Release Notes Chromeleon 7.2.8

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Release Notes

Chromeleon 7

Chromatography Data System

Software Version 7.2.8 • April 2018

Chromeleon 7

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Copyright

For Research Use Only. Not for use in diagnostic procedures. Copyright © 2009-2018 Thermo Fisher Scientific

Inc. All rights reserved.

Trademarks

ACQUITY, Alliance and Waters are registered trademarks of Waters Corporation. Agilent is a registered

trademark of Agilent Technologies. Microsoft, Windows 8.1 Pro, .NET Framework and SQL Server are registered

trademarks of Microsoft Corporation. PerkinElmer and Clarus are registered trademarks of PerkinElmer Inc.

Shimadzu is a trademark of Shimadzu Corporation. Air Server-xr, TD100-xr UNITY-xr and Kori-xr are trademarks

of Markes International Ltd. WibuKey is owned by Wibu Systems.

All other trademarks are 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. The document is copyright protected; any reproduction of the whole or any part of this

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

This document is provided “as is”. The contents of this document are subject to being changed, without notice,

in future revisions.

Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate, or error-free.

Thermo Fisher Scientific Inc. assumes no responsibility and will not be liable for any errors, omissions, damage,

or loss that might result from any use of this document, even if the information in the document is followed

properly.

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. The Terms and Conditions of Sale

shall govern all conflicting information between the two documents.

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Table of Contents

1 Introduction ........................................................................................................................... 6

2 Other Documentation ........................................................................................................... 7

3 What’s New in Chromeleon 7.2.8 ......................................................................................... 8

3.1 New and Updated Thermo Scientific Instrument Drivers .............................................. 8

3.1.1 Vanquish Diode Array Detector FG - New Driver [SWFR-2240] ............................... 8

3.1.2 Vanquish Dual Gradient Pump Flex – New Driver [SWFR-1987] .............................. 8

3.1.3 Vanquish Dual Autosampler (Horizon and Flex) – New Driver [SWFR-1995] ........... 8

3.1.4 Vanquish Diode Array Detectors - Updated Driver [CM7-19402] ............................ 8

3.1.5 ISQ 7000 / TSQ 9000 GCMS - New Driver [SWFR-2542] ......................................... 8

3.1.6 ISQ EC LC/IC MS - Updated Driver [SWFR-3014, SWFR-3015, SWFR-3016, SWFR-

3018, SWFR-3153] .............................................................................................................. 8

3.1.7 TRACE 1300 GC – Updated Driver [SWFR-2758] ....................................................... 9

3.2 New and Updated Third Party Instrument Drivers ......................................................... 9

3.2.1 Agilent 6890 GC – Updated Driver [SWFR-2984, CM-204] ....................................... 9

3.2.2 Agilent 6850 GC – Updated Driver [SWFR-769, CM-296, CM-4393] ........................ 9

3.2.3 Agilent LC – Updated Driver [CM-8569, CM7-25390] ............................................... 9

3.2.4 Waters Driver Pack 2017 R2 – New Version [SWFR-2749, CM-6901, CM-6921] ...... 9

3.3 Vanquish Duo Features ................................................................................................. 10

3.3.1 Dual LC Support [SWFR-2860] ................................................................................. 10

3.3.2 Inverse Gradient [SWFR-2693] ................................................................................ 10

3.3.3 Tandem LC/LC-MS [SWFR-1150] ............................................................................. 10

3.3.4 Fluidic Connections [SWFR-1274] ........................................................................... 10

3.4 Chromeleon Client Enhancements ............................................................................... 10

3.4.1 New Cobra Detection Parameter to define a straight baseline between two data

points in the chromatogram [SWFR-3089] ....................................................................... 10

3.4.2 Simplified overlaying of Chromatograms when comparing injection query results

in the Chromatography Studio [SWFR-1616] ................................................................... 11

3.4.3 Pinning/Unpinning Chromatograms in the Chromatography Studio [SWFR-1616

related] .............................................................................................................................. 11

3.4.4 Enhancements to Tentatively Identified Peaks Pane [SWFR-2291, CM-76, CM-77,

CM-79] .............................................................................................................................. 11

3.4.5 Component Table Retention Time Adjustment [SWFR-1585, CM-71] ................... 12

3.4.6 Using a Syringe Standard to Compute ISTD Recovery [SWFR-1162, CM-3979] ..... 12

3.4.7 Summing Response on Quantitation and Confirming Ions for Calibration [SWFR-

1457, CM-3999] ................................................................................................................ 12

3.4.8 Plot Component Traces of an Associated ISTD [SWFR-3189, CM-4009] ................ 12

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3.5 Chromeleon Client Enhancements for the ICS-6000 .................................................... 12

3.5.1 Progress bar to indicate tag read/write percent complete [SWFR-2394, CM-

7409] 12

3.5.2 Tag read/write status [CM-8332, CM-8874, CM-11087] ........................................ 12

3.5.3 Improved audit trail read/write error messages [CM-8749] .................................. 12

3.5.4 DRS 600 Consumables Installation Guide [CM-10326] ........................................... 12

3.5.5 Improvements to ICS-6000 control [SWFR-3367] ................................................... 13

3.6 Other Enhancements .................................................................................................... 13

3.6.1 Support Chromeleon on Windows 2016 Server [SWFR-2666] ............................... 13

3.6.2 New Station Installation Qualification [SWFR-1058] .............................................. 13

3.6.3 Execute Installation Qualification as part of System Status Report [CM-3203] ..... 13

3.6.4 Automated results export to external application [CM-193] ................................. 14

3.6.5 Post-sequence reporting improvements [SWFR-610, SWFR-1686, SWFR-420] ..... 14

4 Resolved Issues .................................................................................................................... 15

4.1 Issues resolved with the new Station Installation Qualification Tool .......................... 21

5 Limitations and Known Issues ............................................................................................. 22

5.1 Limitations with Thermo Scientific Instruments ........................................................... 22

5.2 Upgrading a Windows 10 PC From Chromeleon 7.2 SR5 to Chromeleon 7.2.8 ........... 25

5.3 Compatibility with Foundation 3.1 ............................................................................... 25

5.4 Limitations with the Waters Driver Pack ...................................................................... 26

5.5 Limitations with Agilent ICF .......................................................................................... 28

5.6 Limitations with Other Third Party Instruments ........................................................... 30

5.7 Other Limitations .......................................................................................................... 31

5.8 Obsolete Drivers ........................................................................................................... 37

5.9 Functional Differences between Chromeleon 7.2 and Chromeleon 6.8 ...................... 37

6 Backward/Forward Compatibility Issues ............................................................................. 38

6.1 Thermo Scientific Vanquish Charged Aerosol Detector [CM6-23499] ......................... 38

6.2 Thermo Scientific Vanquish Autosampler [CM6-23405] .............................................. 38

6.3 Thermo Scientific TriPlus RSH ....................................................................................... 38

6.4 Thermo Scientific TriPlus 300 HS .................................................................................. 38

6.5 Thermo Scientific TriPlus LS-100 ................................................................................... 38

6.6 Thermo Scientific TSQ Quantiva ................................................................................... 38

6.7 Thermo Scientific TSQ Quantiva and Endura ................................................................ 38

6.8 TSQ Quantiva and Endura Instrument Method [CM7-18759] ...................................... 38

6.9 Signed Sequences [CM7-16374] ................................................................................... 39

6.10 Chromeleon Enterprise Compatibility of a Chromeleon 7.2 SR5 Domain Controller

with Newer Versions of Chromeleon Clients and Instrument Controllers ........................... 39

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7 Appendix .............................................................................................................................. 41

7.1 Release Notes................................................................................................................ 41

7.2 Online Help ................................................................................................................... 41

7.3 Contributed Content ..................................................................................................... 41

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1 Introduction

The Thermo Scientific™ Chromeleon™ 7 Chromatography Data System (CDS) is a new-generation

chromatography data system that provides the fastest path from samples to results. Building upon

market-leading innovations of prior Chromeleon software releases – such as dynamic interactive data

displays, an integrated database for rapid data retrieval, and spreadsheet-based reporting –

Chromeleon 7 features a modern user interface, comprehensive new tools for peak detection, and an

innovative workflow management framework, all of which speed up learning, simplify operation, and

deliver results with greater efficiency than any other chromatography data system.

