not

display a resolution label.

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Fragments

The Fragments pane displays fragments in one of two ways:

•All Fragments

•Individual Fragments

All Fragments

The All Fragments view displays a composite of all fragments found in the peak. The

application displays the measured peak as a red line; the application displays the expected peak

as a blue line.

The application displays these headers for the All Fragments view:

Figure 57. Fragments pane with overlaid spectra for all fragments

Processing filter

File name

Minimum number

of fragments

specified in the

method

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Figure 58. Fragments pane with stacked spectra for all fragments

Individual Fragments

The individual fragments view displays the expected and measured peaks for a single

fragment.

The application displays these headers for the individual fragments view:

Minimum number of fragments specified

in the method

Expected m/z

for fragment 1

Measured m/z

for fragment 1 Delta between expected

and measured m/z

Expected ion

ratio range

Measured ion ratio

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Figure 59. Fragments pane with overlaid spectra for a single fragment

Figure 60. Fragments pane with stacked spectra for a single fragment

Intensity

threshold

specified in

the method

Intensity

threshold

specified in the

method

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Quan Peaks Overlay

The Quan Peaks Overlay page displays overlaying quantitation peaks for compounds with

multiple target peaks.

• The first target peak in the peak list appears in black in the overlay pane.

• The second target peak in the peak list appears in red in the overlay pane.

• The selected peak is bolded in the overlay pane.

Figure 61. Quan Peaks Overlay page

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Comparative View for Quantitation Batches

The Comparative View uses three panes to display a list of all compounds available in the

method, all samples in the current batch, and the sample peak plots for all compounds found

in the samples with the horizontal threshold guide.

These are the default panes and their locations:

Related Topics

•Samples Page Features

•Creating a New Batch

•Editing a Batch

•Submitting a Batch

Samples Page Features

Use the Samples page to create a batch.

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Samples Page

The Samples page includes the following features:

•Column Display

•Status Indicators

•Groups

•Sample Weight Calculation

•Instrument Methods

•Toolbar

•Batch View Sample List

•Batch View Shortcut Menu

Column Display

The sample list contains many columns of information. You can scroll to see all the columns,

and you can customize which ones to display and their display order.

To scroll the sample list

Use the horizontal scroll bar at the bottom of the sample list to view all the information.

When you use the scroll bar at the bottom of the sample list, the following columns

remain fixed: Status, Filename, Sample Type, Groups, Level, Sample ID, and Sample

Name, while the other columns scroll right and left.

To customize the column display

1. Right-click the sample list and choose Modify Columns.

The Modify Columns dialog box opens.

2. Use the arrow buttons to move all the columns that you want displayed to the Displayed

Columns pane.

These columns appear after the Status, Filename, Sample Type, Groups, Level, Sample

ID, and Sample Name columns.

3. To arrange the order of the columns, do the following:

a. In the Displayed Columns pane, select a column name.

b. Use Up or Down to move the selected column up or down in the list.

The first column in the list represents the leftmost column in the Batch View sample

list, and the last column in the list represents the rightmost column in the Batch View

sample list.

Note The following columns are fixed: Status, Filename, Sample Type, Groups,

Level, Sample ID, and Sample Name.

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4. To change the width of a column, do the following:

a. In the Displayed Columns pane, select the column width.

b. Type a new value for the width.

5. Repeat step 4 for all columns whose widths you want to change, and click OK.

The columns in the sample list immediately reflect your changes. The application uses

these settings for all sample lists in the Batch View.

Figure 113. Modify Columns dialog box

Table 58. Button descriptions for the Modify Columns dialog box

Button Description

Moves all columns to the Displayed Columns pane.

Moves the selected column to the Displayed Columns pane.

The following buttons apply to all columns, except for those that are fixed: Status, Filename,

Sample Type, Groups, Level, Sample ID, and Sample Name.

Moves the selected column to the Available Columns pane.

Moves all columns except fixed columns.

Moves the selected column name in the Displayed Columns pane one row

up in the column order.

Moves the selected column name in the Displayed Columns pane one row

down in the column order.

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Status Indicators

Status indicators show the current status of each sample during the acquisition and

processing.

Sample is not acquired.

Sample is acquired but not processed.

Sample is acquired and processed.

Sample is currently acquiring.

Groups

Use the Groups feature to assign samples to a group.

To create a group

1. For each sample, type the name of a group in the Groups column.

Repeat this for each sample that you want to include in a group.

2. Create as many groups as you want.

You can create a control group (specify the group name as Control) to use for group

averages in Data Review.

For information about group averages, see Group Averages Pane. For information about

maximum fold analysis, see Cross Sample Peak List Pane.

Status indicators

Note To assign a sample to multiple groups, separate the groups with a comma.

The application uses the first group listed for the Maximum Fold analysis and in

the Group Averages pane.

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Sample Weight Calculation

Use the sample weight features to calculate the conversion factor for a sample. The application

uses different methods to calculate the conversion factor for liquid or solid calculation types.

Liquid: SampleVolume DilutionFactor

Solid: (SampleVolume × DilutionFactor) SampleWeight

Manual: The application does not calculate the Conversion Factor. Instead, you can enter the

Conversion Factor value.

Follow these procedures:

•To display the features for calculating sample weight

•To calculate the conversion factor for a liquid sample

•To calculate the conversion factor for a solid sample

•To manually specify the conversion factor for a sample

To display the features for calculating sample weight

If the Conversion Factor, Sample Volume, Dilution Factor, Sample Weight, Calculation

Type, and Final Units columns are not visible, right-click and choose Enable Sample

Weight Calculation.

To calculate the conversion factor for a liquid sample

1. From the Calculation Type list, select Liquid.

For a liquid sample, the Sample Weight value is not editable.

2. In the Sample Volume column, type the volume in ng/mL for your sample.

3. In the Dilution Factor column, type the value for the dilution.

For example, if you have 1000 ng/mL of a substance that is too concentrated for the mass

spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion

factor is 1000, and your sample amount is 1000.

4. In the Final Units column, type the units that you want to use for the calculated amount

in the Data Review view or in reports.

Note The application uses the following formula to calculate the Conversion Factor:

SampleVolume DilutionFactor

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To calculate the conversion factor for a solid sample

1. From the Calculation Type list, select Solid.

2. In the Sample Weight column, type the weight in ng for your sample.

3. In the Sample Volume column, type the volume in ng/ml for your sample.

4. In the Dilution Factor column, type the value for the dilution.

For example, if you have 1000 ng/ml of a substance that is too concentrated for the mass

spectrometer, you can dilute it by 1000. Then your injection volume is 1, your conversion

factor is 1000, and your sample amount is 1000.

5. In the Final Units column, type the units that you want to use for the calculated amount

in the Data Review view or in reports.

To manually specify the conversion factor for a sample

1. From the Calculation Type list, select Manual.

For a manually calculated sample, the only available columns are the Conversion Factor

and the Final Units.

2. In the Conversion Factor column, type the conversion factor to use for your sample.

3. In the Final Units column, type the units that you want to use for the calculated amount

in the Data Review view or in reports.

Instrument Methods

Use the Instrument Methods column to specify instrument methods for the samples.

To specify instrument methods for samples

1. Display the Instrument Method column in the sample list:

a. Right-click the sample list and choose Modify Columns.

The Modify Columns dialog box opens.

b. In the Available Columns pane, select Instrument Method.

c. Click to move the Instrument Method column to the Displayed Columns

pane.

Note The application uses the following formula to calculate the Conversion Factor:

(SampleVolume × DilutionFactor) SampleWeight

Note The application uses the specified conversion factor when it calculates the

amount for the sample.

Note By default, the Instrument Method column is not displayed in the Batch View

sample list.

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d. Click OK.

The application displays the Instrument Method column, defaulting to the instrument

method specified in the master method.

2. Click the Instrument Method column and select an instrument method from the list.

This list contains all the available instrument methods. Instrument methods from

external sources are prefixed with “Ext:”.

You can specify a different instrument method for each sample.

When you submit the batch for acquisition, the application saves a copy of the selected

instrument methods to the following folders:

External instrument methods:

…\TraceFinderData\4.0\Projects\…\batch\Methods\method\ExternalMethods

Local instrument methods:

…\TraceFinderData\4.0\Projects\…\batch\Methods\method

Toolbar

The Analysis mode includes this toolbar for creating and submitting a batch.

Table 59. Toolbar icons (Sheet 1 of 2)

Icon Description

Adds the specified number of new, empty samples to the end of the

sample list. See the instructions To add samples to the list.

Inserts a new, empty sample or samples above the selected sample. See

the instructions To insert samples into the list.

Removes the selected samples from the sample list. See the

instructions To remove samples from the list.

Adds imported samples from a CSV, an XML, or an SLD file to the

sample list. See the instructions To import samples into the list.

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Submits only the selected samples for acquisition, processing, or

report generation. See the instructions To submit samples in the

batch.

Submits the batch for acquisition, processing, or report generation.

See the instructions To submit samples in the batch.

Submits only the selected samples for processing. See the instructions

To submit selected peaks for processing.

Opens the Acquisition mode where you can use a batch template to

define a standard sequence composed of various sample types to be

assembled into a batch of samples. See Working in Data Review for

Unknown Screening Batches.

Opens the Acquisition mode where you can create a batch template

that contains the basic settings and sample types for your batches. See

Using the Acquisition Mode.

Opens the Quick Acquisition window where you can quickly submit a

single sample. See Appendix A, “Using Quick Acquisition.”

Opens the Audit Viewer where you can view audit logs. See

Chapter 8, “Using the Audit Viewer.” Available only when you enable

Auditing in the Administrator Console. Refer to the instructions in

the TraceFinder Administrator Console User Guide.

Table 59. Toolbar icons (Sheet 2 of 2)

Icon Description

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Batch View Sample List

The sample list displays all the quantitative data for the samples of a batch. Status indicators

for each sample indicate if the sample is currently acquiring, not acquired, acquired, or

processed.

The sample list includes the following columns of information:

Figure 114. Batch View sample list

Table 60. Batch View sample list columns (Sheet 1 of 3)

Column Description

Status Sample is not acquired.

Sample is acquired but not processed.

Sample is acquired and processed.

Sample is currently acquiring.

Note When you include unknown screening features in a quantitation method and you

choose to process with only the unknown screening criteria, both the Sample View and

the Unknown Screening View show the Status for the samples as acquired and processed

().

Note When you include unknown screening features in a target screening method and

you choose to process with only the unknown screening criteria, both the Samples view

and the Unknown Screening View show the Status for the samples as acquired and

processed ( ).

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Filename Name of the raw data file that contains the sample data.

Sample Type Defines how the application processes the sample data. Each sample is classified as one of

the following sample types: Matrix Blank, Solvent, QC Std, or Unknown.

Default: Unknown

Note Unknown Screening does not use calibration sample types (Cal Std).

Groups Threshold group to which a sample belongs.

Level Not used in Unknown Screening processing.

Sample ID A user-defined, alphanumeric string that identifies a sample.

Sample Name A user-defined name that identifies a sample.

Vial Position The tray vial number used for an autosampler acquisition.

Injection Volume The injection volume (in microliters) of the injected sample.

When you are using an autosampler, you can set the default injection volume in the

Autosampler dialog box in the Instrument View. The minimum and maximum injection

volumes that you can use depend on the Autosampler you configure. The usable range

depends on the injection mode and might be smaller than the displayed range.

The Injection Volume value set in the master method overwrites the value in the instrument

method.

Valid range: 0.1 through 5000 μL

Calculation Type Liquid: The application calculates the Conversion Factor as

SampleVolume DilutionFactor

Solid: The application calculates the Conversion Factor as

(SampleVolume × DilutionFactor) SampleWeight

Manual: Sample Volume, Dilution Factor, Sample Weight, and Final Units columns are not

available, and the Conversion Factor value is editable.

Conversion Factor Editable only when Calculation Type is Manual.

Default: 1

Sample Volume Default: 1

Dilution Factor Default: 1

Sample Weight Available only when Calculation Type is Solid.

Default: 1

Table 60. Batch View sample list columns (Sheet 2 of 3)

Column Description

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Batch View Shortcut Menu

The Batch View includes a shortcut menu for creating a batch.

Final Units Specifies the calculated amount in the Data Review view or in reports.

Default: 1

Instrument Method Specifies the instrument to use for the acquisition. This column is hidden by default. To

display this column, see To customize the column display.

Channel Specifies the channel on which the sample was run. If the sample is not acquired, the value is

Pending. The Channel column is available only when you have activated multiplexing in the

Configuration console. Refer to “Multiplexing” in Chapter 1, “Using the Configuration

Console,” in the TraceFinder Lab Director User Guide.

Barcode Expected A user-entered barcode for the vial.

Barcode Actual An actual barcode for the vial. This value is not editable.

Comment A user-defined comment for the sample.

Table 60. Batch View sample list columns (Sheet 3 of 3)

Column Description

Table 61. Batch View shortcut menu commands (Sheet 1 of 2)

Command Description

Add Sample Adds a single empty row to the sample grid.

Insert Sample Inserts a single empty row to the sample grid above the selected row.

Insert Copy Sample Copies the currently selected row and inserts a copy above the row.

Reinject Selected Samples Creates a copy of the selected sample and appends INJ001 to the file name.

Additional reinjections of the same sample are numbered INJ002, INJ003, and so

forth.

Remove Selected Samples Removes selected samples from the sample grid.

Import Samples Opens the Sample Import Tool. See To import samples into the list.

Browse in Raw File (Move) Opens a dialog box where you can select a raw data file to use for the selected sample

row. The application removes the raw data file from the source location.

Browse in Raw File (Copy) Opens a dialog box where you can select a raw data file to use for the selected sample

row. The application copies the raw data file from the source location.

Map Raw Files to Samples Opens a dialog box where you can select multiple raw data files to use for the selected

sample rows.

Copy Down Copies the value in the selected row to all rows below it. This command is available

only when you have selected a value that can be copied down.

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Fill Down Enters sequential values in the column starting with the value in the selected row and

ending with the last row in the column. This command is available only when you

have selected a value that can be filled down.

Modify Columns Opens the Modify Columns dialog box.

Enable/Disable Sample

Weight Calculation

Displays or hides the Sample Volume, Dilution Factor, Sample Weight, Calculation

Type, and Final Units columns.

Copy Copies the data in the selected rows or columns to the Clipboard. Use this command

to copy sample information into a text editor or spreadsheet application. You cannot

paste this data back into the Batch View sample list.

Copy with Headers Copies the data in the selected rows or columns and the associated column headers to

the Clipboard. Use this command to copy sample information into another text

editor or spreadsheet application. You cannot paste this data back into the sample list.

For example

Paste Pastes a single column of copied data from another text editor or spreadsheet

application into the selected column.

Undo Last Paste Removes the last pasted item in the Batch View.

Export to CSV File Opens the Save As dialog box where you can save the current sample list to a CSV

file.

Edit Instrument Method Opens the Instrument Setup window where you can edit the parameters of the

instrument method.

• When you edit an external method, the application updates the method in the

…\Xcalibur\methods folder.

• When you edit an internal method, the application updates the method in the

…\TraceFinderData\4.0\Projects\…\batch\Methods\method folder.

For detailed information about editing instrument methods, refer to Chapter 3,

“Using Instrument Methods in the Method Development Mode,” in the Trace Fin de r

Lab Director User Guide.

Table 61. Batch View shortcut menu commands (Sheet 2 of 2)

Command Description

Copy with Headers

from TraceFinder Paste into an Excel spreadsheet.

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Creating a New Batch

In the Batch View, you can create a new batch.

Follow these procedures:

•To c re a t e a ne w b a t c h

•To add samples to the list

•To insert samples into the list

•To import samples into the list

•To remove samples from the list

•To c o py a sa m pl e

•To reinject a sample

•To edit sample values

•To browse in raw data files

•To customize the column display

To create a new batch

1. Choose File > New > Batch from the main menu.

The Create New Batch Dialog Box opens, displaying all drives that contain projects.

2. Select a drive from the list.

3. Select the folder where you want to store your batch.

To create a new folder for the storage location, see Editing Folders for Batches.

4. Select Unknown Only from the Type list.

The batch list displays all batches in the selected folder. The Method list displays all

methods for the unknown screening type.

5. Select a master method from the Master Method list.

Tip The application displays all configured and enabled repositories.

Tip To activate the Create button, you must enter a unique batch name. If the Create

button is not activated, you have entered a batch name that is already used.

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6. Click Create.

A new batch opens with one Unknown sample.

The batch name in the title bar indicates that you are creating an unknown screening

batch.

To add samples to the list

1. To add a single sample row, right-click the sample list and choose Add Sample.

2. To add multiple sample rows, select the number of rows and then click the Add Sample

icon, .

The application adds the specified number of new, empty samples to the end of the

sample list.

To insert samples into the list

Select the sample above which you will insert new, Unknown samples, and then do one of

the following:

• To insert a single sample row, right-click and choose Insert Sample.

• To insert multiple sample rows, select the number of rows and then click the Insert

Sample icon .

The application inserts the Unknown samples above the selected sample.

Inserted samples

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To import samples into the list

1. Choose Batch > Import Samples from the main menu, or click the Import Samples

icon, .

The Sample Import Tool dialog box opens.

From this dialog box, you can import samples from a CSV, an XML, or an SLD file.

2. Click Browse and select a CSV, an XML, or an SLD file that contains the samples to

import.

3. From the Imported Samples Will Be list, select Appended to the End of the List or

Inserted at the Selected Row.

4. Click Import.

The Sample Import Tool dialog box closes, and the application adds the specified samples

to the sample list.

When you import samples from an Xcalibur sequence file (.sld), the application makes

the following column name substitutions:

When you import samples from an Xcalibur sequence file (.sld), the application makes

the following sample type substitutions:

5. (Optional) When using multiplexing, select a channel for each imported sample.

Imported samples default to Auto.

Xcalibur column TraceFinder column

Position Vial Position

Inj Vol Injection Volume

Dil Factor Conversion Factor

Xcalibur sample type TraceFinder sample type

Blank Matrix Blank

QC QC Std

Std Bracket Cal Std

Note The Channel column is available only when you have activated multiplexing in

the Configuration console. Refer to “Multiplexing” in Chapter 1, “Using the

Configuration Console,” in the TraceFinder Lab Director User Guide.

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To remove samples from the list

1. Select the samples that you want to remove.

2. Right-click and choose Remove Selected Samples.

To copy a sample

1. Select the sample that you want to copy.

2. Right-click and choose Insert Copy Sample.

The application inserts the copy above the selected sample.

To reinject a sample

1. In the sample list, select the sample that you want to reinject.

2. Right-click and choose Reinject This Sample.

The application creates a copy of the selected sample and appends INJ001 to the file

name. Additional reinjections of the sample are numbered INJ002, INJ003, and so forth.

The application copies all parameter values from the original sample.

To edit sample values

1. For each sample, do one of the following:

Type a new file name over the current filename.

–or–

Double-click the Filename column and locate a raw data file to use for the sample.

–or–

Right-click and choose Browse in Raw File, and then locate a raw data file to use for the

sample.

By default, the application sets the Sample Type to Unknown.

2. For each sample, click the Sample Type column and select a sample type from the list.

3. Type a vial position in the Vial Position column for each sample.

4. Type a volume in the Injection Volume column for each sample.

The minimum injection volume value allowed is 0.1 μL; the maximum injection volume

value allowed is 5000 μL.

Tip Use the CTRL or SHIFT keys to select multiple samples.

Available sample types

Matrix Blank Solvent QC Std Unknown

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5. (Optional) Type or edit the values for the remaining columns.

To automatically copy or fill values in these columns, see Appendix B, “Using Copy

Down and Fill Down.”

To browse in raw data files

1. Do one of the following:

Double-click the Filename column.

–or–

Right-click and choose Browse in Raw File.

The What Raw File Would You Like to Use dialog box opens.

2. Select a raw data file to use for the sample or use the CTRL key to select multiple files,

and then click Open.

The application overwrites the selected, unacquired sample in the batch with the first

“browsed in” file and adds any additional browsed in files below the selected sample.

For all browsed-in raw data files, the application sets the Status to Acquired, , and sets

the Sample Type to Unknown.

To customize the column display

1. Right-click the Batch View sample list and choose Modify Columns.

The Modify Columns dialog box opens.

2. Use the arrow buttons to move all the columns that you want displayed to the Displayed

Columns pane.

All the columns you select appear after the Status, Filename, Sample Type, Groups, Level,

Sample ID, and Sample Name columns.

3. To arrange the order of the columns, do the following:

a. In the Displayed Columns pane, select a column name.

b. Use Up or Down to move the selected column up or down in the list.

The first column in the list represents the leftmost column in the Batch View sample

list, and the last column in the list represents the rightmost column in the Batch View

sample list.

Note When you use the scroll bar at the bottom of the sample list, the following

columns remain fixed: Status, Filename, Sample Type, Groups, Level, Sample ID, and

Sample Name, while the other columns scroll right and left.

Note You cannot overwrite an acquired sample. When you select a sample that is

acquired, the application adds all browsed in files below the selected sample.

Note The following columns are fixed: Status, Filename, Sample Type, Groups,

Level, Sample ID, and Sample Name.

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4. To change the width of a column, do the following:

a. In the Displayed Columns pane, select the column width.

b. Type a new value for the width.

5. When you have completed your changes, click OK.

The columns in the sample list immediately reflect your changes. The application uses

these settings for all sample lists in the Batch View.

Figure 115. Modify Columns dialog box

Table 62. Button descriptions for the Modify Columns dialog box

Button Description

Moves all columns to the Displayed Columns pane.

Moves the selected column to the Displayed Columns pane.

The following buttons apply to all columns, except for those that are fixed: Status, Filename,

Sample Type, Groups, Level, Sample ID, and Sample Name.

Moves the selected column to the Available Columns pane.

Moves all columns except those that are fixed.

Moves the selected column name in the Displayed Columns pane one row up in

the column order.

Moves the selected column name in the Displayed Columns pane one row down

in the column order.

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Create New Batch Dialog Box

Use the Create New Batch dialog box to select a folder and method for your batch and to

name the new batch.

Table 63. Create New Batch dialog box parameters (Sheet 1 of 2)

Parameter Description

Create New Folder

Adds one of the following:

• When a drive is selected, adds a new project-level folder to the drive.

• When a project folder is selected, adds a subproject-level folder to the selected project.

• When a subproject folder is selected, adds a lower-level folder to the subproject.

Or, you can right-click and choose Create Folder.

Delete Folder

With no confirmation prompt, immediately removes the selected folder.

You cannot delete a folder that contains lower-level folders; you must delete the lower-level

folders first.

Or, you can right-click and choose Delete.

Rename Folder

Renames the selected folder.

Or, you can right-click and choose Rename.

Batch table

Batch Name of batches in the selected project.

Type Type of batch: Quan, Screening, or Unknown Only.

Date Changed Date that the batch was last updated.

Samples Number of samples in the batch.

Method Name of the method used to create the batch.

Size Size of the batch in megabytes.

Domain TraceFinder domain in which the batch was created.

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Editing Folders for Batches

From the Create New Batch dialog box, you can create new folders for your batches. You can

also delete or rename folders.

Use these procedures:

•To create new project folders

•To delete project folders

•To rename project folders

To create new project folders

1. In the Create New Batch dialog box, select the folder for which you will create a new

lower-level folder.

• You can select the main TraceFinderData\4.0\Projects folder and create a new folder

under it.

• You can select one of the existing folders and create a lower-level folder under it.

2. Click the Create Folder icon, .

The application adds a new lower-level folder to the selected folder.

3. Select the new folder name and type a name for the folder.

Folder names are limited to 30 characters and can contain spaces and special characters,

except for the following special characters: \ / : + ? ” < >

New batch parameters

New Batch Name of the new batch to create.

Note If the Create button is not activated, you have entered a name that is already used or

you have not selected a method.

Type Type of batch to create: Quan, Screening, or Unknown Only.

Method Method used to create the new batch.

Path Path to the project in the TraceFinderData\4.0\Projects folder where the batch is created.

Buttons

Create Creates the specified batch and opens the Batch View for the new batch.

Cancel Closes the Create New Batch dialog box without creating a batch.

Table 63. Create New Batch dialog box parameters (Sheet 2 of 2)

Parameter Description

Note After you add a lower-level folder, you cannot rename the parent folder.

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To delete project folders

1. In the Create New Batch dialog box, select the folder to delete.

2. Click the Delete Folder icon, .

With no confirmation prompt, the application immediately removes the selected folder.

To rename project folders

1. In the Create New Batch dialog box, select the folder to rename.

2. Click the Rename Folder icon, .

3. Type a new name for the folder and press ENTER.

The application saves the new folder name.

Editing a Batch

In the Batch View, you can open a saved batch and edit the sample list. You can add samples,

edit samples, or remove samples. If the batch has already been acquired, you can select specific

samples for reinjection. If the batch has unacquired samples when you complete your edits,

you can save it as a “ready to acquire” batch.

Follow these procedures:

•To o p e n a sa v e d b at c h

•To open a recent batch

•To edit samples in a batch

•To reinject a sample from a previously acquired batch

To open a saved batch

1. Choose File > Open > Batch from the main menu.

The Open Batch dialog box opens.

2. Select a project and a subproject.

3. Select Unknown Only or Any from the Type list.

The batch list displays all batches created with Unknown methods (or all methods of all

types when you select Any).

4. Select a batch from the list.

5. Click Open.

The selected batch opens in the Batch View.

Note You cannot delete folders that contains lower-level folders; you must delete the

lower-level folders first.

Note You cannot rename folders that contain lower-level folders.

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Figure 116. Open Batch dialog box

To open a recent batch

Choose File > Recent Files > batch from the main menu.

The selected batch opens in the Batch View.

Table 64. Open Batch dialog box parameters

Parameter Description

Batch Name of batches in the selected project.

Type Type of batch: Quan, Screening, or Unknown Only.

Date Changed Date the batch was last updated.

Samples Number of samples in the batch.

Method Name of the method used to create the batch.

Size Size of the batch in megabytes.

Domain TraceFinder domain in which the batch was created.

Path Path to the project in the TraceFinderData\4.0\Projects folder where the batch is stored.

Buttons

Type Type of batch to display in the Batch list: Quan, Screening, Unknown Only, or Any.

Open Opens the Batch View for the selected batch.

Cancel Closes the Open Batch dialog box without opening a batch.

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To edit samples in a batch

Use the commands described in Working in the Batch View for Unknown Screening

Batches.

You can add new samples, edit samples, or delete samples.

To reinject a sample from a previously acquired batch

1. In the sample list, select the sample that you want to reinject.

2. Right-click and choose Reinject This Sample.

The application creates a copy of the selected sample and appends INJ001 to the file

name. Additional reinjections of the sample are numbered INJ002, INJ003, and so forth.

The application copies all parameter values from the original sample.

A green status icon indicates previously acquired samples (acquired and processed), and

the sample name is grayed out. A blue status icon indicates samples created for reinjection

(not acquired).

When you submit all samples in this batch, the application acquires all samples (including

previously acquired samples).

3. To save this batch with the new samples for reinjection, choose File > Save > Batch from

the main menu.

The batch is saved as a prepared batch that is ready to submit. You can open this batch

from the Reinject Samples page in the Acquisition mode and submit the batch. The

application acquires only the samples that have not been previously acquired.

Submitting a Batch

In the Batch View, you can submit an entire batch or only selected samples in the batch.

When you submit a batch for acquisition and processing, you can choose to create reports for

the submitted samples. See Submit Options dialog box.

For a description of commands in the shortcut menu, see Batch View shortcut menu

commands.

Follow these procedures:

•To submit selected peaks for processing

•To submit samples in the batch

•To view the output files

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To submit selected peaks for processing

1. In the Peak List, select the Selected check box for the peaks that you want to process.

2. Click the Submit … for Processing icon, .

The application processes the selected peaks and updates the data in the Peak

Identifications pane.

To submit samples in the batch

1. Do one of the following:

• To submit all samples in the batch, click the Submit Batch icon, .

• To submit specific samples, select the samples and click the

Submit Selected Samples icon, .

The Submit Options dialog box opens.

2. To acquire (or reacquire) the submitted samples, select the Acquire Data check box.

• When all submitted samples have been previously acquired, this option is (by default)

not selected.

• When one or more samples in the batch have not been acquired, this option is (by

default) selected.

3. To process the submitted samples, select the Process Data check box.

The application displays processing options for the Unknown Screening method.

4. Select the check box for the unknown screening options that you want to use.

Peak Detect: Performs peak detection. You can process the data with or without

performing peak detection. For example, you might want to turn off peak detection when

reprocessing samples.

Identify: Performs identification. This produces the peak identification data in the

Unknown Screening View.

With RT Alignment: Performs retention time alignment. This produces the heat map

and group averages data in the Unknown Screening View. When you select this option,

the application automatically selects the Peak Detect option.

5. (Optional) Select the Create Reports check box.

Note You can also submit only selected peaks for processing. See To submit selected

peaks for processing.

Tip You can process the data with or without performing peak detection. For

example, you might want to turn off peak detection when reprocessing samples.

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6. (Optional with multiplexing activated) Select the Priority Sequence check box.

The application acquires the priority batch on the next available channel or the assigned

channel.

7. (Optional without multiplexing activated) Select the Priority Sequence check box and

then select one of the following priority options to place the batch in the queue:

•Next Available Batch places the batch immediately after the currently acquiring

batch.

•Next Available Sample places the batch immediately after the currently acquiring

sample.

8. To specify the following optional parameters, click Show Details.

a. Select the Use check box for the device that you want to use for this acquisition.

b. Select the Start Device check box to indicate the device that will initiate

communication with the other instruments.

This is usually the autosampler.

c. Select the Start When Ready check box, which starts all instruments together when

they are all ready.

When this is cleared, individual instruments can start at different times and then have

to wait for the last instrument to be ready.

d. Select the system state after it acquires the last batch: On, Standby, or Off.

9. To start the selected processes, click OK.

The selected processes begin, and the application shows the real-time display at the

bottom of the current window. You can begin another batch in the Analysis mode while

you watch the real-time display of the currently acquiring batch.

Note When you select Full Sequence Submission in the Configuration console, these

options are unavailable because the current batch and the current sample are, in effect,

the same thing.

IMPORTANT After the first processing, you might see an error message stating that the

total number of results is too large for a single batch (more than 500 000). Return to the

Processing pages in the method (refer to Chapter 6, “Using the Method Development

Mode for Unknown Screening Methods,” in the TraceFinder Lab Director User Guide) and

make one or more of these parameter adjustments:

• Limit the RT range.

• Shorten the signal range.

• Specify a lower value for the Number of Top Matches.

• Specify a Simple Search instead of an Exhaustive Search.

• Specify Top Peaks instead of All Peaks.

• Limit the number of search types.

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Figure 117. Submit Options dialog box

Table 65. Submit Options dialog box parameters (Sheet 1 of 3)

Parameter Description

User Name Name of the current user.

Samples Number of samples to be submitted for acquisition, processing, or

reporting.

Workflow Steps to Perform

Acquire Data Submits the current batch to acquisition.

• When all submitted samples have been previously acquired, this

option is (by default) not selected.

• When one or more samples in the batch have not been

acquired, this option is (by default) selected.

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Process Data Processes the data for the current batch using any of the following

options:

Peak Detect: Performs peak detection for all method types. You can

process the data with or without performing peak detection. For

example, you might want to turn off peak detection when

reprocessing samples.

Identify: Performs identification for unknown screening methods.

With RT Alignment: Performs retention time alignment for

unknown screening methods. This produces the heat map and

group averages data in the Unknown Screening View. When you

select this option, the application automatically selects the Peak

Detect option.

Note You can use Unknown Screening features in conjunction

with Quantitation or Target Screening methods.

For specifying processing data for batches that also use

Quantitation methods, see To submit samples in the batch.

For specifying processing data for batches that also use Target

Screening methods, see To submit samples in the batch.

Create Reports Creates reports for the current batch.

Submit as a Priority Sequence?

Priority Sequence With multiplexing activated, places the batch immediately after the

currently acquiring batch.