This new version, Chromeleon 7.2.8 CDS, provides updated and new instrument control for

instruments from Thermo Fisher Scientific. Improvements and enhancements have been made in a

number of areas related to ease of use, data processing and visualization. In addition, this release

introduces support for the Thermo Scientific Vanquish Duo. Please see below for more details on

these and other enhancements present in this release.

The software is developed using modern software development tools and technologies that improve

performance, sustainability and extendibility.

Backward compatibility with Chromeleon 6 is maintained to the greatest practicable extent, to

provide an easy migration path.

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2 Other Documentation

Chromeleon is provided with many other documents that will help you to learn more about the

software. These documents can also be found in electronic form on the installation disk in the

Documents folder.

Please refer to the Installation Guide for information regarding:

• System Requirements

• Supported Operating Systems and Databases

• Required Third-Party Software

• Compatibility with Previous Versions

• Installing and configuring the Chromeleon software

Also available are the Enterprise Documents that were released for Chromeleon 7.2 SR5, which

describe the process for installation of enterprise systems based on Chromeleon 7.2 SR5. These

documents are also applicable for Chromeleon 7.2.8.

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3 What’s New in Chromeleon 7.2.8

Chromeleon 7.2.8 implements a number of new features, including support for the new Vanquish

Duo system providing support for dual LC, tandem LC and inverse gradient workflows. Also included

are several updated drivers and core Chromeleon enhancements. This document will only give a

short overview of all features without going into much detail. For more details, refer to the Online

Help.

3.1 New and Updated Thermo Scientific Instrument Drivers

This chapter lists new and updated Thermo Scientific™ drivers added to Chromeleon 7.2.8. For

details on supported options, required licenses, installation, and control, refer to the Online Help or

the List of Supported Instruments document found on the Chromeleon 7.2.8 DVD.

3.1.1 Vanquish Diode Array Detector FG - New Driver [SWFR-2240]

This release includes support for the new Thermo Scientific Vanquish Diode Array Detector FG (VF-

D11-A). This detector is compatible with all other Vanquish modules.

3.1.2 Vanquish Dual Gradient Pump Flex – New Driver [SWFR-1987]

This release includes support for the new Thermo Scientific Vanquish Dual Gradient Pump Flex (VF-

P32-A-01). This pump is compatible with all other Vanquish modules.

3.1.3 Vanquish Dual Autosampler (Horizon and Flex) – New Driver [SWFR-1995]

This release includes support for the new Thermo Scientific Vanquish Dual Autosampler Horizon

(1500 bar limit, VH-A40-A-02) and Vanquish Dual Autosampler Flex (1034 bar limit, VF-A40-A-02).

These autosamplers are compatible with all other Vanquish modules. Note that for the Vanquish

Dual Autosampler the charger is not yet supported.

3.1.4 Vanquish Diode Array Detectors - Updated Driver [CM7-19402]

The driver for the Vanquish Diode Array Detectors (VH-D10-A, VF-D11-A) has been updated to

include a wellness device in line with drivers for other Vanquish modules.

3.1.5 ISQ 7000 / TSQ 9000 GCMS - New Driver [SWFR-2542]

This release includes drivers to support the new Thermo Scientific ISQ 7000 Single Quadrupole GC

Mass Spectrometer and Thermo Scientific TSQ 9000 Triple Quadrupole GC Mass Spectrometer.

These new drivers also control the ISQ Classic/QD/LT and TSQ 8000 Classic/ Duo and TSQ 8000 Evo.

3.1.6 ISQ EC LC/IC MS - Updated Driver [SWFR-3014, SWFR-3015, SWFR-3016,

SWFR-3018, SWFR-3153]

This release includes an updated driver for the Thermo Scientific ISQ EC Single Quadrupole LC/IC

Mass Spectrometer.

• It is now possible to acquire MS data in profile mode

• The instrument method editor now includes an option to automatically create temporary

channels which may then be used as input for faction collection.

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• Support for Smart Startup, Smart Standby and Smart Shutdown functionality is now

available.

• It is now possible to exchange information via the Windows clipboard between the

instrument method scan table and the processing method component table

• When working in the Real time Scan Window of the ISQ EC, the user can copy the scan

settings from that window to the Windows Clipboard and then paste the values into the ISQ

EC MS method.

3.1.7 TRACE 1300 GC – Updated Driver [SWFR-2758]

With this release a retention time alignment tool has been included on the inlet tab of the Thermo

Scientific TRACE 1300 GC instrument method. This tool compensates for changing column conditions

by adjusting the flow or pressure of the method to maintain the same retention time for

components.

3.2 New and Updated Third Party Instrument Drivers

This chapter lists new and updated third party instrument drivers added to Chromeleon 7.2.8. For

details on supported options, required licenses, installation, and control, refer to the Online Help or

the List of Supported Instruments document found on the Chromeleon 7.2.8 DVD.

3.2.1 Agilent 6890 GC – Updated Driver [SWFR-2984, CM-204]

With this release, timed events for the valves are now entered in a table on a dedicated method tab,

and are sent to the instrument at the start of the run. This results in better accuracy of timed events

as compared to defining valve events in the method script.

3.2.2 Agilent 6850 GC – Updated Driver [SWFR-769, CM-296, CM-4393]

This release allows the Agilent 7693 autosampler to be used with an Agilent 6850 GC, and includes

the same valve events improvements as the Agilent 6890 driver.

3.2.3 Agilent LC – Updated Driver [CM-8569, CM7-25390]

This release includes an updated driver, provided by Agilent Technologies, for control of Agilent LC

instruments. This update contains a fix for issue CM7-25390. More details are available in the

Resolved Issues section, and in the release notes document provided in the \packages\Agilent

Chromeleon Drivers\Documentation folder on the Chromeleon 7.2.8 DVD.

3.2.4 Waters Driver Pack 2017 R2 – New Version [SWFR-2749, CM-6901, CM-6921]

A new version of the Waters Driver Pack is introduced with this version of Chromeleon CDS.

Please refer to the document DP2017 R2 installation and configuration guide 715005543rA.pdf in the

\Packages\Waters Driver Pack\Driver Pack folder on the Chromeleon 7.2.8 DVD for full installation

instructions.

Note: It is necessary to have Windows update KB2999226 installed before attempting to install

the Driver Pack.

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3.3 Vanquish Duo Features

3.3.1 Dual LC Support [SWFR-2860]

This release includes support for a two pump setup which includes a dual autosampler. This allows

running two chromatographic applications at the same time. If only one column compartment is

used, the system ensures that both applications run at the same temperature.

3.3.2 Inverse Gradient [SWFR-2693]

This release includes support for the inverse gradient workflow for a Vanquish Duo system with a

Dual Gradient Pump (DGP), two HPG or two LPG pumps. A wizard supports the user in setting up the

gradient and inverse gradient and provides an inverse gradient offset based on the system fluidics.

3.3.3 Tandem LC/LC-MS [SWFR-1150]

This release includes support for the Tandem LC/LC-MS workflow, where one chromatographic

application is run alternately on two columns. While one column is used for the analytical

application, the other is re-equilibrated. A wizard supports the user in setting up the analytical and

reconditioning part of the gradient and suggests a Minimum Purge Time based on the system fluidics.

3.3.4 Fluidic Connections [SWFR-1274]

The Vanquish Duo system allows for more complex fluidic setups that may involve multiple flows,

valves, columns, and devices. Chromeleon 7.2.8 allows a representation of these more complex

fluidic setups.

A wizard supports the user in describing the fluidic configuration of the system. The fluidic

framework allows drivers to query the flow between components, considering valve positions and

pump flows. The wizard allows the user to select a capillary kit for a specific workflow from those

capillary kits compatible with the current hardware configuration. Alternatively, the user can import

a custom fluidic description from file.

The fluidic configuration describes the fluidics of the system including the capillary volume, flow cell

volume and pre-heater volume. For the inverse gradient workflow, the system in addition reads out

the column volume and/or column dimensions from the column tag and calculates the effective

column volume from the column dimensions. Alternatively, the user can enter the column

dimensions or effective column volume manually.

3.4 Chromeleon Client Enhancements

3.4.1 New Cobra Detection Parameter to define a straight baseline between two

data points in the chromatogram [SWFR-3089]

The Cobra detection algorithm version associated with Chromeleon 7.2.8 offers a new detection

parameter called ‘Fixed Baseline’. This parameter allows to force a straight baseline between two

data points in the chromatogram. A pair of two detection parameters ‘Fixed Baseline = Start’ and

‘Fixed Baseline = End’ defines such a straight baseline via their corresponding retention time values.