Without multiplexing activated, specifies one of the following

priority options to place the batch in the queue:

Next Available Batch: Places the batch immediately after the

currently acquiring batch.

Next Available Sample: Places the batch immediately after the

currently acquiring sample.

Note When you select Full Sequence Submission in the

Configuration console, these options are unavailable because the

current batch and the current sample are, in effect, the same

thing.

Table 65. Submit Options dialog box parameters (Sheet 2 of 3)

Parameter Description

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To view the output files

Locate the files to view from the following directories:

The application writes saved batches to the project folder:

…\TraceFinderData\4.0\Projects\…

For each acquired sample, the application writes an RSX file to the batch Data folder:

…\TraceFinderData\4.0\Projects\…\Data

The application saves method information to the batch Methods folder:

…\TraceFinderData\4.0\Projects\…\Methods

The application writes the reports to the batch Reports folder:

…\TraceFinderData\4.0\Projects\…\batch\Reports

Acquisition pane

Device Name Lists all configured instruments.

If the instrument that you want to use is not configured, close the

TraceFinder application, configure the instrument, and then reopen

the application. You cannot configure an instrument while the

TraceFinder application is running.

Available only when you select the Acquire Data check box.

Use Specifies the instruments used for this acquisition.

Available only when you select the Acquire Data check box.

Start Device Specifies the instrument that initiates the communication with the

other instruments. This is usually the autosampler.

Available only when you select the Acquire Data check box.

Start When Ready Starts the specified device when all the instruments are ready to

acquire data. When this is cleared, individual instruments can start

at different times and then must wait for the last instrument to be

ready.

Post-run System State Specifies the system state after it acquires the last batch: On

(default), Standby, or Off.

Buttons

Hide/Show Details Collapses or expands the acquisition details of the Submit Options

dialog box.

OK Begins the selected processes.

Cancel Closes the Submit Options dialog box without submitting any

tasks.

Table 65. Submit Options dialog box parameters (Sheet 3 of 3)

Parameter Description

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Saving a Batch to a New Location

You can move the current batch to a different project folder, or you can make a copy of the

current batch and save the copy to a different project folder.

Follow these procedures:

•To save a batch to another project folder

•To move a batch to another folder

•To create new project folder

•To delete project folders

•To rename project folders

To save a batch to another project folder

1. Choose File > Save > Save Batch As from the Batch View main menu in the Analysis

mode.

The Save Batch As Dialog Box opens.

2. Select a storage location.

The default storage location is C:\TraceFinderData\4.0\Projects.

3. Select or create a project folder.

4. Type a name for the new batch.

If you are saving the batch to a different folder, you must give it a unique name. You

cannot overwrite an existing batch in a folder.

5. Click Save.

When you save the batch to a different folder, the reports reflect the original project

folders and the application does not save the calibration history.

To move a batch to another folder

1. Choose File > Save > Move Batch from the Batch View main menu in the Analysis

mode.

The Save Batch As Dialog Box opens.

2. Select a storage location.

The default storage location is C:\TraceFinderData\4.0\Projects.

3. Select or create a project folder.

4. Type a name for the new batch.

You must give the batch a unique name in the new subproject folder. You cannot

overwrite an existing batch.

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5. Click Save.

When you move the batch, the reports reflect the original project and subproject folders

and the application does not save the calibration history.

To create new project folder

1. In the Save Batch As dialog box, select the folder for which you will create a new

lower-level folder.

• You can select the main TraceFinderData\4.0\Projects folder and create a new folder

under it.

• You can select one of the existing folders and create a lower-level folder under it.

2. Click the Create Folder icon, .

The application adds a new lower-level folder to the selected folder.

3. Select the new folder name and type a name for the folder.

Folder names can contain spaces and special characters, except for the following special

characters: \ / : + ? ” < >

To delete project folders

1. In the Save Batch As dialog box, select the folder to delete.

2. Click the Delete Folder icon, .

With no confirmation prompt, the application immediately removes the selected folder.

To rename project folders

1. In the Save Batch As dialog box, select the folder to rename.

2. Click the Rename Folder icon, .

3. Type a new name for the folder and press ENTER.

The application saves the new folder name.

Note After you add a lower-level folder, you cannot rename the parent folder.

Note This feature is not available for folders that contain lower-level project or batch

folders; you must first delete the lower-level project or batch folders.

Note This feature is not available for folders that contain lower-level project or batch

folders; you must first delete the lower-level project or batch folders.

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Save Batch As Dialog Box

Use the features in the Save Batch As dialog box to save a batch to a new name or to move a

batch to a different project folder.

Figure 118. Save Batch As dialog box

Table 66. Save Batch As dialog box parameters (Sheet 1 of 2)

Parameter Description

Create New Folder

Adds one of the following:

• When a drive is selected, adds a new project-level folder to the drive.

• When a project folder is selected, adds a subproject-level folder to the selected project.

• When a subproject folder is selected, adds a lower-level folder to the subproject.

Or, you can right-click and choose Create Folder.

Delete Folder

With no confirmation prompt, immediately removes the selected folder.

You cannot delete a folder that contains lower-level project or batch folders; you must first

delete the lower-level project or batch folders.

Or, you can right-click and choose Delete.

Rename Folder

Renames the selected folder.

You cannot rename a folder that contains lower-level project or batch folders; you must first

delete the lower-level project or batch folders.

Or, you can right-click and choose Rename.

Batch table

Batch Name of batches in the selected project.

Type Type of batch: Quan, Screening, or Unknown Only.

Date Changed Date that the batch was last updated.

Samples Number of samples in the batch.

Method Name of the method used to create the batch.

Size Size of the batch in megabytes.

Domain TraceFinder domain in which the batch was created.

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New batch parameters

New Batch Name of the new batch to create.

Note If the Create button is not activated, you have entered a name that is already used or

you have not selected a method.

Path Path to the project in the TraceFinderData\4.0\Projects folder where the batch is created.

Buttons

Save Saves the batch to the specified name and folder and opens the Batch View for the new

batch.

Cancel Closes the Save Batch As dialog box without saving the batch.

Shortcut menu commands

Create Folder Adds one of the following:

• When a drive is selected, adds a new project-level folder to the drive.

• When a project folder is selected, adds a subproject-level folder to the selected project.

• When a subproject folder is selected, adds a lower-level folder to the subproject.

Delete Folder Immediately removes the selected folder. There is no prompt to confirm that you want to

delete the selected folder.

You cannot delete a folder that contains lower-level project or batch folders; you must first

delete the lower-level project or batch folders.

Rename Folder Renames the selected folder.

You cannot rename a folder that contains lower-level project or batch folders; you must first

delete the lower-level project or batch folders.

Expand Child Nodes Expands all project and subproject folders in the Project tree.

Collapse Child Nodes Collapses all project and subproject folders in the Project tree.

Table 66. Save Batch As dialog box parameters (Sheet 2 of 2)

Parameter Description

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Working in Data Review for Unknown Screening Batches

The Data Review view displays the data generated by the master method. Use Data Review to

verify the data for identified peaks before you generate reports.

When you run samples in an experiment, you can check for peaks that are not already

identified in either an associated target screening or quantitation method and take appropriate

steps when the application finds these peaks and proposes whether they match one or more

compounds using various identification sources.

Follow these procedures:

•To open the Data Review view

•To display or hide a pane on the Unknown Screening View page

•To move, dock, or float Data Review panes

•To restore the default layout

To open the Data Review view

1. Click Analysis in the navigation pane.

The Analysis navigation pane opens.

2. Click Data Review.

The Data Review navigation pane opens.

IMPORTANT When unknown screening features are associated with a quantitation or

target screening method, the unknown screening results do not include any compounds

(other than internal standards) that were identified by the quantitation or target screening

methods.

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To display or hide a pane on the Unknown Screening View page

From the View menu, choose to display or hide any of the following panes.

A check mark indicates a displayed pane.

To move, dock, or float Data Review panes

Follow the instructions in Appendix C, “Moving Data Review Panes.”

To restore the default layout

Choose View > Restore Default Layout.

The Unknown Screening View displays the default panes in their default locations.

Cross Sample Peak List Pane

Use the Cross Sample Peak List pane to compare peak values across all samples in a batch.

To use the Cross Sample Peak List pane

1. In the Peak List pane, select a peak.

The application scrolls the Cross Sample Peak List pane to the specified peak and selects

the peak.

2. Use the scroll bar at the bottom of the pane to scroll across the values for the selected peak

in all samples and groups in the batch.

Displays the Peak List Pane.

Displays the TIC Chromatogram Pane.

Displays the Spectrum Pane.

Displays the Sample List Pane.

Displays the Fragments Pane.

Displays the Isotopes Pane.

Displays the Cross Sample Peak Overlay Pane.

Displays the Heat Map Pane.

Displays the Peak Identifications Pane.

Displays the Library Search Pane.

Displays the Chemical Structure Pane.

Displays the Group Averages Pane.

Displays the XIC Pane.

Displays the Cross Sample Peak List Pane.

Displays the XIC Overlay Pane.

Displays the Peak Chromatogram Pane.

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Figure 119. Cross Sample Peak List pane

Table 67. Cross Sample Peak List pane columns (Sheet 1 of 2)

Column Description

Selected Identifies peaks to display when you select the Selected option in

the XIC Overlay pane, or identifies which peaks to process when

you click the Submit … for Processing icon, .

Do not confuse a check mark in the Selected column with the

currently selected peak. The row for a currently selected peak is

highlighted in blue.

Retention Time The time after injection when the compound elutes. The total

time that the compound is retained on the column.

M/Z Mass-to-charge ratio found in the spectra for the peak. Assumes

that the charge is 1.

Mass The uncharged mass found in the spectra for the peak.

Monoisotopic Mass The most abundant mass in the spectra for the peak.

Maximum Fold The maximum difference of the group average response from the

control average response.

Compound Name Displays the compound name found in the library or compound

database. This column is displayed only when the peaks are

aligned and you have performed a simple search. Refer to

Chapter 6, “Using the Method Development Mode for Unknown

Screening Methods,” in the TraceFinder Lab Director User Guide.

Sample n MS Area The MS peak area for each sample.

Default Average Area The averaged response of all peak occurrences in the sample.

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Heat Map Pane

Use the Heat Map pane to display the response of each peak occurrence in the batch. The

Heat Map pane displays all MS Area values for all peaks in all samples in the batch that are

above the peak threshold value specified in the method. When you select a peak in the Heat

Map pane, the application displays the associated results for the selected peak in all panes of

the Unknown Screening view.

The Heat Map pane is available only when you select the Alignment and Gap Filling option

in the method (refer to Chapter 6, “Using the Method Development Mode for Unknown

Screening Methods,” in the TraceFinder Lab Director User Guide) or select the RT Alignment

option when you submit the batch (see Submitting a Batch).

Follow these procedures:

•To use the Heat Map pane

•To use the Heat Map pane with the TIC Chromatogram pane

•To use the Heat Map pane with the XIC chromatogram pane

Default % CV The coefficient of variance for each sample.

The coefficient of variance is calculated as the standard deviation

of the multiple samples of one level, multiplied by 100, and

divided by the average of the multiple samples of that level. This

calculation is based on the areas of the peaks.

Default Fold The maximum difference of the sample average response from the

control average response.

Group n Average Area The averaged response of all peak occurrences in the group. The

minimum value is 1, even when the peak never occurs in the

group.

Group n % CV The coefficient of variance for each sample.

The coefficient of variance is calculated as the standard deviation

of the multiple samples of one level, multiplied by 100, and

divided by the average of the multiple samples of that level. This

calculation is based on the areas of all the peaks in the group of

samples.

Group n Fold The maximum difference of the average response of all samples in

a group from the control average response.

Table 67. Cross Sample Peak List pane columns (Sheet 2 of 2)

Column Description

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To use the Heat Map pane

1. Click the Heat Map tab to display the pane.

For detailed descriptions of all parameters in the Heat Map pane, see Heat Map pane

columns.

2. In the Peak List pane, select a peak.

The application scrolls the Heat Map pane to the specified peak and selects the peak.

For each found peak in the batch, the application assigns a color code indicating the

relative MS area value from highest (orange) to lowest (green).

To use the Heat Map pane with the TIC Chromatogram pane

1. Click the TIC Chromatogram tab to display the pane.

The total ion current (TIC) chromatogram pane displays the relative intensity of all

found peaks in the batch.

2. In the Heat Map pane, select a peak.

The application identifies the selected peak in the TIC Chromatogram pane and indicates

it with a red marker.

Or, you can select a peak in the TIC Chromatogram pane, and the application scrolls the

heat map to the selected peak.

Highest

Lowest

A red marker

indicates the

selected peak in

the TIC

Chromatogram

pane.

Select a peak.

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To use the Heat Map pane with the XIC chromatogram pane

1. Click the XIC tab to display the pane.

The extracted ion chromatogram (XIC) pane displays the absolute intensity of the

selected peak.

2. In the Heat Map pane, select a peak.

The application identifies the selected peak in the XIC, scales the chromatogram’s y axis

to fit the peak, and indicates it with a red marker.

Or, you can select a peak in the XIC pane, and the application scales the chromatogram

to fit the peak, indicates it with a red marker, and scrolls the heat map to the selected

peak.

Figure 120. Heat Map pane

Table 68. Heat Map pane columns

Column Description

Retention Time The time after injection when the compound elutes. The total

time that the compound is retained on the column.

M/Z Mass-to-charge ratio found in the spectra for the peak. Assumes

that the charge is 1.

Mass The uncharged mass found in the spectra for the peak.

Sample n MS Area The MS peak area for each sample.

A red marker

indicates the

selected peak in

the XIC pane.

Select a peak.

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Sample List Pane

Use the Sample List pane to select a sample of interest. The application displays the associated

results for the selected sample in all panes of the Unknown Screening view.

To hide or display columns in the Sample List pane

1. Click the Field Chooser icon, , in the upper left corner of the pane.

The Field Chooser displays all available columns of data for the Sample List pane.

2. Select the check box for each column that you want to display, or clear the check box for

each column that you want to hide.

The application immediately displays or hides the column in the Sample List pane.

3. When you are finished modifying the column display, click to close the Field

Chooser.

Figure 121. Sample List pane

Table 69. Sample List pane columns

Column Description

Batch Order The order in which the samples were acquired.

Filename A user-defined name that identifies a sample.

Sample Type Defines how the application processes the sample data. Each

sample is classified as one of the following sample types: Matrix

Blank, Solvent, Cal Std, QC Std, or Unknown.

Default: Unknown

Status Sample is not acquired.

Sample is acquired but not processed.

Sample is acquired and processed.

Sample is currently acquiring.

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Peak List Pane

Use the Peak List pane to select a specific peak found in the selected sample. The Peak List

displays each peak that the application identified in the sample.

To display information for a peak

In the Peak List, click anywhere in the peak row.

The application displays information for the selected peak in the other Data Review

panes.

Figure 122. Peak List pane

Note Do not confuse a check mark in the Selected column with the currently selected

peak. The row for the current, selected peak is highlighted in blue. A selected check

box in the Selected column does not indicate the current, selected peak (see Selected).

Table 70. Peak List pane columns (Sheet 1 of 2)

Column Description

Selected Identifies peaks to display when you select the Selected option in

the XIC Overlay pane, or identifies which peaks to process when

you click the Submit … for Processing icon, .

Do not confuse a check mark in the Selected column with the

currently selected peak. The row for the current, selected peak is

highlighted in blue.

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Peak ID Identifies the peak as “peak @ retention time m/z.”

Example: peak @ 0.80 203.05

m/z Mass-to-charge ratio found in the spectra for the peak. Assumes

the charge is 1.

Retention Time The time after injection when the compound elutes. The total

time (in minutes) that the compound is retained on the column.

Area The area obtained by integrating peak intensities from the start to

the end of the peak.

Height The distance from the peak maximum to the peak base, measured

perpendicular to the ordinate.

Potential ID The number of returned peak IDs.

Mass The uncharged mass found in the spectra for the peak.

Monoisotopic Mass The sum of the masses of the most abundant isotope.

Charge State The charge state of the ion (the z value in m/z). For example, a

charge state of 2 with a negative polarity means that the

compound has 2 more electrons than protons.