The new detection parameter (pair) can be entered in various ways:

• Processing Method Editor: the detection table offers the new parameter in the Cobra

detection parameter dialog.

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• Chromatogram View: drawing a mouse rectangle with the right mouse button offers a

dedicated ‘Set Fixed Baseline’ entry in the corresponding context menu. The rectangle

start/end time defines the retention times for the Fixed Baseline detection parameter pair.

• Chromatogram View: the Insert button in the group ‘Detection Parameter’ of the Processing

ribbon offers ‘Fixed Baseline’ as well. After selecting this option you can set the fixed

baseline start and end point via a dedicated mouse tool interactively.

All peaks which are detected automatically between fixed baseline start and end or which are

inserted manually later are evaluated in respect to this straight baseline.

Note: For processing methods created or updated with a Chromeleon version prior to 7.2.8 the

new detection parameter is only available and offered in the UI if the Cobra detection algorithm

version is update to the latest version.

3.4.2 Simplified overlaying of Chromatograms when comparing injection query

results in the Chromatography Studio [SWFR-1616]

When running an injection query and getting hits from different sequences with different channels

the selection of chromatograms in a corresponding Chromatography Studio session has been

improved. In Chromeleon versions prior to 7.2.8 the channel which has been selected in the

navigation area of the Chromatography Studio is used for all injections of the query. This created a

“Channel is not available” message in the chromatogram plot area if the selected injection was from

a sequence where this channel has not been acquired. Now with version 7.2.8 the default channel of

the corresponding sequence is used in this case. That way you can easily overlay and compare two

chromatograms from two different sequences with different channels.

3.4.3 Pinning/Unpinning Chromatograms in the Chromatography Studio [SWFR-

1616 related]

The chromatogram plot in the Data Processing Category of the Chromatography Studio is extended

to allow the pinning of single chromatograms. In Chromeleon versions prior to 7.2.8 one could pin

injections and channels only separately. Yet if an injection has been pinned a different channel

selection in the navigation area did select a different chromatogram (with the newly selected

channel). If a channel has been pinned all corresponding chromatogram of all selected injections

were overlaid in the chromatogram plot. With version 7.2.8 the chromatogram plot offers to pin

single chromatograms, i.e. the combination of injection and channel. Selecting a different channel or

injection afterwards does not remove or change this chromatogram. The pinned chromatograms are

kept in the chromatogram plot window and overlaid with other selected chromatograms until they

are explicitly unpinned. Both the pin and unpin operation can be only executed via the context menu

in the title bar of the chromatogram plot area. Pinned chromatograms are marked with a red pin icon

( ) on the left side of the title bar.

3.4.4 Enhancements to Tentatively Identified Peaks Pane [SWFR-2291, CM-76, CM-

77, CM-79]

This release enhances the Tentatively Identified Peaks pane to:

• Generate peak results for any acquisition channel (not just the TIC)

• Display the compound CAS number (when available from a library)

• Allow entry of a compound CAS number (when available from a library)

• Transfer a tentatively identified peak to the component table of the method

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3.4.5 Component Table Retention Time Adjustment [SWFR-1585, CM-71]

This release adds the ability to adjust the expected retention times of one or multiple components in

the processing method by a fixed amount or fixed percentage.

3.4.6 Using a Syringe Standard to Compute ISTD Recovery [SWFR-1162, CM-3979]

This release supports the ability to assign an internal standard to another internal standard as a

‘Syringe Standard’ in order to compute the percent recovery of the internal standard. The

implementation uses a special component custom variable named “CM7_Syringe_Standard” to make

the syringe standard assignment.

3.4.7 Summing Response on Quantitation and Confirming Ions for Calibration

[SWFR-1457, CM-3999]

When performing calibration related calculations it is now possible to add the results (e.g. area) of

the confirming ion traces to that of the quantitation ion trace.

3.4.8 Plot Component Traces of an Associated ISTD [SWFR-3189, CM-4009]

The MS Components pane now includes an option to plot the quantitation and confirming ion plots

for the ISTD of a component as well as the quantitation and confirming ion plots of the component

itself. This is useful in applications that use isotope dilution (such as dioxin analysis), where it is

important to be able to visually compare the RT alignment.

3.5 Chromeleon Client Enhancements for the ICS-6000

3.5.1 Progress bar to indicate tag read/write percent complete [SWFR-2394, CM-

7409]

A progress bar has been added to the Consumables Inventory user interface to better indicate how

much time is left for an ongoing tag read/write.

3.5.2 Tag read/write status [CM-8332, CM-8874, CM-11087]

The Consumables Inventory user interface has been enhanced with two new table columns. The

first, titled ‘Last Write’, shows the time since the tag information became outdated. The second,

‘Status’, indicates a read, write or read/write error.

In addition, a modified audit trail has been added to the interface, which is filtered to show only

errors and warnings.

3.5.3 Improved audit trail read/write error messages [CM-8749]

Tag read/write error messages reported in the audit trail for ICS-6000 instruments equipped with the

CDM module have been revised to show the product part and serial numbers to help make

identification of the effected consumable easier.

3.5.4 DRS 600 Consumables Installation Guide [CM-10326]

A DRS 600 Installation Guide has been added to the Consumables Inventory user interface. This

guide will help users better understand the difference between the new DRS 600 and other

suppressor offerings and instructs on how to install it on an IC system.

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3.5.5 Improvements to ICS-6000 control [SWFR-3367]

The control of the ICS-6000 has been improved in a number of areas; instrument configuration,

creation of the instrument method, handling of the consumables inventory, and Smart Startup,

Smart Standby and Smart Shutdown.

3.6 Other Enhancements

3.6.1 Support Chromeleon on Windows 2016 Server [SWFR-2666]

Chromeleon 7.2.8 has been tested on the Windows 2016 Server operating system.

The following Chromeleon components can be installed on run on Windows 2016 Server:

• Chromeleon Domain Controller

• Chromeleon Data Vault Server

• Chromeleon Raw Data Server

• Chromeleon Client

3.6.2 New Station Installation Qualification [SWFR-1058]

The Station IQ tool has been rewritten from the ground up to support extensibility, enhanced

checking, an easy to read report, and the following enhancements:

• Station IQ now checks Windows Firewall rules [CM7-5175]. When a third party firewall is

used, Station IQ shows a recommendation to check the firewall rules of the third party

firewall [CM7-24538].

• The Station IQ reference data ("inventory" files) are now digitally signed to prevent

manipulation. [CM7-8879]

• Station IQ now records system and user locale settings such as number and date format.

[CM7-10995]

• A summary of errors and warnings is now shown at the top of the report. The entries are

linked to the corresponding section of the report containing further details. [CM7-1579,

CM7-14315]

• In the "Packages" section, IQ now reports the installed version of packages which are

installed with Chromeleon, such as Microsoft components, mass spectrometry components,

and third party drivers. It also checks that the expected version is installed [CM7-17246]

Note: A warning is issued if a newer version than expected is found.

The new Station IQ also fixes many issues that were present in the old Station IQ tool, see section 4.1

3.6.3 Execute Installation Qualification as part of System Status Report [CM-3203]

The System Status Report contains a new option; "Installation Qualification".

• When set to ON, a new IQ report is generated and included in the SSR Zip Archive

• When set to OFF, no IQ report is generated or included in the SSR Zip Archive

The content of an SSR-generated IQ report is identical to an IQ report created by any other

mechanism.

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3.6.4 Automated results export to external application [CM-193]

If Chromatography results are being exported from Chromeleon to an external application (such as

Thermo Scientific SampleManager LIMS), Chromeleon 7.2.8 introduces a way for Chromeleon System

Administrators to integrate this export as an automated step in the Electronic Signature workflow.

A new configuration option in the Electronic Signature policy allows the export to be triggered at one

of the following transitions:

• When the Sequence is Submitted into the eSignature workflow

• When the Sequence is marked as Reviewed

• When the Sequence is marked as Approved

Exporting results to SampleManager requires the Chromeleon-to-SampleManager link components

to be installed and configured on each Chromeleon client.

3.6.5 Post-sequence reporting improvements [SWFR-610, SWFR-1686, SWFR-420]

Prior to Chromeleon 7.2.8, in order to automatically generate a report at the end of acquisition of a

Sequence, the user would need to open the Instrument Queue tab, select a post-sequence or post-

injection reporting option, and leave the Chromeleon Client application open until all reports had

been produced.

Chromeleon 7.2.8 introduces a number of improvements in this area:

• The Instrument Queue tab no longer needs to be opened for reporting to take place

• Reporting is performed even if the Chromeleon Client gets closed after starting the sequence

acquiring

• Post-injection and post-sequence report options are now defined in the Sequence. These

can be pre-defined in the eWorkflow, selected in the Sequence before acquisition starts, or

edited in the Sequence while it is acquiring

• System Administrators can also ‘enforce’ reporting options in the Queue Settings tab of the

Instrument Properties dialog box. These options will then be applied to all sequences

acquired on that Instrument

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4 Resolved Issues

This chapter describes the issues that have been resolved with the release of Chromeleon 7.2.8.

Many trivial and minor issues have been resolved, but are not mentioned here. If you require

information about the status of an issue observed in a Chromeleon 7 release, but which is not listed

here, please contact your local Thermo Fisher Scientific representative for more information.

The numbers in the first column of the table below refer to the Thermo Fisher Scientific tracking IDs.

ID Description

CM7-5339 Audit Trail: Restoring an older version of a Spectral Library produced two entries in the

data audit trail of the containing sequence instead of one as expected. Now the

spurious entry "Changed Library Spectrum" is no longer generated.

CM7-7292 Administration Console: Local Machine: A second log-in would be required when

launching a subordinate tool (Discovery, Data Vault Manager) from the Administration

Console, instead of the logged-in credentials being passed through to the subordinate

tool.

CM7-15336 Client: Import/Export: Non-Unicode characters in a Sequence name would be replaced

by underscore(s) if the sequence was exported to .pdf.

CM7-16248 Client: Import/Export: If an acquiring sequence was exported, the data path displayed

in the Export dialog box was incorrect.

CM7-18239 Instruments: GC Drivers: TRACE 1300 GC: The ECD Acquisition Rate was limited to 60 Hz

(when line frequency is 60 Hz) or 100 Hz (when line frequency is 50 Hz) instead of 300

Hz for either line frequency.

CM7-19018 Client: Console: When a sequence was first assigned to one instrument's queue, then to

a second, and the sequence was started for the second, the run would fail. Now

Chromeleon will throw an error when the sequence is added to the second queue that

states that the sequence is already assigned to another instrument's queue.

CM7-19204 Client: Console: Data: Import External: The Method Path field was incorrectly displayed

for import types which don't support this field.

CM7-20261 Client: Studio: After signing a sequence using an external report, the report would stay

locked until the user who signed the sequence logged out.

CM7-20435 Sequence Queue: Improved the download speed for sequences with many injections, in

particular if versioning is enabled and injections were added to the sequence many

times.

For very large sequences, the download may still take several minutes, and may fail due

a timeout. As a workaround, split the sequence into several smaller sequences, or

increase the timeout on the IPCs by setting the system environment variable

REQUEST_TXP_TIMEOUT. The value is in milliseconds. The default is 300000 (i.e. 5

minutes).

The same speed improvement also applies to the creation of CMBX files with such

sequences.

CM7-20637

User Management: In the event of a loss of network connection on a system using LDAP

logon, attempting to logon to Chromeleon again with the same account details resulted

in a misleading error message "The user name or password are incorrect." This has

been fixed. It is now possible to logon to Chromeleon with the same account again after

a loss of network connection.

CM7-20975 Panels: WPS-3000FC: The Tube Position and Tube Number ePanel values now update

correctly during a run.

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ID Description

CM7-21054 Corrupt Report Template / Electronic Report: In some rare cases when the size of a

report template or an electronic report of a single injection reached exactly a specific

size, an error message (e.g. “The electronic report of the injection is corrupt and cannot

be read”) showed up in the corresponding window. This is fixed now. Such report

templates or electronic reports can now be opened without an error.

CM7-21905 Client: Console: Data: In some circumstances it was possible to set the minimum value

for a Sequence table's column to an invalid value, but doing so would then cause a

"Value out of range" error to be displayed in the Sequence.

CM7-22296 Client: Studio: Electronic Report: If more than 255 characters were used in the

comment field when removing the signature on a signed Sequence, the Sequence

would be un-signed, but the associated Report would still be signed. Any subsequent

attempt to Submit the Sequence would fail with the error "An error occurred during

submitting: The signature status 'Submitted' cannot be applied if the current status is

'Submitted'"

CM7-22707 Client: Import/Export: The way Chromeleon handled an attempt to re-import a .cmb via

drag-and-drop was incorrect, and the messages that Chromeleon displayed were

misleading.

CM7-22795 Setup: when a reboot was needed, the task bar icon still displayed a progress indicator.

If the Setup window was hidden behind other windows. It was therefore not clear that

Setup was waiting for the user to confirm the reboot.

Now the icon flashes instead to indicate that it needs attention.

CM7-23046 Instrument Controller: When editing the injection following the running injection, then

saving the change(s) shortly (5 seconds or less) before the injection is started, in some

instances the injection used the old properties. This has been addressed in Chromeleon

7.2.8.

CM7-23103 Import: Chromeleon 6 Data: when importing or viewing Chromeleon 6 data sets and

using EN-US regional settings but with a modified decimal separator, e.g. comma

instead of the default period, chromatogram results have not been imported correctly.

In particular retention times of peaks have been converted to very large values so that

the chromatogram plot normally didn’t show peaks any more. Chromeleon is now using

always the invariant decimal separator period for such import procedures which

prevents such incorrect number conversions.

CM7-23161 Panels - UltiMate DAD-3000: In the "More Options" subpanel a spurious Mode property

was available.

CM7-23284 Instruments, DDK Driver: In an instrument setup with several instruments, a DDK driver

that was no longer working resulted in an abort message "The communication FIFO of

the DDK driver is corrupted." being posted to all instruments. This has been fixed. A

DDK driver that is no longer working now only posts the abort message to those

instruments the DDK driver is installed on.

CM7-23327 Services: Discovery: The Discovery service would not start if the

DiscoverySubscriberInfo.dat file was corrupt, causing the service to fail and throw an

incorrect, unhandled SerializationException error.

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ID Description

CM7-23527 Fraction Collection: Running a fraction collection method with a WPS-FC and reaching

the limit of collection tubes CM put a corresponding error message “Illegal vial position

…” but didn’t stop running the current injection and sequence. The default error level

for this error message is now raised from ‘Error’ to ‘Abort Error’ thus aborting the

current injection and sequence run.

Note: Error levels are stored in the instrument configuration. So for existing

installations either the error level of this error message above either needs to be raised

manually or the WPS-driver needs to be removed from the instrument configuration

and added afterwards again.

CM7-23550 Setup: When an error occurred during the configuration phase (at the end of the

installation), Setup only reported "Configuration failed" without giving a reason. Now

the reasons are listed.

CM7-23586

PerkinElmer GC: If the PerkinElmer GC stops with no response, the Real Time Kernel

would crash. This has been fixed. If the PerkinElmer GC stops with no response, a

message is written to the audit trail, the driver is disconnected and the Real Time

Kernel does not crash.

CM7-24143 Data Audit Trail: For injections, the data audit trail did not track changes in the Status,

Inject Time, and GUID fields.

When displaying all properties, the current value was shown for the previous and new

value. If the user changed injection properties before running the injection, this lead to

the misleading impression that the user changed properties of a finished injection.

CM7-24519 Import: Chromeleon 6 Data: when importing Chromeleon 6 CMB-Files containing

locked sequences a misleading and incorrect error message “The data item … is read-

only. Write access is denied” was shown during the import procedure. Nevertheless all

sequences were imported correctly. This has been fixed. This error message no longer

appears.

CM7-24572 Chromeleon XPS: If an eWorkflow, which uses relative vial positions in the

Header/Footer block, was used to create a sequence in Chromeleon XPS, the resulting

sequence could contain invalid vial positions for any Unknown samples.

CM7-24592 UltiMate Drivers - WPS-3000/ACC-3000: The autosamplers (WPS-3000/ACC-3000)

would create dump files containing all USB communication without being requested to

do so.

CM7-24608 Data Audit Trail: when opening the data audit trail for a huge number of records (e.g.

for a complete datavault including subfolders) it could happen that an empty window

without any content was shown.