Valid range: 1 through 10

Default: 1

Filter String Filter used to identify the peak. Specified in the raw data file or the

master method.

NIST The NIST match result name for the identified peak. If there is no

match or if the Library search was not specified in the method,

this shows as “N/A.”

mzVault The library match result name for the identified peak. If there is

no match or if the Library Search was not specified in the method,

this shows as “N/A.”

Elemental

Composition

The chemical formula for the identified peak. If there is no match

or the Elemental Composition search was not specified in the

method, this shows as “N/A.”

Database The compound database match result name for the identified

peak. If there is no match or the Database Search was not specified

in the method, this shows as “N/A.”

ChemSpider The ChemSpider database match result name for the identified

peak. If there is no match or the ChemSpider Search was not

specified in the method, this shows as “N/A.”

Table 70. Peak List pane columns (Sheet 2 of 2)

Column Description

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Peak Identifications Pane

Use the Peak Identifications pane to display the name and formula for identified peaks and

the source of the identification.

Figure 123. Peak Identifications pane

Table 71. Peak Identifications pane columns (Sheet 1 of 2)

Column Description

Selected Identifies peaks to display when you select the Selected option in

the XIC Overlay pane, or identifies which peaks to process when

you click the Submit … for Processing icon, .

Do not confuse a check mark in the Selected column with the

currently selected peak. The row for a currently selected peak is

highlighted in blue.

ID Source Specifies the search type used to identify the peak (Database

Search, Library Search [NIST or mzVault], Elemental

Composition, or ChemSpider Search). Refer to the instructions

“To specify the search options” in Chapter 6, “Using the Method

Development Mode for Unknown Screening Methods,” in the

TraceFinder Lab Director User Guide.

ID Source Detail Specifies the name of the library, the compound database, or the

ChemSpider hyperlink where the peak was identified.

Match Result Name Specifies the compound name that was found in the library, in

the compound database, or in the ChemSpider hyperlink.

Formula Specifies the chemical formula that was found in the library, in

the compound database, in the elemental composition, or in the

ChemSpider hyperlink.

Isotope Pattern Score % Specifies the percentage of matched isotopes in the total number

of isotopes.

Number of Isotopes

Matched

Specifies the number of isotopes matched in the calculated

isotope spectra relative to the total number of isotopes used in

the score calculation, in the format “x of y”, where

• x = the number of isotopes matching the elemental

composition used for the Isotope Pattern Score calculation.

• y = the total number of isotopes considered in the Isotope

Pattern Score calculation. This is the number of isotope

peaks expected to be above the spectral noise.

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TIC Chromatogram Pane

Use the TIC Chromatogram pane to display the relative intensity of a trace along the length

of the sample data retention window.

To focus on a specific peak

In the TIC Chromatogram pane, click any displayed peak.

The application indicates the selected peak with a red, vertical marker and updates the

focus in the other Data Review panes with data for that peak.

Figure 124. TIC Chromatogram pane

Score Specifies the score from the library fit. When the application

finds a match in the library, in the compound database, or

through the ChemSpider hyperlink, this column displays the

highest score associated with the Match Result Name parameter.

Valid range: 1 through 100%

SI/Dot Product Specifies the search index method used to search the NIST

library.

RSI/Rev Product (Reverse search index) Specifies the method used to search the

NIST library. A reverse search compares a library entry to an

unknown compound (whereas a forward search compares the

mass spectrum of an unknown compound to a mass spectral

library entry).

Library Probability

Percent

Specifies the probability ranking from the NIST library. When

you use a reverse search, this value is “N/A.”

Fragments Specifies the number of fragments matched in the calculated

spectra relative to the total number of expected fragments.

Table 71. Peak Identifications pane columns (Sheet 2 of 2)

Column Description

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XIC Pane

Use the XIC pane to display the absolute intensity of an extracted trace along the length of the

sample data retention window.

To focus on a specific peak

In the XIC pane, click any displayed peak.

The application indicates the selected peak with a red, vertical marker and updates the

focus in the other Data Review panes with data for that peak.

Figure 125. XIC pane

XIC Overlay Pane

Use the XIC Overlay pane to view specific groups of peaks. You can choose to view all peaks,

selected peaks only, or the top 20 most intense peaks (by area). The XIC Overlay plot is a

collection of overlaid, extracted m/z ion plots that use a different color for each peak.

Follow these procedures:

•To display all peaks in a sample

•To display only selected peaks in a sample

•To display the top 20 peaks in a sample

•To focus on a specific peak

To display all peaks in a sample

1. In the Sample List pane, select the sample whose peaks you want to view.

2. In the XIC Overlay pane, select the All check box.

The application displays all the peaks in the selected sample. See XIC Overlay plot

showing all peaks.

Note If there are more than 1000 peaks in the sample, performance might be slow.

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Figure 126. XIC Overlay plot showing all peaks

To display only selected peaks in a sample

1. In the Sample List pane, select the sample whose peaks you want to view.

2. In the Peak List pane, select the Selected check box for each peak that you want to view.

3. In the XIC Overlay pane, select the Selected option.

The application displays all selected peaks.

Figure 127. XIC Overlay plot showing selected peaks

To display the top 20 peaks in a sample

1. In the Sample List pane, select the sample whose peaks you want to view.

2. In the XIC Overlay pane, select the Top 20 check box.

The application displays the top 20 peaks in the selected sample.

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Figure 128. XIC Overlay plot showing the top 20 peaks

To focus on a specific peak

In the XIC Overlay pane, click any displayed peak.

The application indicates the selected peak with a red, vertical marker and updates the

focus in the other Data Review panes with data for that peak.

Group Averages Pane

Use the Group Averages pane to compare the peak areas of different samples to a control

group of samples.

The Group Averages pane is available only when you select the Alignment and Gap Filling

option in the method (refer to Chapter 6, “Using the Method Development Mode for

Unknown Screening Methods,” in the TraceFinder Lab Director User Guide) or select the RT

Alignment option when you submit the batch (see Submitting a Batch).

The control group is displayed to the left, and other samples and groups are listed in the order

in which they appear in the Batch View. To specify a group as the control group, see Groups.

Each group displays a colored bar that indicates the average response of the group, as

displayed in the Average Area column in the Cross Sample Peak List Pane. The color of the

bar matches the colors assigned to the samples and peaks in the Cross Sample Peak Overlay

Pane.

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Figure 129. Group Averages pane

To display areas for each sample in the batch

Hold the cursor over an indicator icon ( , ).

The application displays the area for the selected compound in each represented sample.

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To use the Group Averages pane with the Cross Sample Peak Overlay pane

Display both the Group Averages pane and the Cross Sample Peak Overlay pane.

The color of the bars in the Group Averages pane matches the colors assigned to the

group samples and peaks in the Cross Sample Peak Overlay pane.

Peak Chromatogram Pane

Use the Peak Chromatogram Pane to display the selected chromatogram peak. The pane

initially displays only the apex scan for the detected peak. You can manually integrate the peak

and use the updated peak to generate reports.

Follow these procedures:

•To zoom in on a peak

•To remove a peak

•To customize the labels in the display

•To display surrounding apex times

•To manually integrate a peak

•To switch between Method and Manual integration modes

To zoom in on a peak

1. In the chromatogram plot, drag the cursor to delineate a rectangle around the peak.

The delineated area expands to fill the view.

2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling.

To remove a peak

Right-click the Peak Chromatogram pane, and choose Delete Peak.

The application removes the peak displayed in the Peak Chromatogram pane. All data for

this peak are removed from the Unknown Screening View panes.

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To customize the labels in the display

1. Right-click the Peak Chromatogram pane, and choose Peak Display Settings.

The Peak Settings Dialog Box opens.

2. To display labels for the peak retention time (RT), mass height (MH), mass area (MA), or

signal-to-noise (SN), select the appropriate check box.

3. Click OK in the Peak Settings dialog box.

The chromatogram plot displays the selected labels.

Figure 130. Example of displayed labels

To display surrounding apex times

1. Right-click the Peak Chromatogram pane, and choose Peak Display Settings.

The Peak Settings Dialog Box opens.

2. Select the Show All Apex Times check box.

3. Click OK in the Peak Settings dialog box.

Figure 131. Example of displayed apex times

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To manually integrate a peak

1. Right-click the Peak Chromatogram pane and then choose Swipe Manual Integration,

or click the Swipe Manual Integration icon, .

The cursor changes to indicate the manual integration mode.

2. Drag the cursor to define the beginning and ending base points for the new peak. See

Manually integrated peak.

Figure 132. Manually integrated peak

The application updates the area of the peak to the baseline that you just added. When

you regenerate the reports, they display the manually modified data.

3. To return to the original peak as defined by the method, right-click and choose

Integration Settings > Method.

To switch between Method and Manual integration modes

Right-click the Peak Chromatogram pane and choose Integration Settings > Manual or

Integration Settings > Method.

Initially, the method integration and manual integration settings that are stored for a

compound and file are identical. When you switch modes, the saved result set does not

change. However, when manual data are available, both the Peak Chromatogram plots

and the result set update as you switch between method and manual modes.

As you switch between modes, each pane reflects the changes. The generated reports for

the data identify the manual modifications.

Note You must drag the cursor inside the x axis and y axis.

Drag the cursor across the peak at

the base points for the new peak.

The application identifies the peak and

indicates the manual integration in the labels.

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Peak Chromatogram Pane

Use the Peak Chromatogram pane to display the selected chromatogram peak.

Figure 133. Peak Chromatogram pane

Table 72. Peak Chromatogram pane shortcut menu commands

Command Description

Reset Scaling Resets the original scaling after a zoom operation.

Copy to Clipboard Copies the graphic display to the Clipboard.

Swipe Manual

Integration

Switches to manual integration mode, where you can manually

define the peak.

Also available from the icon in the upper right corner, .

Integration Settings

(Manual or Method)

Switches the display between manual and method integration modes.

Delete Peak Removes the peak and all data for this peak from the Unknown

Screening View panes.

Also available from the icon in the upper right corner, .

Peak Display

Settings

Opens the Peak Settings Dialog Box.

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Peak Settings Dialog Box

Use the Peak Settings dialog box to custom the display settings.

Figure 134. Peak Settings dialog box

Table 73. Peak Settings dialog box parameters (Sheet 1 of 2)

Command Description

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific Notation Displays the y-axis scale in scientific notation.

Peak Labels

RT Displays the retention time (RT) label in the peak

chromatogram pane.

Height Displays the peak height (AH) label in the peak

chromatogram pane.

Area Displays the peak area (AA) label in the peak

chromatogram pane.

Signal to Noise Displays the signal-to-noise (SN) label in the peak

chromatogram pane.

Plot Header

Sample ID Displays a user-defined, alphanumeric string that

identifies a sample.

Threshold Displays the peak threshold.

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Cross Sample Peak Overlay Pane

Use the Cross Sample Peak Overlay Pane to compare instances of a selected peak across all

samples in the batch. The application overlays all occurrences of the peak in the batch.

The application displays the names of all samples in the batch where the selected peak is

found. Samples that are assigned to groups are color coded, and the peaks found in those

samples are color coded in the plot. To assign samples to groups, see Groups.

The retention time window displayed in the Cross Sample Peak Overlay pane is the RT

window that you specified in the method.

Follow these procedures:

•To select the peak to display in the Cross Sample Peak Overlay pane

•To zoom in on a peak

•To use the Cross Sample Peak Overlay pane with the Group Averages pane

m/z Displays the mass-to-charge ratio found in the spectra for

the peak. Assumes the charge is 1.

Sample Filename Displays the name of the current, selected sample where

the peak was found.

Compound Name Displays the compound name match in the library or

compound database.

Filter String Displays the filter used to identify the peak. Specified in

the raw data file or the master method.

Plot Style

Point To Point Displays chromatograms in the following format:

Stick Displays chromatograms in the following format:

Chromatogram

Show All Apex Times Displays all surrounding apex times in the plot.

Table 73. Peak Settings dialog box parameters (Sheet 2 of 2)

Command Description

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To select the peak to display in the Cross Sample Peak Overlay pane

Select a peak in either the Peak List Pane or the Cross Sample Peak List Pane.

To zoom in on a peak

1. In the chromatogram plot, drag the cursor to delineate a rectangle around the peak.

The delineated area expands to fill the view.

2. To restore the default view, right-click the chromatogram plot and choose Reset Scaling.

To use the Cross Sample Peak Overlay pane with the Group Averages pane

Display both the Cross Sample Peak Overlay pane and the Group Averages pane.

The color of the bars in the Group Averages pane matches the colors assigned to the

group samples and peaks in the Cross Sample Peak Overlay pane.

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Cross Sample Peak Overlay Pane

Use the Cross Sample Peak Overlay pane to compare instances of a selected peak across all

samples in the batch

Figure 135. Cross Sample Peak Overlay pane

Library Search Pane

The Library Search Pane displays the best library matches for the selected peak, with the

highest score listed first.

Follow these procedures:

•To view the spectrum for a library match

•To display the difference between experimental and library spectra

Table 74. Cross Sample Peak Overlay pane shortcut menu commands

Column Description

Reset Scaling Resets the original scaling after a zoom operation.

Copy to Clipboard Copies the graphic display to the Clipboard.

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To view the spectrum for a library match

In the Library Search pane, select a library entry.

The Experimental plot displays the measured spectra for the selected compound. Library

matches are colored red.

The Library plot displays the expected spectra in the library. Library matches are colored

blue.

The spectra header displays the following:

• The library match name

• The chemical formula for the peak

• The score from the library fit when the library type is mzVault or NIST

• SI and RSI when the library type is NIST

• Dot Prod or Rev Dot Prod when the library is HRAM

• Molecular weight when the library type is NIST

• The ID record from the library when the library type is mzVault or NIST

• The scan number and scan filter when either is present in the library

Library matches Experimental spectrum

Library spectrum

Library match name Library score

Score ID Chemical formula Filter

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To display the difference between experimental and library spectra

1. Right-click the spectrum plot and choose Show Difference Plot.

The application displays the Experimental and Library plots and a Difference plot that

shows the difference between the experimental and library spectra. When you read a

difference plot, the match between the experimental and library spectra is better when

fewer peaks appear.

Figure 136. Library Search pane showing a Difference plot

2. To specify how the difference plot displays the mass tolerance, do the following:

a. Right-click the spectrum plot and choose Set Difference Plot Mass Tolerance.

b. In the dialog box that opens, select either MMU or PPM as the unit of measure.

The default value is the tolerance set in the NIST library or mzVault library.

c. Type a mass tolerance value.

d. Click OK.

Note This command is available only when you display the difference plot.

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Library Search Pane

Use the Library Search pane to display the best library matches for the selected peak.

Figure 137. Library Search pane

Chemical Structure Pane

Use the Chemical Structure pane to view the chemical formula and structure for the peak that

is currently selected in the Peak List pane.

The application displays the chemical formula (and CAS number when available) that was

found in the search database that you specified in the method. Refer to Chapter 6, “Using the

Method Development Mode for Unknown Screening Methods,” in the TraceFind er Lab

Director User Guide.

Figure 138. Chemical Structure pane

Table 75. Library Search pane shortcut menu commands

Command Description

Reset Scaling Resets the original scaling after a zoom operation.

Copy to Clipboard Copies the graphic display to the Clipboard.

Display Overlay Spectra

Display Stack Spectra

Overlays the two spectrum displays, or stacks the

Experimental and Library spectra.

When you display the Difference plot, this spectrum

also displays the Difference spectrum.

Show/Hide Difference Plot Displays or hides the Difference spectrum plot.

Set Difference Plot Mass Tolerance Opens a dialog box where you specify the mass

tolerance in either MMU or PPM units. Available

only when you display the Difference Plot.

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Fragments Pane

The Fragments pane displays the maximum number of fragments as specified in the unknown

screening method. Refer to Chapter 6, “Using the Method Development Mode for Unknown

Screening Methods,” in the TraceFinder Lab Director User Guide.

When a compound database search returns a match for a peak that has fragments, the

Fragments pane displays the theoretical fragments.