Note: Opening such a data audit trail with a huge number of records (e.g. for a

complete datavault with 10,000 sequences or more) will still take quite some time. You

might have to wait hours until you can see all the data audit trail records. There is also a

chance that CM clients runs into an out-of-memory exception. To avoid that you can

open the data audit trail in every subfolder of the datavault root to reduce the number

of visible records.

CM7-24684 Agilent ICF: In rare cases, up-to-date tray configuration information was not received

from ICF. Chromeleon would then improperly request the instrument to perform runs

without injecting samples. This condition is now detected and results in an Error during

Queue Ready Check.

CM7-24709 Client: Console: If a user was not part of the Access Group for a folder, then attempting

to move or copy a file into that folder resulted in the software crashing.

Chromeleon 7

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ID Description

CM7-24730 Vanquish Drivers: Column Compartment: If using a column compartment with only one

valve configured, where the position of the valve should change for each injection, and

the command for this is immediately following a temperature control or nominal

command where the temperature hadn't changed compared with the preconditions,

then occasionally the column compartment would appear not ready for use.

CM7-24808 Third Party Device Drivers: Waters Acquity: In some cases an intermittent error was

observed with an Acquity H-Class, leading to interrupted runs within the sequence and

the message "Unsupported data format in the data header submitted by the module"

in the audit trail.

CM7-24845 ICS-6000/5000+: Injection valve settings page no longer displays in the Instrument

Method Wizard when no injection valve is configured for the DC module.

CM7-24879 PerkinElmer TurboMatrix HS Sampler: If the sampler was set into a special

communication mode before (either by the PerkinElmer TurboChrom software or a

different program such as a tool used by PE service technicians), then the sequence

would crash when starting a headspace sequence.

CM7-24899 ICS-6000: In Dual EGC mode, the Smart Startup, Smart Standby and Smart Shutdown

concentration settings have been removed from Standby and Shutdown method

scripts, since they are not required. Chromeleon will no longer throw a preflight error

due to these settings.

CM7-24921 Instruments: GC Drivers: Trace Ultra: Data packages which have been resent by the GC

Driver were not being handled correctly, and could incorrectly appear in the

Chromatogram.

CM7-24924 ICS-5000+: High-pressure valves are now properly displayed on the DC module's ePanel

and are no longer displayed as low-pressure valves.

CM7-24925 ICS-5000+: Low-pressure valves controls now display on the DC module's ePanel when

the valves are installed in the Automation Manager

CM7-24931 Rheodyne MXII: If a queue contains a large number of commands to set the position of

the Rheodyne MXII to the same position as was previously set, then occasionally this

would lead to an interrupted queue.

CM7-24974 Client: Console: Import/Export: Importing of CMBX could result in the following error:

(1): Dionex.Chromeleon.Data.DataException: The command 'INSERT INTO CJ_VERSION

(VERSION_ID, VERSION_OBJECT_ID, NAME, UNIQUE_NAME, TYPE, PARENT_ID,

PARENT_RELATION_TYPE, RELATIVE_ID, COPIED_ID, ITEM_TYPE_VERSION, COMMENT,

VERSION_CREATE_TXN_ID, VERSION_INVALIDATE_TXN_ID, VERSION_CREATE_TXN_NO,

VERSION_INVALIDATE_TXN_NO, VERSION_LAST_SIBLINGS_TXN_NO,

EXTENSION_DATA) VALUES (@P0, @P1, @P2, @P3, @P4, @P5, @P6, @P7, @P8, @P9,

@P10, @P11, @P12, @P13, @P14, @P15, @P16) {rest of SQL skipped} ); ' failed.

(2): System.Data.SqlClient.SqlException: Cannot insert duplicate key row in object

'dbo.CJ_VERSION' with unique index 'IX_VERSION_NAME_TYPE_PARENT'. The duplicate

key value is (1cb7e1e3-7b80-4a8c-8be1-460c1370afe7, 5609976132718149,

172606000, 9, 100).

if the Sequence(s) in the CMBX had been created in Chromeleon 7.2 SR3, with

versioning enabled, and a processing method had been saved while the sequence was

downloading.

CM7-24995 Instruments: GC Drivers - TriPlus RSH: If a TriPlus RSH autosampler was being used in

shared mode, servicing two GCs, and a sequence was started on the 'main' GC while the

autosampler was performing actions for the 'virtual' GC, Chromeleon would

immediately report "Can't access the TriPlus" for the 'main' GC sequence, instead of

waiting until the TriPlus had completed its actions for the 'virtual' GC.

Chromeleon 7

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ID Description

CM7-25011 ICS-6000/5000: With either the CDM or the I/O board installed in the DC module, TTL

Inputs can now be assigned to open or close the AC Relays 1 and 2.

CM7-25056 Instruments: Vanquish Drivers: Pumps: If the pump is in 'hold' mode when the injection

is started, this results in a flow command not being executed. The pump continues to

pump with the initial flow. The flow command is now correctly executed even if the

pump was in 'hold' mode when the injection started.

CM7-25068 Client: Studio: When two users have the same sequence open, and user A locks a

certain injection, if user B then tries to modify the chromatogram of this injection, user

B was (correctly) notified that the change cannot be saved due to user A's change.

However, if user B then discarded the change and repeated it, the injection was saved.

This should not be possible as the injection is locked. Now Chromeleon correctly

recognizes that the injection is locked and prevents the change in this scenario.

CM7-25070 Lock Injection: If a sequence is opened by user A and B at the same time in different CM

client sessions it may happen that the changes of user A are not immediately visible for

user B. In such a scenario user B could lock an injection although the results of this

injection might change if the changes of user A would have been applied in the

meantime. In a rare scenario an injection could have been even locked twice by both

users. This incorrect multi-user behaviour is fixed now. User B will not be allowed to

lock an injection if the sequence has been changed in the meantime by user A so that

results of this injection might be affected. In particular an injection cannot be locked

anymore twice by two users at the same time.

CM7-25093 Sequence editor: in rare cases, when creating a new sequence from an existing finished

sequence via "Save As..." (without raw data), the new sequence retained Inject Time

and Status values from the original sequence (but not the raw data).

CM7-25100 Instrument Configuration / Chromeleon Domain Controller: When invalid characters

were used in instrument names for the entire Chromeleon Domain, access to data

vaults and instruments was not possible in a reliable way anymore.

CM7-25123 Administration Console: Password Recovery: Having activated authorization for

privileged action ‘LDAP Logon’ in section ‘Administration User Policies’ and having

deactivated LDAP Logon by mistake but not having any emergency CM Admin account

with a non-LDAP-password, it is still possible to logon to the Chromeleon

Administration Console using the administrator password recovery workflow. Yet it is

not possible to correct the damaged LDAP Logon policy settings as this requires

authorization and this is not possible until the LDAP Logon policy settings are corrected.

With 7.2.8 the authorization request for changing the LDAP Logon policy settings is now

skipped if the logon has been done via the administration password recovery.

CM7-25126 Instrument Controller: Data vaults sometimes disappeared momentarily from the

network, in particular during startup. As a result, the Instrument Audit Trail was written

to different local data vault or even the XVault.

CM7-25148 eWorkflows: When a data vault had a large number of eWorkflows, the Console would

become unresponsive and could report an out of memory error when switching

categories.

CM7-25189 ICS-6000: Running two channels on an ICS-6000 system with one channel set to allow

tag read/writes during runs no longer adds an additional injection count between

blanks on that channels tags.

CM7-25190 ICS-5000+: The suppressor current setting on the DC ePanel now displays properly.

CM7-25191 Custom Variable: It was not possible for a 'Numeric' custom variable to have a default

of 'Blank', even if empty values were allowed

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ID Description

CM7-25197 ICS-6000: When switching between two Chromeleon Instruments, the Consumables

Inventory no longer opens automatically, unless that page is open immediately prior to

switching.

CM7-25198 ISQ-EC: When running a sequence, the ISQ-EC occasionally disconnected between

injections, resulting in the sequence being aborted. The instrument audit trail reported:

"communication FIFO of the DDK is corrupted". To recover it was necessary to stop and

restart the instrument controller.