When the data has an MS/MS element that is identified as belonging to the chromatographic

peak, the Fragments pane displays the fragments found in the MS/MS scan.

The Fragments pane displays the fragments in one of two ways:

•All Fragments

•Individual Fragments

All Fragments

The All Fragments view displays a composite of all fragments found in the peak. The

application displays the measured peak as a red line; the application displays the expected peak

as a blue line. The application displays these headers for the All Fragments view:

Figure 139. Fragments pane with overlaid spectra for all fragments

Processing filter

File name

Minimum number

of fragments

specified in the

method

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Figure 140. Fragments pane with stacked spectra for all fragments

Individual Fragments

The individual fragments view displays the expected and measured peaks for a single

fragment. The application displays these headers for the individual fragments view:

Minimum number of fragments specified

in the method

Expected m/z

for fragment 1

Measured m/z

for fragment 1 Delta between expected

and measured m/z

Expected ion ratio range Measured ion ratio

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Figure 141. Fragments pane with overlaid spectra for a single fragment

Figure 142. Fragments pane with stacked spectra for a single fragment

Isotopes Pane

The isotopes pane displays isotopic pattern results for all adducts of a compound according to

the threshold and deviation parameters defined in the unknown method.

To identify or confirm the presence of a compound, the resulting score percentage from

isotopic pattern matching must be higher than the specified fit threshold percentage.

• An isotope peak is not found if its intensity, relative to the monoisotopic ion’s intensity, is

more than the specified intensity deviation percentage away from the theoretical relative

intensity of the isotope ion.

• An isotope peak is found if its measured m/z is less than the specified mass deviation

amount away from its expected m/z.

Intensity

threshold

specified in

the method

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To specify the peak threshold and deviation parameters, refer to Chapter 6, “Using the

Method Development Mode for Unknown Screening Methods,” in the TraceFind er Lab

Director User Guide.

The Isotopes pane displays the isotopes in one of three ways:

•All Isotopes

•Multi-Isotopes

•Individual Isotopes

All isotopes panes use a shortcut menu so that you can specify how to display the data. See

Isotopes pane shortcut menu commands.

All Isotopes

The All Isotopes view displays a composite of all isotopes found in the compound. The

application scales the window with respect to the most intense isotope. The most intense

isotope is usually the first isotope unless you are using halogenated compounds. The

application displays the measured peak as a solid red line; the application displays the

expected peak as a dashed blue line.

The application displays these headers for the All Isotopes view:

Scan range for

the isotopes

Retention time

range for all scans

Number of averaged scans

Processing filter

Sample file name

Percentage of total isotopes to the

number of matched isotopes

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Figure 143. Isotopes pane with stacked spectra for all isotopes

Figure 144. Isotopes pane with overlaid spectra for all isotopes

Multi-Isotopes

The Multi-Isotopes view displays individual plots for each isotope. You can individually stack

or overlay the plots for each isotope.

The application displays these headers for the Multi-Isotopes view:

Measured spectrum Expected spectrumExpected m/z of the isotope

Measured spectrum in redExpected spectrum in blue

Scan range for the isotopes

Retention time

range for all scans

Number of averaged scans

Percentage of total isotopes to the

number of matched isotopes

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Figure 145. Isotopes pane with overlaid spectra for multi-isotopes

Figure 146. Isotopes pane with stacked spectra for multi-isotopes

Figure 147. Isotopes pane with stacked and overlaid spectra for multi-isotopes

Expected spectrum in blue Measured spectrum in red

Measured spectrum in redExpected spectrum in blue

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Individual Isotopes

The individual isotopes view displays the expected and measured peaks for a single isotope.

The application displays these headers for the individual isotopes view:

Figure 148. Isotopes pane with overlaid spectra for a single isotope

Figure 149. Isotopes pane with stacked spectra for a single isotope

Scan range for

the isotopes

Retention time

range for all

scans

Number of averaged

scans

Expected m/z

for isotope 5

Measured m/z

for isotope 5

Delta between expected

and measured m/z

Percentage of total isotopes to

the number of matched isotopes

Measured spectrum in redExpected spectrum in blue

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Spectrum Pane

When data is available, the plot width is the full mass range in the raw data file. Otherwise,

the application scales the width to the scan range.

Figure 150. Spectrum pane

Table 76. Isotopes pane shortcut menu commands

Command Description

Reset Scaling Resets the original scaling after a zoom operation.

Copy to Clipboard Copies the graphic display to the Clipboard.

Display Overlay Spectra

Display Stack Spectra

Overlays the two spectrum displays, or stacks the simulated

spectrum and the peak apex spectrum.

Show/Hide Noise Label Adds a noise label to each peak. Expected isotope peaks

(displayed in blue) do not display a noise label.

Show/Hide Resolution

Label

Adds a resolution label to each peak. Expected isotope peaks

(displayed in blue) do not display a resolution label.

Table 77. Spectrum pane shortcut menu commands

Command Description

Reset Scaling Resets the original scaling after a zoom operation.

Copy to Clipboard Copies the graphic display to the Clipboard.

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Working in the Report View for Unknown Screening Batches

The Report View displays example reports for the current batch. You must have an open

batch to use the features in the Report View.

Follow these procedures:

•To open the Report View

•To preview a report

•To generate a report as a PDF, an Excel, or a CSV file

•To print a report

•To display a generated report

•To e d i t a re po r t t e m p l a t e

•To create a new report template

To open the Report View

Click Report View in the navigation pane.

The application opens the Report View.

To preview a report

1. In the Template pane, select a report template.

The template list shows all the report templates that you configured in the Configuration

console. Refer to Chapter 1, “Using the Configuration Console,” in the TraceFi nder Lab

Director User Guide.

Figure 151. Example template list for unknown screening batches

2. Click Preview, .

The application opens the Report Designer, showing the report information for the

current batch in the selected report template format.

For details about using the Report Designer, see Chapter 7, “Using the Report Designer.”

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To generate a report as a PDF, an Excel, or a CSV file

1. In the Template pane, select a report template.

2. Select the check box for each of the file types that you want to create: PDF, Excel, or

CSV.

3. Click Generate, .

The application does the following:

• Displays a green progress bar as it generates the reports.

• Creates a report for the current batch as a PDF, an Excel, or a CSV file, using the

selected report template format.

• Adds information about the generated report to the Generated Reports pane.

For details about the Generated Reports pane, see Report View.

• Saves the report files to the …\TraceFinderData\4.0\Projects\batch\ReportOutput

folder.

To print a report

1. In the Template pane, select a report template.

2. Select the check box for the Print file format.

3. Click Generate, .

The application does the following:

• Creates a report for the current batch using the selected report template format.

• Prints the report to your default printer.

• Adds information about the generated report to the Generated Reports pane.

For details about the Generated Reports pane, see Report View.

• Saves the report files to the …\TraceFinderData\4.0\Projects\batch\ReportOutput

folder.

To display a generated report

In the Generated Reports pane, click View for the report that you want to see.

Figure 152. Generated Reports pane showing a PDF report

The application opens the output file.

Opens the generated file.

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To edit a report template

1. In the Template pane, select a report template.

2. Click Open, .

The application opens the Report Designer showing the template in an Excel spreadsheet.

See Report Designer showing the template for the selected report.

Figure 153. Report Designer showing the template for the selected report

3. Use the features in the Report Designer to edit the template.

See Chapter 7, “Using the Report Designer.”

4. When you finish your changes, choose File > Save from the Report Designer menu bar.

To create a new report template

1. Click New, .

The application opens the Report Designer showing an empty template in an Excel

spreadsheet. See Report Designer showing a new, empty template.

The Report Type is None.

In the left pane, the spreadsheet lists all samples in the current batch and all compounds

in the method used for the batch.

Note You cannot edit report templates that were provided with the TraceFinder

application; however, you can open a TraceFinder template, make changes, and save it

to a new template name.

Note When user security is activated, you must have Template Editing permission to

edit report templates created by your laboratory. If the Open button is not active, user

security is activated and you do not have Template Editing permission.

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Figure 154. Report Designer showing a new, empty template

2. Use the features in the Report Designer to create the report template.

See Chapter 7, “Using the Report Designer.”

3. When you finish your changes, choose File > Save from the Report Designer menu bar.

The Save Template dialog box opens.

Figure 155. Save Template dialog box

4. Type a name for the new report template and click OK.

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Report View

Use the features in the Report View to display example reports for the current batch.

Figure 156. Report View

Table 78. Report View parameters (Sheet 1 of 2)

Parameter Description

Template

Displays all available unknown screening report templates.

Rules

Sheet Name Specifies each sheet in the report.

Rules Specifies the type of data used in each sheet in the selected report.

•Batch

• EachSample

• SampleType: SampleType

•CompoundType: CompoundType

•SampleCustomFormula:

Buttons

View Report Templates Displays the C:\TraceFinderData\4.0\Templates\ReportTemplates folder that contains

all report templates.

Opens the selected report template in the Report Designer.

Opens a blank report template in the Report Designer.

Opens the Report Designer showing the report information for the current batch in the

selected report template format.

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PDF Writes the generated report to a PDF file in the

…\TraceFinderData\4.0\Projects\batch\ReportOutput folder.

Excel Writes the generated report to a PDF file in the

…\TraceFinderData\4.0\Projects\batch\ReportOutput folder.

CSV Saves the generated report as a PDF file in the

…\TraceFinderData\4.0\Projects\batch\ReportOutput folder.

When the report contains multiple sheets, the application writes each sheet as a separate

CSV file.

Print Prints the generated report to your default printer.

Generates the selected type of reports for the current batch using the selected report

template.

Generated Reports

Template Report template used for the report. See Example template list for unknown screening

batches.

Rule Type of data used in each sheet of the report. See Rules.

Sample For sample-level reports, the name of each sample in the report.

Output Type of output specified for the report: PDF, Excel, CSV, or Print.

Generated Report File Lists the output file name for each report in the …\TraceFinderData\4.0\Projects folder.

View Displays the generated output file.

View Generated Reports Displays the C:\TraceFinderData\4.0\Projects folder that contains all report outputs.

Clear Removes all reports from the Generated Reports display. This does not delete the reports

from the C:\TraceFinderData\4.0\Projects folder.

Table 78. Report View parameters (Sheet 2 of 2)

Parameter Description

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Working in the Local Method View for Unknown Screening Batches

A local method is a copy of a master method associated with a batch. You can edit only the

local copy of the method, or you can edit the master method and overwrite the local copy

with the edited master method.

In the Local Method view, you can edit the local method parameters. A local method is a copy

of a master method associated with a batch. Local methods are named Batch_MasterMethod.

To open the Local Method View

1. Click Analysis in the navigation pane.

2. Click Local Method.

The Local Method View for the currently selected batch opens.

You can edit many of the method parameters in a local method. Editing the local method

does not affect parameters in the master method.

For detailed descriptions of method parameters, refer to Chapter 6, “Using the Method

Development Mode for Unknown Screening Methods,” in the Tra c eFin der L ab D i re ct o r

User Guide.

3. Enter any local changes to the method.

4. When you have finished editing the local method, choose File > Save.

5. To process the batch or create new reports with the edited local method, return to the

Batch View and submit the batch.

To overwrite the local method with the master method in the Batch View

In the Batch View, click Update.

The application overwrites the local method with the master method of the same name.

You can use this feature to overwrite an edited local method with the original master

method or to overwrite the local method with an updated master method.

6 Using the Analysis Mode for Unknown Screening Batches

Working in the Local Method View for Unknown Screening Batches

Thermo Scientific TraceFinder User Guide 381

Figure 157. Local Method View

6 Using the Analysis Mode for Unknown Screening Batches

Working in the Local Method View for Unknown Screening Batches

382 TraceFinder User Guide Thermo Scientific

Thermo Scientific TraceFinder User Guide 383

Using the Report Designer

Use the features in the Report Designer to create or edit report templates.

You can create new report templates or edit your laboratory’s report templates. You cannot

edit report templates that were provided with the TraceFinder application; however, you can

open a TraceFinder template, make changes, and save it to a new template name.

When user security is activated, you must have Template Editing permission to edit report

templates created by your laboratory. To use the administration tools to set Reports

permissions, refer to the instructions in the TraceFinder Administrator Console User Guide.

With the Report Designer, you can do any of the following to create or edit a report template:

• Make changes to the template as you would in an Excel application.

• Add or remove graphics.

• Add repeated areas of many types.

• Format fonts and colors.

• Add or edit formulas.

• Edit template text and headers.

In addition to the procedures in this chapter, you can view video instructions at

http://mytracefinder.com/plugins/reporting/.

Contents

•Editing a Template

•Toolbar Reference

•Plot Display Properties

•Quick Tips

Note To edit or create a template, you must have an open batch.

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Editing a Template

384 TraceFinder User Guide Thermo Scientific

Editing a Template

Use the Report Designer to add or remove graphics, add tables, add repeated areas, and

format headings, data, or cells.

Follow these procedures:

•To insert graphics into a report template

•To resize an inserted graphic

•To move an inserted graphic

•To i n se r t a t a b l e

•To r e m ov e a n i n se r t ed t a bl e

•To make changes to a table

•To format header text in the spreadsheet

•To format data in the report grid

•To format cells in the report grid

•To add repeated areas

•To insert a new sheet in a report

To insert graphics into a report template

1. Click the Insert tab.

The Insert page displays the available objects that you can insert in a quantitation, a target

screening, or an unknown screening report template.

Figure 158. Quan Plots features for quantitation batch report templates

For a description of each graphic element, see Insert Toolbar – General Features.

Figure 159. Screening Plots features for target screening batch report templates

For a description of each graphic element, see Insert Toolbar – Target Screening Reports.

Figure 160. Unknown Plots features for unknown screening batch report templates

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Editing a Template

Thermo Scientific TraceFinder User Guide 385

For a description of each graphic element, see Insert Toolbar – Unknown Screening

Reports.

2. In the template grid, drag to select cells where you want to place the item.

3. Select a sample from the list of samples in the left pane.

The application uses graphical data from the selected sample when you insert a graphical

plot.

4. Click a graphical plot in the toolbar to insert into the selected cells.

The application inserts the selected plot in the template grid.

Figure 161. Inserted peak chromatogram

To resize an inserted graphic

1. Right-click the graphic to make it editable.

Figure 162. Editable graphic

Note When the method for a quantitation or target screening batch includes

unknown screening, the Insert features for the report templates include Unknown

Plots.

Note You can also select a single row, and the application inserts the upper left corner

of the graphic at the first cell, using a minimum default size.

The border indicates that the

graphic is editable.

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Editing a Template

386 TraceFinder User Guide Thermo Scientific

2. Grab a corner of the graphic and stretch it to the new size.

Figure 163. Resized graphic

To move an inserted graphic

1. Right-click the graphic to make it editable.

Figure 164. Editable graphic

2. Click the graphic (notice the cursor change), and drag it to a new location.

Figure 165. Moved graphic

Note In this example, the original graphic was too small to display all the

chromatogram data. Stretching the graphic reveals the sample name, mass, filter, and

labeling.

The border indicates that the

graphic is editable.

Cursor for moving a graphic

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Editing a Template

Thermo Scientific TraceFinder User Guide 387

To insert a table

1. Select a row in the report grid where you want to insert the table.

2. Click the Insert tab, and then click the Ta bl e icon, .

The New Table dialog box opens.

3. Select the type of table that you want to insert and click Select Table.

The Edit Table Dialog Box opens.

The dropdown list in the upper left corner displays the data type for the table you

selected.

The left pane displays an alphabetical list of all available fields for the selected data type

that you can include in the table. To display fields for a different data type, see step 4.

The right pane lists the fields that are included in the new table.

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388 TraceFinder User Guide Thermo Scientific

You can select as many additional fields as you want. The table you create displays each

selected field as a table column. By default, all available fields for the original data type are

included in the table. The first field in the list is the leftmost column in the table. The last

field in the list is the rightmost column in the table. To change the order of the columns,

see step 6.

4. To add fields to the table from a different data type, do the following:

a. Click the dropdown list and select a different data type.

The left pane displays an alphabetical list of all available fields for the new data type.

b. Select a field in the left pane and then click .

The application moves the selected field to the rightmost pane to indicate that it is

included in the inserted table.

5. To select a field that you do not want in the table, in the rightmost pane, clear the check

box next to the field name.

6. To move a column up or down in the table, select the field name in the rightmost pane

and click the Up arrow, , or Down arrow, .

7. To edit the header for a table column, select the field in the list on the right, and then type

new header text in the Header box in the Field Details area.

The default header name is the same as the field name.

8. To find the formula for a field, select the field.

The application displays the formula in the Formula box.

This video demonstrates how to use the Report Designer to create your own formula:

Working with Formulas.

Field not selected

Field selected (blue background)

Details for the selected field

7 Using the Report Designer

Editing a Template

Thermo Scientific TraceFinder User Guide 389

9. To create a custom column, do the following:

a. Click Custom, .

The application adds a Custom field to the fields list.

b. Select the Custom field in the list.

The application display the details for the new, custom column.

c. Enter values for the Formula and Header.

10. To create a pivot table, do the following:

a. Select the Pivot Table check box.

The Pivot Table area expands to display the pivot table options.

b. Select the Use Key check box for the row label.

c. Select the Use Key check box for the column label.

d. Select the operation that you want to use to calculate the aggregate value: Sum,

Count, Average, First, or Last.

11. When you have made all your table selections, click OK.

The application inserts the table into the report template.

To remove an inserted table

1. Select all rows and cells in the table.

2. Right-click and choose Delete – Delete Cells and Shift Cells Left.

The application removes the entire table from the report template.

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390 TraceFinder User Guide Thermo Scientific

To make changes to a table

1. In the table that you want to edit, right-click and choose Data Table.

The Edit Table Dialog Box opens, displaying all of the available fields for the selected

template. The Edit Table dialog box is virtually identical to the dialog box that you used

to create a table.

2. Edit the fields for the table and click OK.

To format header text in the spreadsheet

1. In the Report Designer window, select the header in the spreadsheet table.

To change all headers, select the entire header row.

To change a single header, select the specific header cell.

2. Click the Home tab.

3. Use the Font icons to change the font format.

To format data in the report grid

1. Select the data that you want to format.

To format all rows in a column, select the header row.

To format a single cell of data, select only that cell.

2. Click the Home tab and use the toolbar icons to edit the font or cells as appropriate:

• Change the font or font size.

• Make the selected text bold.

• Make the selected text italics.

Tip You can also use the SHIFT key to select sequential cells or the CTRL key to

select nonsequential cells anywhere in the grid.

Tip You can also use the SHIFT key to select sequential cells or the CTRL key to

select nonsequential cells anywhere in the grid.

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Thermo Scientific TraceFinder User Guide 391

• Underline the selected text.

• Apply borders to the currently selected cells.

• Increase or decrease font size.

• Apply color to the background for selected cells.

• Change the font color.

To format cells in the report grid

1. Select the cells that you want to modify:

To change all cells in a row, select the entire row.

To change a single cell, select only that cell.

2. Click the Home tab and use the Alignment or Cells toolbar icons to edit the cells.

3. To align the cell text to the top, center, or bottom of the cell, click one of these icons:

4. To align the cell text to the left, center, or right of the cell, click one of these icons:

5. To make all contents visible within a cell, click Wrap Text.

6. To join selected cells into one cell, click Merge Cells.

7. To insert cells, rows, or columns into the template, click Insert.

8. To delete rows or columns from the template, click Delete.

9. To change the row height or column width, organize sheets, or protect or hide cells, click

Format.

10. To highlight or emphasize useful cells based on specific criteria, click Conditional

Formatting to use data bars, color scales, or icon sets.

11. To show formulas for selected cells instead of the resulting value, click Show Formulas.

Tip You can also use the SHIFT key to select sequential cells or the CTRL key to

select nonsequential cells.

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392 TraceFinder User Guide Thermo Scientific

To add repeated areas

1. To define a repeat area, select the cells that you want to repeat.

You can repeat only one area per worksheet, but you can repeat it many times. You cannot

insert data tables beneath a repeated area. See Example of repeated areas.

2. Click the Insert tab and then click Repeat.

The Repeat Area Definition dialog box opens.

3. To filter the repeat area according to the filter criteria, type the string syntax in the Filter

String box.

4. Select to repeat for each sample, for each compound, or for both.

5. Define whether the repeat area repeats first for samples or first for compounds:

• To have the repeat area repeat first for samples and then for compounds, clear the

Compound Centric check box.

• To have the repeat area repeat first for compounds and then for samples, select the

Compound Centric check box.

6. To define the number of times to repeat horizontally before wrapping to the next row,

type a number in the Max Horizontal Repeats box.

7. To define the number of times to repeat vertically before inserting an auto-page break,

type a number in the Max Vertical Repeats Per Page box.

8. To define the maximum suggested number of repeats, type a number in the Repeats in

Design Mode box.

This maximum number of repeats is intended to limit the size of the report while you are

editing the report in the Report Designer. When generating an actual report, the

application does not enforce this limit.

7 Using the Report Designer

Editing a Template

Thermo Scientific TraceFinder User Guide 393

In this example, the repeated area (outlined in red) displays the peak chromatogram, target

peak, total area, peak area, retention time, theoretical amount, actual amount, and reported

flags, if any, for each compound.

Figure 166. Example of repeated areas

To insert a new sheet in a report

1. Click the Home tab.

2. In the Cells area, choose Insert Sheet from the Insert menu.

The application adds a new sheet to the report.

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Editing a Template

394 TraceFinder User Guide Thermo Scientific

Edit Table Dialog Box

Use the options in the Edit Table dialog box to edit the fields in a table.

Figure 167. Edit Table dialog box

Table 79. Edit Table dialog box parameters (Sheet 1 of 2)

Parameter Description

Dropdown List Specifies the type of table you are editing.

Field List Lists all available table fields.

Table Displays the selected table type and the fields included in the table.

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Field Details

Formula Specifies the functions and arguments used to define the field.

Preview Specifies the name of the raw data file used for the report.

Header Specifies the header name for the column in the spreadsheet.

Description Specifies the type of field.

Table Filter

Table Filter Specifies the filter used for the sample compounds.

Preview –

Sort By Sorts the data by ascending or descending values.

Pivot Table

Pivot Table Enables the Pivot Table features.

Row Label –

Row Key –

Column Label –

Column Key –

Value –

Operation Specifies the operation used to calculate the aggregate value.

Valid values: Sum, Count, Average, First, Last

Box Format –

Additional Values –

Delete Deletes the selected table from the template.

Table 79. Edit Table dialog box parameters (Sheet 2 of 2)

Parameter Description

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Toolbar Reference

396 TraceFinder User Guide Thermo Scientific

Toolbar Reference

The Report Designer includes the following toolbars.

•Home Toolbar

•Insert Toolbar – General Features

•Insert Toolbar – Quantitation Reports

•Insert Toolbar – Target Screening Reports

•Insert Toolbar – Unknown Screening Reports

•Page Layout Toolbar

Home Toolbar

Use the options in the Home toolbar to modify fonts, align cell data, and format cells.

Table 80. Home toolbar options (Sheet 1 of 2)

Option Description

Clipboard

Paste Paste the contents of the Clipboard. You can also paste only formating or only a

formula.

Copy Copy text or graphics to use in another place.

Font

Font and size lists Use the dropdown lists to change the font or font size.

Bold Make the selected text bold.

Italic Make the selected text italics.

Underline Underline the selected text.

Border Apply borders to the currently selected cells.

Font size Increase or decrease the font size.

Fill color Apply color to the background for selected cells.

Font color Change the font color.

Alignment

Align the cell text to the top, center, or bottom of the cell.

Align the cell text to the left, center, or right of the cell.

Wrap text Make all contents visible within a cell.

7 Using the Report Designer

Toolbar Reference

Thermo Scientific TraceFinder User Guide 397

Insert Toolbar – General Features

Use the features on the Insert page to create and edit tables, formulas, graphic plots, charts,

and illustrations.

Graphic plots can represent data from quantitative, target screening, or unknown screening

data. The Insert page displays the available data plots for the type of batch: quantitation,

quantitation plus unknown screening, target screening, target screening plus unknown

screening, or unknown screening only.

The following graphic outlines all three plot types for illustrative purposes only.

Merge cells Join selected cells into one cell.

Cells

Insert Insert cells, rows, columns, or sheets into a template.

Delete Delete rows or columns from a template.

Format Change the row height or column width, organize sheets, or protect or hide cells.

Conditional Formatting Based on specific criteria, highlight or emphasize useful cells using data bars, color

scales, and icon sets.

Show Formulas Show formulas for selected cells instead of the resulting value.

Table 80. Home toolbar options (Sheet 2 of 2)

Option Description

Table 81. Insert toolbar options (Sheet 1 of 2)

Option Description

Tables

Table Create a table to manage and analyze data.

Field Edit the formula for a field by choosing functions and editing

arguments.

Repeat

Repeat Repeat text, cell, or graphic elements.

Refresh Update the view to reflect recent changes.

Quan Plots Can be stand-alone or used with Unknown plots. For descriptions of

quantitation plots, see Insert Toolbar – Quantitation Reports.

Screening Plots Can be stand-alone or used with Unknown plots. For descriptions of

target screening plots, see Insert Toolbar – Target Screening Reports.

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Toolbar Reference

398 TraceFinder User Guide Thermo Scientific

Insert Toolbar – Quantitation Reports

Use the options in the Insert toolbar to add graphics, plots, and other objects to a template or

report. You can also set up repeating objects and define functions.

For each inserted plot, you can customize the display properties. See Quantitation and Target

Screening Plots.

Unknown Plots

Can be stand-alone or used with either Quan plots or Screening plots.

For descriptions of unknown screening plots, see Insert Toolbar –

Unknown Screening Reports.

Charts

Adds a custom chart. To define the chart, double-click the inserted

blank chart.

Illustrations

Insert a picture from a file.

Table 81. Insert toolbar options (Sheet 2 of 2)

Option Description

Table 82. Insert toolbar Quantitation options (Sheet 1 of 2)

Option Description

Adds a sample TIC.

For information about sample TIC data in the Data Review results, see Peaks Pane.

Adds a peak chromatogram.

For information about peak chromatogram data in the Data Review results, see Quan Peak.

Adds an ion overlay.

For information about ion overlay data in the Data Review results, see Ion Overlay.

Adds a quantitation peaks overlay plot.

For information about quantitation peaks overlay data in the Data Review results, see Quan Peaks

Overlay.

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Thermo Scientific TraceFinder User Guide 399

Adds a spectral plot.

For information about spectral data in the Data Review results, see Spectra.

Adds a comparative spectral plot.

For information about comparative spectral data in the Data Review results, see Spectra.

Adds a calibration curve plot.

For information about calibration curve data in the Data Review results, see Calibration Curve.

Adds an isotope plot to display the number of isotopes found, the score, a pass/fail flag, and a plot

of the isotopes.

For information about isotope plot data in the Data Review results, see Isotope.

Adds a fragment plot.

For information about fragment plot data in the Data Review results, see Fragments.

Adds a library plot.

For information about library plot data in the Data Review results, see Library Match.

Adds a group averages plot.

For information about group averages data in the Data Review results, see Group Averages.

Adds an RT summary plot.

For information about retention time summary data in the Data Review results, see Retention

Time Summary.

Adds an XIC summary plot.

For information about XIC summary data in the Data Review results, see XIC Overlay.

Adds a Batch Quan Peaks Overlay plot that displays all quantitative peaks in the batch.

Table 82. Insert toolbar Quantitation options (Sheet 2 of 2)

Option Description

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Insert Toolbar – Target Screening Reports

Use the options in the Insert toolbar to add graphics, plots, and other objects to a template or

report. You can also set up repeating objects and define functions.

For each inserted plot, you can customize the display properties. See Quantitation and Target

Screening Plots.

Table 83. Insert toolbar Target Screening options (Sheet 1 of 2)

Option Description

Adds a sample TIC plot.

Adds a peak chromatogram plot.

For information about peak chromatogram data in the Data Review results, see

Chromatogram Pane.

Adds an ion overlay plot.

Adds a quantitation peaks overlay plot.

Adds a spectral plot.

For information about spectral plot data in the Data Review results, see Spectrum.

Adds an isotope plot to display the number of isotopes found, the score, a pass/fail flag, and a

plot of the isotopes.

For information about isotope plot data in the Data Review results, see Isotopes.

Adds a fragment plot.

For information about fragment plot data in the Data Review results, see Fragments.

Adds a library plot.

For information about library plot data in the Data Review results, see Library.

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Toolbar Reference

Thermo Scientific TraceFinder User Guide 401

Insert Toolbar – Unknown Screening Reports

Use the options in the Insert toolbar to add graphics, plots, and other objects to a template or

report. You can also set up repeating objects and define functions.

For each inserted plot, you can customize the display properties. See Unknown Screening

Plots.

Adds a group averages plot.

For information about group averages data in the Data Review results, see Groups.

Adds an RT summary plot.

Adds an XIC summary plot.

Adds a Batch Quan Peaks Overlay plot that displays all quantitative peaks in the batch.

Table 83. Insert toolbar Target Screening options (Sheet 2 of 2)

Option Description

Table 84. Insert toolbar Unknown Screening options (Sheet 1 of 2)

Option Description

Adds a peak chromatogram.

For information about peak chromatogram data in the Data Review results, see Peak

Chromatogram Pane.

Adds a TIC chromatogram.

For information about TIC chromatogram data in the Data Review results, see TIC

Chromatogram Pane.

Adds a spectral plot.

For information about spectral plot data in the Data Review results, see Spectrum Pane.

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Adds an XIC overlay plot.

For information about XIC overlay data in the Data Review results, see XIC Overlay Pane.

Adds a library plot.

For information about library plot data in the Data Review results, see Library Search Pane.

Adds an XIC plot.

For information about XIC plot data in the Data Review results, see XIC Pane.

Adds a cross-sample peak overlay plot.

For information about cross-sample peak overlay data in the Data Review results, see Cross

Sample Peak Overlay Pane.

Adds a fragments plot.

For information about fragments plot data in the Data Review results, see Fragments Pane.

Adds an isotopes plot.

For information about isotopes plot data in the Data Review results, see Isotopes Pane.

Adds a chemical structure plot.

For information about chemical structure plot data in the Data Review results, see Chemical

Structure Pane.

Adds a group averages plot.

For information about group averages data in the Data Review results, see Group Averages

Pane.

Table 84. Insert toolbar Unknown Screening options (Sheet 2 of 2)

Option Description

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Thermo Scientific TraceFinder User Guide 403

Page Layout Toolbar

Use the options in the Page Layout toolbar to adjust margins, orientation, paper size, and page

breaks. To see your changes, click Print Preview.

Table 85. Page Layout toolbar options

Option Description

View the report before printing it.

Define page details.

Select page margins for the current view or the entire document.

Switch the pages from portrait to landscape view.

Choose a page size for the current view or the entire document.

Specify where a new page begins in the printed copy.

Template Properties Open the Template Properties dialog box where you can specify

the expected batch type for the report template.

The Template Properties dialog box also displays the Used Range

so that you can identify when there is empty white space in the

report template. Extra white space to the right or left of the

report content can cause unwanted page breaks.

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Plot Display Properties

404 TraceFinder User Guide Thermo Scientific

Plot Display Properties

For plot types that you insert in the spreadsheet, you can change the display properties.

To change the plot display properties

1. Insert a plot in the spreadsheet.

2. Right-click the plot to select it.

3. Right-click the plot again to display the shortcut menu.

4. Choose Properties.

The Plot Properties dialog box opens, displaying the editable display properties for the

selected plot type.

The following topics show the plots in the report templates and describe their properties.

•Quantitation and Target Screening Plots

•Unknown Screening Plots

Quantitation and Target Screening Plots

To customize the display in the quantitation and target screening reports, use the Plot

Properties dialog box for each plot.

•Sample TIC Plot

•Peak Chromatogram Plot

•Ion Overlay Plot

•Quan Peaks Overlay Plot

•Spectral Plot

•Comparative Spectral Plot (quantitation reports only)

•Calibration Curve Plot (quantitation reports only)

•Isotope Plot, Fragment Plot, or Library Plot

•Group Bar Graph Plot

•RT Summary Plot

•XIC Overlay Plot

•Batch Quan Peaks Overlay Plot

Note This topic shows examples of all plot types; however, the following plots do not have

editable plot properties: Calibration Curve, Group Bar Graph, and RT Summary.