CM7-25209 eWorkflows: When a data vault had a large number of eWorkflows, it could take

several minutes for the list of eWorkflows to be updated on other machines in the

Chromeleon Domain

CM7-25213 Aquion/ICS-2x00/ICS-1x00: Selecting a suppressor type other than None in the

Instrument Method Wizard/Editor will now correctly populate the Concentration and

Current fields on the Suppressor Options page, ensure that Current Set is editable and

that the Suppressor_Current command is added to the Instrument Method.

CM7-25214 Reporting: When working with MS sequences containing a very large number of XICs, it

would take a very long time to open a report template containing a consolidated report

table.

CM7-25256 DC-6000: 'CDM Connected' control is now connected to the correct

commands/properties and functions correctly.

CM7-25260 eWorkflows: When restoring an eWorkflow from an ewfx file, if an eWorkflow with the

same name already existed, an exception error occurred if you attempted to overwrite

the eWorkflow.

CM7-25268 Processing Method: When identifying peaks based on a reference mass spectrum, if the

MS baseline correction settings were changed, the component assignments were not

re-evaluated.

CM7-25270 Vanquish FLD and UltiMate 3000 FLD: It was not possible to acquire the FLField at the

same time as the Flowcell temperature channel. This was the case only if using

Chromeleon 7.2.7.

CM7-25302 eWorkflow Editor: Renaming an injection template was not stored, although it was

logged in the audit trail.

This only happened if the rename was combined with another change (property

update) in the same save operation. The property update was not necessarily

something that is triggered by the user, as there some scenarios where an eWorkflow is

immediately changed after opening due to internal metadata updates (issue CM7-

25321).

CM7-25369 Integrion: After consumables tag approval some consumables, when selected in the

Consumables Inventory list, would not show the detailed tag information. Instead, the

"Get Details" button would be displayed.

CM7-25390 Third Party LC Drivers - Agilent Chromeleon Drivers: On rare occasions, especially when

the acquisition PC has an extremely high CPU utilisation, a high degree of RAM capacity

utilisation and very high Input / Output (I/O) activity, there was an infrequent possibility

that an injection location is ignored and the previous injection location was used again,

without being correctly noted in the Audit Trail. Agilent Chromeleon Drivers 1.1 Update

1 should be installed to prevent this occuring.

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ID Description

CM7-25426 Cobra Peak Detection: Detect Negative Peaks: The Cobra peak detection algorithm

associated with version 7.2.7 does not evaluate the parameter 'Detect Negative Peaks'

if it is switched on and the Baseline Types 'Lock at current level' or 'Lock at global

minimum' are not active. Version 7.2.8 introduces a new version of the Cobra algorithm

which fixes this.

Note: Processing methods associated with version 7.2.7, i.e. which have been created

with 7.2.7 or have been modified via 7.2.7 and explicitly updated the Cobra algorithm

are still using the version of the Cobra algorithm which cannot detect negative peaks. If

you want to apply negative peak detection with these processing methods you have to

update the Cobra algorithm to the latest version associated with 7.2.8. Processing

methods associated with a version prior to 7.2.7 are not affected.

CM7-25462 Services: Data vaults sometimes disappeared momentarily from the network, in

particular during startup. This sometimes caused running sequences to be aborted with

the error:

The running or preparing injection with the URL "[...]" has been deleted or moved to a

different location.

CM7-25479 Audit Trails: When moving an object (e.g. Processing Method) from a folder to a sub-

folder, the action was recorded in the audit trail of the container folder, but was not

tracked in the audit trail of the object itself.

CM7-25509 Instrument Controller: Data vaults sometimes disappeared momentarily from the

network, in particular during startup. This sometimes caused sequences to be

downloaded to a regular local data vault instead of the XVault.

CM7-25546 ICS-2100/2000: Eluent cartridge information is now being shown in the Instrument

Method Wizard and Editor when creating new or reviewing existing instrument

methods.

4.1 Issues resolved with the new Station Installation Qualification Tool

The rewritten Station IQ tool fixes these issues that were present in the old Station IQ tool:

ID Description

CM7-4994 Cancelling Installation Qualification no longer results in an incomplete report.

CM7-9291 The summary at the top of the report contained some very confusing counts (No. of

failing files / errors / warnings) that apparently did not match the actual number of

errors and warnings. (The numbers were "technically correct", but the representation

was misleading.)

The new report summary presents this in a much clearer manner.

CM7-11699 For many files, CmIqData.xml contained wrong reference information. Station IQ

nevertheless reported no deviation as long as the digital signature ("strong name") was

correct.

Note that due to the digital signature check, modified files were still properly detected.

The wrong reference information would only affect the expected values that have

been reported in an error.

CM7-19853 The Agilent SFC package (part of ICF) was not listed in the IQ report

Chromeleon 7

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5 Limitations and Known Issues

The following sections list known issues and limitations. The numbers in the first column of the table

below refer to the Thermo Fisher Scientific tracking IDs.

5.1 Limitations with Thermo Scientific Instruments

ID Description

CM7-15457 ESA Drivers: Coulochem III: Before setting the cell state to ON manually, please ensure

that eluent is flowing into the detector. Otherwise the detector can be damaged.

CM7-15632 TSQ Quantiva and Endura: When removing the source from a TSQ Quantiva or Endura in

mid-acquisition, the sequence does not abort.

CM7-16030 TSQ Quantiva and Endura: With these instruments the standby state reports that the

instrument is on, regardless of the real instrument state.

CM7-16154 TSQ Quantiva and Endura: When creating an Instrument Method for the TSQ Endura or

TSQ Quantiva, the MS run time is not the same as the Chromeleon run time. The user

should enter the correct run time on the MS page of the Wizard.

CM7-16557 MSQ Plus and Tune Application: When using the MSQ Plus with Chromeleon the user has

to wait for the Chromeleon Instrument Controller to be in idle mode before opening the

Tune application. Without waiting, the MSQ Plus will not be able to change the operating

mode (On, Off, Standby), or it will not be possible to run injections. To recover from this

error both the PC and the MSQ Plus would have to be restarted.

CM7-16851 UltiMate 3000 MWD-3000 and DAD-3000: In the Instrument Method Editor for these

devices, the script page offers one additional option for the data collection rate (20 Hz)

that is not present in the Instrument Method Wizard. This additional option is a valid

value for this parameter. Although it is possible to manually type in a value for the data

collection rate that is not in the list, these values will be rejected by the Ready Check

when a sequence is submitted.

CM7-17500 Exactive Series: Exactive Series instruments are usually shipped with a PC (“Exactive PC”)

that includes all the necessary instrument data files, such as calibration files, for

operating the instrument. If you want to control an Exactive instrument using a different

PC, make sure that the specific instrument data files residing on the Exactive PC are

backed up and transferred to the new PC. For details on performing the data backup on

the Exactive PC, refer to the Thermo Exactive Series 2.5 SP1 Release Notes, section

Backup provided on the Chromeleon installation disk in the Packages\Thermo

Exactive\Documentation folder.

CM7-17668 TSQ Quantiva and Endura: TSQ Endura and TSQ Quantiva instruments are usually

shipped with a PC (“Endura/Quantiva PC”) that includes all the necessary instrument

data files, such as calibration files, for operating the MS instrument. If you want to

control an instrument using a different PC, make sure that the specific instrument data

files residing on the Endura or Quantiva PC are backed up and transferred to the new PC.

For details on performing this process, please consult with your local MS field service

engineer.

CM7-18098 Accela Open Autosampler: Sequences cannot be run when the sampler does not include

the DLW option. This configuration is not supported and requires a custom script.

CM7-18129 TSQ Quantiva and Endura: After an upgrade of the TSQ Endura/Quantiva instrument

driver, an error may occur when opening the Chromeleon Instrument Configuration. To

resolve the error, remove the Chromeleon Mass Spectrometer driver from the

configuration and then add it again. This will update the configuration information in

Chromeleon to match the updated TSQ Endura/Quantiva instrument driver version.

Chromeleon 7

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ID Description

CM7-20295 TSQ 8000 and ISQ Series: When a GC-MS instrument method includes a scan event

containing multiple SIM ions (e.g. “SIM 115, 152, 188”) then data from matching filters

collected at different time ranges will not be combined into a single filter in the data for

that injection.

CM7-20547 247 Instrument Controller: TDS4: Due to the smaller internal storage space available on

TDS4 models of 247 Instrument Controller, and the larger data files created by 3D

acquisition, TDS4 models of 247 should only be used to acquire 2D data. To acquire 3D

data, a TDS5 model of 247 should be used.