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Thermo Scientific TraceFinder User Guide 405

Sample TIC Plot

Use the icon to insert a sample TIC Chromatogram plot.

Figure 168. TIC Chromatogram plot

Figure 169. Plot Properties dialog box for a TIC Chromatogram plot

Table 86. Plot Properties parameters for a TIC Chromatogram (Sheet 1 of 2)

Command Description

TIC Polarity Specifies the polarity of adducts displayed in the plot.

All: Displays positive, negative, and analog adducts.

Positive: Displays only positive adducts.

Negative: Displays only negative adducts.

Analog: Displays only analog adducts.

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

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Peak Chromatogram Plot

Use the icon to insert a Peak Chromatogram plot.

Figure 170. Peak Chromatogram plot

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Header Displays the raw data file path at the top of the plot.

Show Grid Lines Displays the grid lines in the plot background.

Peak Plot Labels

RT Displays the retention time (RT) for each peak in the plot.

Show All Apex Times Displays all surrounding apex times in the plot.

Nominal Level Displays the nominal level (NL) values for each peak in the

plot.

Table 86. Plot Properties parameters for a TIC Chromatogram (Sheet 2 of 2)

Command Description

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Figure 171. Plot Properties dialog box for Peak Chromatogram plot

Table 87. Plot Properties parameters for a Peak Chromatogram plot (Sheet 1 of 2)

Command Description

Peak Type Specifies the type of peak to display in the plot:

•Quan

• Confirming

• InternalStandard

• InternalStandardConfirming

Integration:

Always Show Processed

Peak

Specifies that the plot always displays the processed peak.

Quan Peak Index Valid values: 1 through 9

Time Range Specifies that the plot display one of the following:

• View Width: Zooms the display on the peak of interest.

• Full Window: Displays the full width of the scan.

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

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Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Grid Lines Displays the grid lines in the plot background.

Peak Plot Labels

RT Displays the retention time (RT) label in the peak

chromatogram plot.

Area Displays the peak area (AA) label in the peak chromatogram

plot.

Height Displays the peak height (AH) label in the peak

chromatogram plot.

Signal to Noise Displays the signal-to-noise (SN) label in the peak

chromatogram plot.

Show All Apex Times Displays all surrounding apex times in the plot.

Sample Filename Displays the name of the sample file.

Compound Name Displays the compound name.

Nominal Level Displays the nominal level (NL) values for each peak in the

plot.

Filter Displays the filter used for the scan. The plot displays the

filter name below the raw data file name.

Plot Style

Point To Point Displays chromatograms in the following format:

Stick Displays chromatograms in the following format:

Table 87. Plot Properties parameters for a Peak Chromatogram plot (Sheet 2 of 2)

Command Description

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Ion Overlay Plot

Use the icon to insert an Ion Overlay plot.

Figure 172. Ion Overlay plot

Figure 173. Plot Properties dialog box for Ion Overlay plot

Table 88. Plot Properties parameters for an Ion Overlay plot (Sheet 1 of 2)

Command Description

Peak Type Specifies the type of peak to display in the plot: Quan or

InternalStandard

Quan Peak Index Valid values: 1 through 9

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Quan Peaks Overlay Plot

Use the icon to insert a quantitation peaks overlay plot.

Figure 174. Quan Peaks Overlay plot

Time Range Specifies that the plot display one of the following:

• View Width: Zooms the display on the peak of interest.

• Full Window: Displays the full width of the scan.

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Header Displays the raw data file name and compound name.

Show Grid Lines Displays the grid lines in the plot background.

Table 88. Plot Properties parameters for an Ion Overlay plot (Sheet 2 of 2)

Command Description

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Thermo Scientific TraceFinder User Guide 411

Figure 175. Plot Properties dialog box for a Quan Peaks Overlay plot

Table 89. Plot Properties parameters for a Quan Peaks Overlay plot

Command Description

Peak Type Specifies the type of peak to display in the plot: Quan or

InternalStandard

Quan Peak Index Valid values: 1 through 9

Time Range Specifies that the plot display one of the following:

• View Width: Zooms the display on the peak of interest.

• Full Window: Displays the full width of the scan.

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Header Displays the raw data file name and compound name.

Show Grid Lines Displays the grid lines in the plot background.

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Spectral Plot

Use the icon to insert a Spectral plot.

Figure 176. Spectral plot

Figure 177. Plot Properties dialog box for a Spectral plot

Table 90. Plot Properties parameters for a Spectral plot

Command Description

Target Peak Index Valid values: 1 through 9

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Header Displays the raw data file name and compound name.

Show Grid Lines Displays the grid lines in the plot background.

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Thermo Scientific TraceFinder User Guide 413

Comparative Spectral Plot (quantitation reports only)

Use the icon to insert a Comparative Spectral plot.

Figure 178. Comparative Spectral plot

Figure 179. Plot Properties dialog box for a Comparative Spectral plot

Table 91. Plot Properties parameters for a Comparative Spectral plot (Sheet 1 of 2)

Command Description

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

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Calibration Curve Plot (quantitation reports only)

Use the icon to insert a Calibration Curve plot.

Figure 180. Calibration Curve plot

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Grid Lines Displays the grid lines in the plot background.

Table 91. Plot Properties parameters for a Comparative Spectral plot (Sheet 2 of 2)

Command Description

Note There are no plot properties for a calibration curve plot.

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Thermo Scientific TraceFinder User Guide 415

Isotope Plot, Fragment Plot, or Library Plot

Do one of the following:

• Use the icon to insert an Isotope plot.

• Use the icon to insert a Fragment plot.

• Use the icon to insert a Library plot.

The Isotope, Fragment, and Library plots use identical plot properties.

Figure 181. Isotope plot

Figure 182. Fragment plot

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Figure 183. Library plot

Figure 184. Plot Properties dialog box for an Isotope plot, a Fragment plot, or a Library plot

Table 92. Plot Properties parameters for an Isotope plot, a Fragment plot, or a Library plot

(Sheet 1 of 2)

Command Description

Target Peak Index Specifies the number of peak plots to display.

Valid values: 1 through 9

Confirmation Plot

Type

Specifies that the plot display one of the following:

• All: Displays isotopes, fragments, or library hits.

• Multi: Displays individual plots for each isotope. You can

individually stack or overlay the plots for each isotope.

• Single: Displays only the selected isotope, fragment, or

library hit.

For examples of these display types, see Isotope, Fragments, or

Library Match.

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Thermo Scientific TraceFinder User Guide 417

Group Bar Graph Plot

Use the icon to insert a Group Bar Graph plot.

Figure 185. Group Bar Graph plot

RT Summary Plot

Use the icon to insert an RT Summary plot.

Figure 186. RT Summary plot

Confirmation Plot

Style

Specifies that the plot display one of the following:

• Stacked: Stacks the simulated spectrum and the peak apex

spectrum.

• Overlay: Overlays the two spectrum displays.

For examples of these display types, see Isotope, Fragments, or

Library Match.

Table 92. Plot Properties parameters for an Isotope plot, a Fragment plot, or a Library plot

(Sheet 2 of 2)

Command Description

Note There are no plot properties for a group bar graph plot.

Note There are no plot properties for an RT summary plot.

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XIC Overlay Plot

Use the icon to insert an XIC Overlay plot.

Figure 187. XIC Overlay plot

Figure 188. Plot Properties dialog box for an XIC Overlay plot

Table 93. Plot Properties parameters for an XIC Overlay plot

Command Description

Selected Peaks

Top 20 Displays the top 20 peaks.

Selected Peak Displays only the selected peak.

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Thermo Scientific TraceFinder User Guide 419

Batch Quan Peaks Overlay Plot

Use the icon to insert a Batch Quan Peaks Overlay plot.

Figure 189. Batch Quan Peaks Overlay plot

Figure 190. Plot Properties dialog box for a Batch Quan Peaks Overlay plot

Table 94. Plot Properties parameters for a Batch Quan Peaks Overlay plot (Sheet 1 of 2)

Command Description

Quan Peak Index Valid values: 1 through 9

Time Range Specifies that the plot display one of the following:

• View Width: Zooms the display on the peak of interest.

• Full Window: Displays the full width of the scan.

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Unknown Screening Plots

To customize the display in the unknown screening report, use the Plot Properties dialog box

for each plot.

•Peak Chromatogram Plot

•TIC Chromatogram Plot

•Spectral Plot

•XIC Overlay Plot

•Library Plot, Fragments Plot, or Isotopes Plot

•XIC Plot

•Cross Sample Peak Overlay Plot

•Chemical Structure Plot

•Group Bar Graph Plot

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Header Displays the raw data file name and compound name.

Show Grid Lines Displays the grid lines in the plot background.

Number of Columns Specifies the number of columns that you want to display in

the inserted graphic. The application resizes the images to fit

the specified number of columns.

Table 94. Plot Properties parameters for a Batch Quan Peaks Overlay plot (Sheet 2 of 2)

Command Description

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Thermo Scientific TraceFinder User Guide 421

Peak Chromatogram Plot

Use the icon to insert a Peak Chromatogram plot.

Figure 191. Peak Chromatogram plot

Figure 192. Plot Properties dialog box for Peak Chromatogram plot

Table 95. Plot Properties parameters for a Peak Chromatogram plot (Sheet 1 of 2)

Command Description

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

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TIC Chromatogram Plot

Use the icon to insert a TIC Chromatogram plot.

Figure 193. TIC Chromatogram plot

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Grid Lines Displays the grid lines in the plot background.

Peak Plot Labels

RT Displays the retention time (RT) label in the peak

chromatogram plot.

Area Displays the peak area (AA) label in the peak chromatogram

plot.

Height Displays the peak height (AH) label in the peak

chromatogram plot.

Signal to Noise Displays the signal-to-noise (SN) label in the peak

chromatogram plot.

M/Z Displays the peak mass.

Show All Apex Times Displays all surrounding apex times in the plot.

Sample Filename Displays the name of the sample file.

Filter Displays the filter used for the scan. The plot displays the

filter name below the raw data file name.

Table 95. Plot Properties parameters for a Peak Chromatogram plot (Sheet 2 of 2)

Command Description

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Thermo Scientific TraceFinder User Guide 423

Figure 194. Plot Properties dialog box for a TIC Chromatogram plot

Table 96. Plot Properties parameters for a TIC Chromatogram plot (Sheet 1 of 2)

Command Description

TIC Polarity Specifies the polarity of adducts displayed in the plot.

All: Displays positive, negative, and analog adducts.

Positive: Displays only positive adducts.

Negative: Displays only negative adducts.

Analog: Displays only analog adducts.

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Header Displays the raw data file name.

Show Grid Lines Displays the grid lines in the plot background.

Peak Plot Labels

RT Displays the retention time (RT) label in the TIC

chromatogram plot.

Show All Apex Times Displays all surrounding apex times in the plot.

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Spectral Plot

Use the icon to insert a Spectral plot.

Figure 195. Spectral plot

Figure 196. Plot Properties dialog box for a Spectral plot

Nominal Level Displays the nominal level (NL) values for each peak in the

plot.

Filter Displays the filter used for the scan. The plot displays the

filter name below the raw data file name.

Table 96. Plot Properties parameters for a TIC Chromatogram plot (Sheet 2 of 2)

Command Description

Table 97. Plot Properties parameters for a Spectral plot (Sheet 1 of 2)

Command Description

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

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Thermo Scientific TraceFinder User Guide 425

XIC Overlay Plot

Use the icon to insert an XIC Overlay plot.

Figure 197. XIC Overlay plot

Figure 198. Plot Properties dialog box for an XIC Overlay plot

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Header Displays the name of the sample file, the name of the

compound, the retention time, the nominal level, and the

filter used for the scan.

Show Grid Lines Displays the grid lines in the plot background.

Table 97. Plot Properties parameters for a Spectral plot (Sheet 2 of 2)

Command Description

Table 98. Plot Properties parameters for an XIC Overlay plot

Command Description

Selected Peaks

Top 20 Displays the top 20 peaks.

Selected Peak Displays only the selected peak.

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Library Plot, Fragments Plot, or Isotopes Plot

Do one of the following:

• Use the icon to insert a Library plot.

• Use the icon to insert a Fragments plot.

Use the icon to insert an Isotope plot.

The Library, Fragments, and Isotopes plots use identical plot properties.

Figure 199. Library plot

Figure 200. Fragments plot

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Thermo Scientific TraceFinder User Guide 427

Figure 201. Isotopes plot

Figure 202. Plot Properties dialog box for a Library plot, a Fragments plot, or an Isotopes plot

Table 99. Plot Properties parameters for a Library plot, a Fragments plot, or an Isotopes plot

Command Description

Confirmation Plot Type Specifies that the plot display one of the following:

• All: Displays isotopes, fragments, or library hits.

• Multi: Displays individual plots for each isotope. You

can individually stack or overlay the plots for each

isotope.

• Single: Displays only the selected isotope, fragment, or

library hit.

For examples of these display types in the Data Review, see

Library Search Pane, Fragments Pane, or Isotopes Pane.

Confirmation Plot Style Specifies that the plot display one of the following:

• Stacked: Stacks the simulated spectrum and the peak

apex spectrum.

• Overlay: Overlays the two spectrum displays.

For examples of these display types in the Data Review, see

Library Search Pane, Fragments Pane, or Isotopes Pane.

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XIC Plot

Use the icon to insert an XIC plot.

Figure 203. XIC plot

Figure 204. Plot Properties dialog box for an XIC plot

Table 100. Plot Properties parameters for an XIC plot (Sheet 1 of 2)

Command Description

TIC Polarity Specifies the polarity of adducts displayed in the plot.

All: Displays positive, negative, and analog adducts.

Positive: Displays only positive adducts.

Negative: Displays only negative adducts.

Analog: Displays only analog adducts.

Y-Axis Type

Relative Displays the y-axis scale from 0 through 100.

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Thermo Scientific TraceFinder User Guide 429

Cross Sample Peak Overlay Plot

Use the icon to insert a Cross Sample Peak Overlay plot.

Figure 205. Cross Sample Peak Overlay plot

Absolute Displays the y-axis scale from 0 to the actual value of the

most intense peak in the group.

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Labels

Show Label for Y-Axis Displays the relative intensity value on the y axis.

Show Label for X-Axis Displays the retention time (RT) value on the x axis.

Show Header

Show Grid Lines Displays the grid lines in the plot background.

Peak Plot Labels

RT Displays the retention time (RT) values for each peak in the

plot.

Show All Apex Times Displays all surrounding apex times in the plot.

Nominal Level Displays the nominal level (NL) values for each peak in the

plot.

Filter Displays the filter used for the scan. The plot displays the

filter name below the raw data file name.

Table 100. Plot Properties parameters for an XIC plot (Sheet 2 of 2)

Command Description

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Figure 206. Plot Properties dialog box for a Cross Sample Peak Overlay plot

Chemical Structure Plot

Use the icon to insert a Chemical Structure plot.

Figure 207. Chemical Structure plot

Figure 208. Plot Properties dialog box for a Chemical Structure plot

Table 101. Plot Properties parameter for a Cross Sample Peak Overlay plot

Command Description

Label in Scientific

Notation

Displays the y-axis scale in scientific notation.

Table 102. Plot Properties parameter for a chemical structure plot

Command Description

Library Position Specifies the hierarchical position in the library when there

are multiple chemical structures.

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Group Bar Graph Plot

Use the icon to insert a Group Bar Graph plot.

Figure 209. Group Bar Graph plot

Note There are no plot properties for a group bar graph plot.

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432 TraceFinder User Guide Thermo Scientific

Quick Tips

Follow these tips to make the most of the Report Designer features.

To move a report to the Archive folder

1. With a report open for editing, choose File > Archive from the Report Designer main

menu.

2. At the confirmation prompt, click Yes.

The application deletes the report from the …batch\ReportOutput folder.

To insert items in the Report Designer

• Insert a data table when the selected cell is above or below any other table, but not in the

same row as a field. You cannot insert tables in repeat areas.