CM7-21342 Vanquish Variable Wavelength Detector: For acquiring data on a single channel only

using the Vanquish VWD it is necessary to use channel UV_VIS_1.

CM7-21967 TSQ Quantiva and Endura: The TSQ Endura and Quantiva mass spectrometer method

editor is supported on English operating systems with English/United States regional

settings only.

CM7-22490 Exactive Series: When setting the divert valve parameters for an Exactive Series MS with

a 2-position valve, the valve positions are recorded in the MS raw data opposite of how

the divert valve parameters were configured.

CM7-23138 MSQ Plus: It is recommended to use only the MS driver provided on the Chromeleon

installation medium. Other versions of the MSQ Plus driver may not be compatible with

Chromeleon. Please consult your local field service engineer for additional details.

CM7-23295 Exactive Series: Due to differences in how the Exactive 2.8 SP1 driver writes the scan

header in MS data files during acquisition, non-targeted peak detection will not work

correctly when data generated from both the Exactive 2.8 SP1 driver and older drivers

are present in the same sequence.

CM7-23442 Reporting: In order to display the date and time in the Header/Footer of reports one can

use the spreadsheet placeholders &D and &T respectively. During report creation these

placeholders are replaced by the current date and time and formatted via the regional

settings of the currently logged on Windows user account. Yet this doesn’t work correctly

for every regional settings, e.g., 24 hour time formatting.

Instead of using &D and &T one can use the Chromeleon report formula gen.currentTime

or gen.reportTime together with the necessary format, e.g. {gen.currentTime;

“dd.mm.yyy hh:mm”}.

Note: the formula gen.currentTime is replaced by the current date/time during the

electronic report creation. If you want to display the date/time when the electronic

report is really printed or exported you have to use the formula gen.reportTime.

CM7-23669 TSQ 8000 Series: If you attempt to abort an acquisition of multiple timed acquisitions

while the MS is acquiring data, the MS will not cycle back to a Ready state and the

sequence will not end. It is necessary to stop and restart the Instrument Controller to

regain access to the instrument.

CM7-24348 Privileged Actions: When privileged actions are configured to require authentication and

a comment, if a user action caused the "Authorization and Comment" dialog box to be

displayed, then if the dialog was left open for more than a minute before clicking Ok, an

error message was displayed. This was observed when clicking ‘Save As’ on a processing

method in the Studio.

CM7-24384 Setup: When Chromeleon 7.2 SR5 is installed on a Windows 10 PC, upgrading that PC to

Chromeleon 7.2.6 will appear to complete successfully, with no IQ errors or warnings.

However, attempting to export a sequence to PDF will fail with an error stating “Printer

not activated, error code – 30”.

To resolve this problem, rerun the Chromeleon 7.2.6 setup, selecting ‘Repair’ on the

opening screen of the setup program.

Chromeleon 7

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ID Description

CM7-24445 TSQ Quantiva and Endura: Instrument methods written with an earlier version of the

method editor cannot be opened with a newer version thereof.

CM7-24471 Shared Devices: When configuring an Ultimate 3000 DGP or a Vanquish Dual Pump, a

Vanquish Dual Autosampler, or Vanquish Column Compartment that is shared between

two instruments, make sure to use non-identical device names for the instrument

devices (e.g., PumpLeft and PumpRight).

If an Ultimate 3000 DGP or a Vanquish Dual Pump, a Vanquish Dual Autosampler, or

Vanquish Column Compartment are shared between two instruments with identical

device names (e.g., "Pump") in both instruments, removing the driver from one

instrument and moving it to the other instrument results in a fatal error.

Workaround: Rename the instrument devices to non-identical device names (e.g.,

rename the pump units to PumpLeft and PumpRight). Save the instrument configuration

and restart the server. Alternatively, remove the driver, save the configuration, restart

the server and re-add the driver again.

CM7-24600 Spectral Library: If an older Chromeleon version than Chromeleon 7.2.7 is used to create

and name components from library screening results, then upon selecting the folder

reference attempts to close the dialogue with OK will result in an exception being

thrown.

CM7-24825 Client: Studio: Processing Method: A sample with a processing method created in

Chromeleon 7.2.7 when opened in the Chromeleon 7.2.6 in the Studio should show a

notification bar indicating that the evaluation results may differ from those using the

version which was used to create/save the processing method. This notification bar is

not displayed.

CM7-25295 Vanquish Drivers: For the Vanquish Dual Split Sampler (VH-A40-A-02 and VF-A40-A-02)

relays are shared between instruments. Manual changes on one instrument also affect

the other instrument. If a sequence is running on the other instrument, no warning is

issued.

CM7-25296 Vanquish Drivers: For the Vanquish Dual Pump F (VF-P32-A-01) relays are shared

between instruments. Manual changes on one instrument also affect the other

instrument. If a sequence is running on the other instrument, no warning is issued.

CM7-25337 Vanquish Drivers: For an instrument with the Vanquish Dual Split Sampler (VF-A40-A or

VH-A40-A) and an instrument method configured for the left sampling unit using the

default Smart Shutdown settings, Smart Shutdown purges the right sampling unit (and

vice versa).

CM7-25370 Client: Studio: Instrument Method, Electronic Report: An inverse gradient method

created on Chromeleon 7.2.7 (or earlier) can be run on Chromeleon 7.2.8. However,

Chromeleon 7.2.8 does not support Smart Startup, Smart Standby or Smart Shutdown

settings for inverse (or tandem) gradient methods. Hence in Chromeleon 7.2.8, for an

inverse gradient method created on Chromeleon 7.2.7 (or earlier) any Smart Startup,

Smart Standby and/or Smart Shutdown settings included in the method are neither

executed nor reported with Chromeleon 7.2.8.

CM7-25447 Vanquish Drivers - Vanquish Duo Autosampler: If the user adjusts the needle height, this

is only adjusted for the left hand sampler unit, and not for both sampling units as would

be expected. The user should use the property Sampler2.SampleHeight to set the height

for the right hand sampling unit

CM7-25466 Instruments: Vanquish Drivers: For a Dual Autosampler in shared mode, where both

instrument methods have different temperatures set, the temperature setting of the

sequence started first is overwritten by the setting of the sequence started second.

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ID Description

CM7-25532 Client: Studio: Instrument Method – Method Translation: When creating an instrument

method for a given instrument configuration, then removing a module from the

instrument configuration and using the Method Translation Tool to update the

instrument method, in some cases there is no indication in the Method Translation Tool

that the initial instrument method contained settings for the removed module. However,

these settings are correctly removed from the instrument method by the tool.

CM7-25553 Client: Studio: Instrument Method - Method Translation: The method translation is not

working when attempting to translate an instrument method for a Waters UPLC

instrument, for which a module was deleted after the instrument method was created.

The method translation is not enabled for such an instrument method and the steps for

the deleted module remain in the method.

CM7-25567 ISQ EC: Under some circumstances, the parameters for Start Startup, Smart Standby and

Smart Shutdown will not be sent to the hardware, even though the instrument audit trial

indicates that the values were sent. It is recommended not to use Smart Startup, Smart

Standby and Smart Shutdown with this release.

CM7-25600 Instruments: GC Drivers: When running the TriPlus RSH or TriPlus 100 in Clone mode

(Autosampler serves two GCs), if the Virtual Terminal is opened from the ePanel of one

of the GCs and a Sequence is started for the other, the Sequence fails with an error;

"Sample - Error while validating script. (Trayplate 1: Slot 1:3)". This can be worked-

around by closing the Virtual Terminal on GC1 before attempting to start the run on GC2.

CM6-21321 Accela Open Autosampler: When using this autosampler, a dot (‘.’) must be used as

decimal separator.

CM6-22760 TRACE 1300 GC: The autozero function does not work correctly for the FID, NPD, ECD

and FPD detector types.

CM6-23614 TriPlus RSH: When using the TriPlus RSH in constant double pro headspace mode,

starting a sequence that includes a constant double pro method will generate a

validation error.

CM6-24043 TriPlus RSH: If firmware version 2.2 is installed on the TriPlus RSH autosampler, then tool

changes on the instrument are not immediately recognized in Chromeleon. It is

necessary to disconnect and reconnect the instrument after such changes are made;

they will then be detected.