• Insert a data field when the selected cell is not in the same row as a table.

• Use these shortcut keys:

To format cells and group headers

Because the first row of a data table retains formatting information, edit the formatting of

the first row.

The application copies the formatting to all other rows.

For group header items, the application copies the formatting of the first group header to

the remaining group headers.

To sort fields

Select a field, and then click A-Z to sort the data in ascending or descending order.

CTRL+T Insert a table.

CTRL+T Edit a table when the selected cell is inside a table.

CTRL+SHIFT+T Insert or edit a field.

CTRL+R Insert or edit a repeating area.

Thermo Scientific TraceFinder User Guide 433

Using the Audit Viewer

The TraceFinder application records all user access, including logging in, logging out, data

creation and editing (batches, methods, and templates), and manual integration. You can use

the Audit Viewer to view the resulting log files to track modifications to the data. When an

event requires confirmation (as specified in the Administrator Console), the Audit Viewer

records who confirmed each change to a batch, method, or template. When no confirmation

is required, then the Audit Viewer records the user who was logged in when the change

occurred.

In the Administration Console, a user with Auditing permissions can configure the auditing

service by specifying which events are logged, which events require confirmation, a list of

default reasons for a specific event, and whether a user can submit a custom reason. To use the

auditing administration tools, refer to the instructions in the TraceFinder Administrator

Console User Guide.

Audit Trail Log Files

The application creates the following audit trail log files:

• Application: Records all user access, such as starting and stopping the application, logging

in, logging out, or accessing or saving data in batches and methods. The application saves

the data in the following log file: C:\Thermo\TraceFinder\4.0\Logs\AuditLog.adb.

• Master Method: Records all user interactions with master methods, such as creating,

opening, or editing a master method. The application saves the data in the following log

file: C:\TraceFinderData\4.0\Methods\MasterMethodName\AuditLog.adb.

IMPORTANT TraceFinder 4.1 uses the same data as TraceFinder 4.0. By default, the application

stores the log files for the 4.1 release in the TraceFinderData\4.0 or TraceFinder\4.0 folders.

Contents

•Audit Trail Log Files

•Audit Log File Functions

•Audit Viewer

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434 TraceFinder User Guide Thermo Scientific

• Batch Template: Records all user interactions with batch templates, such as creating,

opening, or editing a batch template. The application saves the data in the following log

file: C:\TraceFinderData\4.0\Templates\Batches\BatchTemplateName\AuditLog.adb.

• Batch: Records all user interactions with batches, such as creating, opening, editing,

acquiring, processing, or generating reports for a batch. The application saves the data in

the following log file:

C:\TraceFinderData\4.0\Projects\SubFolder\BatchName\AuditLog.adb.

Audit Log File Functions

The Audit Viewer displays all saved audit log files, and you can filter and sort the audit data.

Follow these procedures:

•To access the Audit Viewer

•To select an audit log

•To view only application, method, batch, or batch template events

•To create a filter for audit log events

•To view audit event details

•To create a filter for an audit log history

•To display the history for an event

To access the Audit Viewer

Choose To ol s > Aud i t Tra il from the TraceFinder main menu or click the Audit Viewer

icon, .

The Audit Viewer opens.

Note The Audit Viewer is available only when you have enabled auditing from the

Administration Console. Refer to the TraceFinder Administrator Console User Guide.

Note The Tools > Audit Trail menu command always opens to application log files,

whereas the Audit Viewer icon is context sensitive and opens to the appropriate type

of log files (application, method, batch, or batch template).

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Thermo Scientific TraceFinder User Guide 435

To select an audit log

1. Click the Open Audit Log icon, .

The application opens the Audit Log Selection dialog box.

2. Expand a log folder to select an application, batch, method, or batch template audit log

file, and click OK.

The Audit Viewer displays the contents of the selected audit log file, as in this example for

a method.

To view only application, method, batch, or batch template events

1. In the Active Log list, select an Active Log file.

• Application logs include application and security events.

• Method logs include application and method events.

• Batch logs include application, method, and batch events.

• Batch template logs include application and batch template events.

The Audit Viewer displays icons for each of the event types included in the log file.

2. Click an icon to turn the display on or off.

In this example, the Events pane displays Batch and Method events and hides Application

events.

Note There is no icon for security events in an application log file. You cannot hide

the display of security events.

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To create a filter for audit log events

1. In the Events pane, click the Create New Filter icon, .

The Filter Editor dialog box opens.

2. In the View box, type a name for the new filter.

You can also leave the View box empty when you enter your filter criteria. When you

finish adding conditions and click OK (step 8), the application filters the current events

list based on the filter criteria you specify, but the filter is not saved. The Filter list in the

viewer identifies this filter as (Custom).

3. Click the Add icon, .

The application adds a new, undefined condition to the Condition list.

4. In the Field list, select one of the following field types.

5. In the Operator list, select one of the available operators.

The available operators depend on the field type that you selected.

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Thermo Scientific TraceFinder User Guide 437

6. In the Value box, type a value or select a value from the list.

• For the Date/Time field, type a numerical value in the Value box.

• For the User, Reason, Context, or Details field, type the appropriate text in the Value

box. This value is case sensitive.

• For the Type of Event field, select one of the following values.

The Filter at the bottom of the dialog box displays the complete definition for the filter.

7. Repeat step 3 (on page 436) through step 6 (on this page) for each condition that you

want to include in your filter.

8. When you have added all your conditions, click OK.

The application creates the new filter with the specified conditions.

Note You can also click the Tokens icon, , and select a token for the Value.

Tokens are predefined values, such as dates and sample or compound identifiers.

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To view audit event details

In the Events pane, select an event.

The Details pane displays key values based on the type of log you select.

To create a filter for an audit log history

1. In the History pane, click the Create New Filter icon, .

The Filter Editor dialog box opens.

2. In the View box, type a name for the new filter.

You can also leave the View box empty when you enter your filter criteria. When you

finish adding conditions and click OK (step 8), the application filters the current history

list based on the criteria you specify, but the filter is not saved. The Filter list in the viewer

identifies this filter as (Custom).

3. Click the Add icon, .

The application adds a new, undefined condition to the Conditions list.

Details for batch log files include the name of the batch.

Details for method log files include the name of the method and

the method type.

Details for batch template log files include the name of the batch

template, the location of the data repository, and the subproject

folder where the template was created.

Details for Application log files include whether the events are for a

batch or method, the location of the data repository, and, for a

batch, the subproject folder where the batch was created.

Details for Security log files include the authentication method

used (Windows Active Directory or local machine) and the

location of the administrator repository.

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4. In the Field list, select one of the following field types.

5. In the Operator list, select from equals, less than/greater than, or contains.

The available operators depend on the field type that you selected.

6. In the Value list, type or select a value from the list.

• For the Name, Context, or Details field, type the appropriate text in the Value box.

This value is case sensitive.

• For the OldValue or NewValue field, type a numerical value in the Value box.

• For the ChangeType field, select one of the following values.

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• When the selected Field is ItemType, select one of the following values.

The Filter at the bottom of the dialog box displays the complete definition for the filter.

7. Repeat steps 3 through 6 for each condition that you want to include in your filter.

8. When you have added all your conditions, click OK.

The applications created the new filter with the specified conditions.

To display the history for an event

1. In the Events pane, select an event that has a selected check box in the History column.

Note You can also click the Tokens icon, , and select a token for the Value.

Tokens are predefined values, such as dates and sample or compound identifiers.

Select an event that has the

History check box selected.

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The History pane displays all unsaved (queued) actions for the selected event.

2. To limit the actions in the history list, select a filter from the Filter list.

See To create a filter for an audit log history.

Figure 210. Example History filter

When you select this filter,

the History pane displays only these actions for the selected event:

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Audit Viewer

442 TraceFinder User Guide Thermo Scientific

Audit Viewer

Use the Audit Viewer to view the audit log files to track user access and modifications to the

data. See Audit Viewer parameters.

Figure 211. Application log in the Audit Viewer

Figure 212. Batch log in the Audit Viewer

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Thermo Scientific TraceFinder User Guide 443

Table 103. Audit Viewer parameters (Sheet 1 of 2)

Parameter Description

Active Log Name of the current audit log file.

Opens the Audit Log Selection dialog box where you can open a different audit log file.

You can select from these audit log files: application, batch, method, or batch template.

Refreshes the current audit log file in the viewer.

Show Select to display only specific types of events in the Events list. The selected log file can

contain batch, method, and application events.

Events

Filter Select a filter view to use for displaying the event log entries.

Opens the Filter Editor dialog box where you can create a filter view.

Opens the Filter Editor dialog box where you can edit the current filter view.

Deletes the current event filter view.

Log

Indicates an event that occurred at the main application level, such as

logging in or opening a batch.

Indicates an event that occurred in the Administration Console.

Indicates an event that occurred in a method template.

Indicates an event that occurred in a method.

Indicates an event that occurred in a batch.

Date/Time Time stamp of the event.

User When an event requires confirmation (as specified in the Administrator Console), User is

the user who confirmed each change to a batch, method, or template.

When no confirmation is required, User is the user who was logged in when the change

occurred.

Computer Name Name of the computer on which the application recorded the event.

Event Type Specific event that triggered the log file entry. For a complete list of event types, refer to

the TraceFinder Administration Console User Guide.

Context Name of the sample, batch, method, or application version where the event occurred.

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History Indicates that there is a history log of queued actions for the event.

Reason Default or custom reason that the user entered for the event.

Details

Key/Value

Identifying parameters and their values for the selected auditing event. These key

parameters are different for each type of auditing event.

History

Filter Select a filter view to use for displaying the change history.

Opens the Filter Editor dialog box where you can create a filter view.

Opens the Filter Editor dialog box where you can edit the current filter view.

Deletes the current history filter view.

Order The sequence of actions that occurred.

Change Type One of the predefined ChangeType values.

Context Name of the specific value on which the action occurred.

Item Type One of the predefined ItemType values.

Item Name A user-defined name for the filter.

Old Value/New Value Original parameter value and the changed value.

Details

Key/Value

Identifying parameters and values for the selected history event.

Table 103. Audit Viewer parameters (Sheet 2 of 2)

Parameter Description

Thermo Scientific TraceFinder User Guide 445

Using Quick Acquisition

Use the quick acquisition feature to quickly submit samples from any mode in the

application.

To run a quick acquisition

1. Choose Tools > Quick Acquire Sample from the main menu or click the Quick Acquire

Sample icon, .

The TraceFinder Quick Acquisition window opens.

2. To create the sequence of samples that you want to acquire, do any of the following:

• Use the Sequence buttons in the toolbar to open and save Xcalibur sequence (.sld)

files.

Note The Quick Acquisition feature is available only when you activate it in the

Configuration console. Refer to Chapter 1, “Using the Configuration Console,” in the

TraceFinder Lab Director User Guide.

Button Description

Replaces the current sequence with a new sequence that contains one

Unknown sample.

Opens the Open dialog box where you can open a saved SLD file.

Saves the current sequence as an SLD file in the

C:\TraceFinderData\Sequences folder.

Opens the Save As dialog box where you can save the current sequence

to a new file name or location.

A Using Quick Acquisition

446 TraceFinder User Guide Thermo Scientific

• Use the Samples buttons in the toolbar to create a sequence of samples.

• (Optional) Use the Tools buttons in the toolbar to open a qualitative browser or the

NIST library browser.

3. When you have completed your sequence of samples, click either of the Acquire buttons.

The application submits the samples for acquisition, processing, and report generation.

See Real Time Status – Acquisition Page.

To see how to use the Quick Acquisition wizard

1. Choose Help > Animations.

2. From the list of animation topics, click Quick Acquisition.

Button Description

Adds the specified number of new, empty samples to the end

of the sample list.

Inserts a new, empty sample or samples above the selected

sample.

Removes the selected samples from the sample list.

Button Description

Opens the qualitative explorer that you configured as your

default qualitative explorer in the Configuration console. See

Launching a Qualitative Explorer.

Opens the NIST library browser. See Launching the NIST

Library Browser.

Button Description

Submits only the selected samples for acquisition, processing, or

report generation.

Submits the sequence for acquisition, processing, or report

generation.

Thermo Scientific TraceFinder User Guide 447

Using Copy Down and Fill Down

This appendix describes the Copy Down and Fill Down commands that you can use to make

entering column values easier.

• Use the Fill Down command for the Filename, Sample Name, Sample ID, and Vial

Position columns.

• Use the Copy Down command for the Sample Type, Vial Position, Injection Volume,

Conv Factor, Level, Comment, and other columns.

Follow these procedures:

•To automatically copy column values

•To automatically enter sequential column values

•To use Copy Down or Fill Down for a range of samples

To automatically copy column values

1. Select the cell whose value you want to copy to all cells below it.

Observe the difference between a selected and nonselected cell.

2. Right-click and choose Copy Down.

The value is copied to all rows below the selected row.

To automatically enter sequential column values

1. Enter a value for the first row of the fill down sequence.

This does not have to be the first sample row. You can begin the fill down procedure from

any row in the sequence.

Selected

Not selected

B Using Copy Down and Fill Down

448 TraceFinder User Guide Thermo Scientific

2. Select the cell whose value is the first in the fill down sequence.

Observe the difference between a selected and nonselected cell.

3. Right-click and choose Fill Down.

The application enters sequential column values starting with the value in the selected

row and ending with the last row in the column.

You can repeatedly use the Fill Down command to create multiple sequences.

When you use the Fill Down command for the Vial Position column with an autosampler

configured, the application knows the number of vial positions configured in your

autosampler and numbers the positions accordingly.

Selected

Not selected

B Using Copy Down and Fill Down

Thermo Scientific TraceFinder User Guide 449

To use Copy Down or Fill Down for a range of samples

1. To select a range of sample values, do one of the following:

Drag your cursor to select a contiguous group of sample values.

–or–

Hold down the SHIFT key to select a contiguous group of sample values.

2. Right-click and choose the appropriate command from the shortcut menu.

The column values are copied or entered sequentially starting with the value in the first

selected row and ending with the last selected row.

Thermo Scientific TraceFinder User Guide 451

Moving Data Review Panes

This appendix describes the procedures you can use to move, dock, or float panes in all Data

Review views. The procedures have accompanying animations.

Follow these procedures:

•To move a docked pane

•To make a pane floating or dockable

•To change a pane from a docked pane to a tabbed pane

To move a docked pane

1. Grab the title bar of the pane and begin dragging the pane.

The application displays docking arrows.

2. Drag the pane over one of the arrows.

As you hold the cursor over a docking arrow, the application displays a blue region

indicating where this arrow will place the pane.

3. Drop the pane onto one of the arrows.

This animation shows the various ways that you can use the docking mechanism to move a

pane. To view the animation, click the filmstrip, and then right-click and choose Full Screen

Multimedia. To stop the animation, press ESC.

C Moving Data Review Panes

452 TraceFinder User Guide Thermo Scientific

To make a pane floating or dockable

Do one of the following:

• To make a dockable pane floating, right-click the title bar of the pane and choose

Floating.

While a pane is set as floating, you cannot use the docking arrows to dock it or make

it a tabbed pane.

• To make a floating pane dockable, right-click the title bar of the pane and choose

Dockable.

This animation shows how to switch a pane from docked to floating and back to docked. To

view the animation, click the filmstrip, and then right-click and choose Full Screen

Multimedia. To stop the animation, press ESC.

To change a pane from a docked pane to a tabbed pane

1. Grab the title bar of the pane and begin dragging the pane.

The application displays docking arrows.

2. Hold the cursor over the center of the docking arrows to display a blue region indicating

the location of the tabbed pane.

3. Drop the pane over the center of the docking arrows.

This animation shows how to change a pane from a docked pane to a tabbed pane and back to

a docked pane. To view the animation, click the filmstrip, and then right-click and choose

Full Screen Multimedia. To stop the animation, press ESC.

Note To change a floating pane to a tabbed pane, you must first make the pane a dockable

pane, and then you can make it a tabbed pane.

Drop the pane on the center location to create a tabbed pane.

Tracefinder User Guide For General Quantitation, Version 4.1 Manual Trace Finder

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