5.2 Upgrading a Windows 10 PC From Chromeleon 7.2 SR5 to

Chromeleon 7.2.8

When Chromeleon 7.2 SR5 is installed on a Windows 10 PC, upgrading that PC to Chromeleon 7.2.8

will appear to complete successfully, with no IQ errors or warnings. However, attempting to export a

sequence to PDF will fail with an error stating “Printer not activated, error code – 30”.

To resolve this problem, rerun the Chromeleon 7.2.8 setup, selecting ‘Repair’ on the opening screen

of the setup program.

5.3 Compatibility with Foundation 3.1

Chromeleon is only compatible with Thermo Foundation 3.0 SP2. Users may encounter situations

where PCs provided with mass spectrometers come pre-installed with Foundation 3.1 or newer. In

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these instances, the factory procedure to uninstall any MS instrument control component software

must first be followed before reinstalling Foundation 3.0 SP2 and the mass spectrometer driver.

This procedure must only be carried out by individuals that have completed the necessary software

and hardware training.

5.4 Limitations with the Waters Driver Pack

ID Description

CM7-19830 Waters Acquity: When using the Waters Acquity driver in a Citrix environment, the

Acquity console does not update correctly and therefore doesn't show current log file

entries. This is due to a problem in the Acquity console, and can be mitigated by using

the instrument audit trail on remote clients.

CM7-20374 Waters Acquity: If the user attempts to open an Instrument method on a PC where the

Waters Driver Pack is installed, but then selects "work offline", an error message will be

shown. This is a problem of the Waters Driver Pack, the workaround is to ensure that the

instrument can be reached, i.e. work online.

CM7-22872

CM7-15225

Waters Acquity - Console: When using the Waters Acquity driver, some Chromeleon

screens may not appear properly, such that text from the previous screen is still visible.

This has been observed with the Sequence Properties and the Chromeleon Log on

screen.

CM7-23504 Waters Acquity: In rare circumstances when the user configures and then deletes an

Acquity PDA, the module will still be shown in the Acquity Console. If a command is then

executed (e.g. lamp on), the module disappears from the console, after which the user

then needs to reconfigure the instrument in the Chromeleon Instrument Configuration

Manager in order e.g. to turn off the lamp.

CM7-23730 Waters Acquity: When using the Waters Acquity Driver Pack4 and trying either to create

a new instrument method, or to open the Acquity console from the ePanel a problem

sometimes occurs. A message appears informing the user that launching the application

had failed, and that the Acquity driver pack may not be installed. If this occurs, the user

should contact Thermo Fisher Scientific for further advice.

CM7-24022 Waters Acquity: If the user has two Acquity systems connected to one Instrument

Controller, the range for the column temperature in the Waters method editor does not

always match the hardware configuration. This is affecting the method editor only, and

occurs when opening a method for instrument A while the Acquity console for

instrument B is open.

CM-9703 Waters Driver Pack 2017 R2: When installing Waters Driver Pack 2017 R2 ensure that

Microsoft Windows Universal C Runtime (KB2999226) is installed. This is to avoid failure

of Waters Driver Pack 2017 R2's DM.exe application, which depends on the Windows

Universal C Runtime that this hotfix provides for older Windows platforms.

CM6-21112 Waters 2998 PDA: Localization to a non-English regional setting for the PC (e.g., German)

does not function correctly for the timed events table, e.g., using a Waters 2998 PDA

detector and setting a timed event in the program file (e.g., wavelength change at 5

minutes). The event is recorded, but without the event time.

CM6-23194 After removing the Sample Organizer from the Instrument Configuration, the plate setup

is not updated correctly. Manually updating the plate settings in the plate setup

configuration dialog avoids this issue. If the total length of the instrument name plus

detector name is more than 32 characters, the sequence will abort shortly after initial

injection. The affected detectors are: 2489, 2998, and Acquity FLR.

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ID Description

CM6-24158 Waters 2489 PDA: After changing the Instrument Method from single to dual-wavelength

mode (without changing Channel A wavelength), the data rate for Channel B is set

incorrectly and incomplete data collection occurs.

CM6-24164 When the Waters Driver Pack 4 is installed in a Citrix environment, the World WIde Web

Publishing Service is automatically disabled, so that after restarting the PC, the Citrix web

application is no longer reachable. The service should be reset to automatic start, after

which the application can be reached

CM6-24191 In extremely rare cases the Acquity PDA server stops working, which then causes the

running sequence to be interrupted.

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5.5 Limitations with Agilent ICF

For a general overview regarding the Agilent Instrument Control Framework, please refer to the

document Chromeleon and Agilent ICF - Quick Start Guide - Chromeleon 7.2 .pdf, found in the

\Documents\ folder of the Chromeleon 7.2 CDS DVD.

ID Description

CM7-19347 Agilent G1312B DAD: When using a G1312B DAD in combination with an old JetDirect

card, the user may experience problems collecting data at 80Hz. If the user observes this,

they should get in touch with their local Thermo Fisher Scientific representative for

advice on possible solutions.

CM7-19540 Agilent ICF: The Agilent GC System Configuration dialog includes entries to configure the

7697A Headspace, G1888A Headspace, 7890 GC, 6890 GC, 68550 GC, and 7820 GC.

Currently, it is only possible to configure the 7697A Headspace sampler. Attempting to

configure any of the other modules will result in a message indicating that the modules

are not supported.

CM7-19863 Agilent ICF: The Agilent LC System Configuration dialog includes entries to configure the

following devices, which are not supported by the release:

All ELS Detectors (Drivers are not included, so they cannot be configured)

Multi-sampler and DAD HDR (Although configurable, they have several known issues and

are therefore not supported)

CM7-19975,

CM7-20451

Agilent 7697A: The Soft Config option, available via the ICF for Agilent LCs, is not

supported for the Agilent 7697 HS. It should not be added to any custom ePanel as its

use can cause issues by allowing configuration changes to be applied to the sampler

during acquisition.

CM7-19993 Agilent 7697A: If the 7697A loses its connection to the network, an audit trail message is

added indicating this fact. However, the ePanel will still show the unit as ‘Ready’.

CM7-20047 Agilent VWD G1314B: When using a G1314B VWD, occasionally the chromatogram is half

the expected length.

CM7-20259 Agilent 7697A: Although the vial position may be assigned in the instrument method

script, unless this is done in the Instrument Setup Stage, the sequence table will not be

updated. This can result in misleading information in reports and should be avoided.

CM7-20991 Agilent ICF: Occasionally when performing injections with ICF controlled instruments the

injection volume is incorrectly displayed, although the injection itself was performed

correctly.

CM7-21172 Agilent ICF: If the user has the monitor DPI settings on their PC set at greater than 100%,

then some parts of the Agilent LC system device ePanel are not visible.

CM7-21427,

CM7-18984

Agilent ICF with 1100 or 1200 LC DAD: When acquiring data from an Agilent 1100 or 1200

LC DAD, the signal trace may be shifted to the start of the run, and the end time is

inconsistent. No data points are lost with a data rate of

10 Hz and slower (>= 0.025 min 0.5 sec)

20 Hz and a low number of spectra (all other than ALL Spectra)

20 Hz and spectrum range 190- 400 step 2

CM7-22051 Agilent LC ICF: Aborting an injection after the start of a sequence but before the injection

resulted in an error, requiring the instrument controller to be restarted

CM7-22567 Agilent ICF: When using a Diode Array Detector with the Agilent ICF, it is necessary to

enable spectra collection initially (this also allows to specify the wavelength range to be

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used in this run). If no spectra are needed for a specific time window during the run, use

the timetable to temporarily set the mode to "None".

CM7-23096 Agilent ICF: If a Fraction Collector with Thermostat is installed, the channel mapping is

not correct. This can be resolved by removing the <Channel name="FC: Delay Sensor">

node from DefaultConfiguration.xml before adding the driver. After this, the user can

configure the mapping for the two channels manually on the Signals (2D) tab of the

configuration dialog.

CM7-23242 Agilent 7697A: Running multiple 7697A Headspace autosamplers on a single 247

Instrument Controller can cause Windows "Out Of Memory" errors, requiring a reboot of

the 247 to resolve. Thermo Fisher therefore recommends that only one 7697A is

connected to any 247 Instrument Controller.

CM7-23341 Setup - Uninstall: When Agilent ICF is installed, un-install of either Chromeleon or Agilent

ICF fails if the Instrument Controller is running:

Failed to execute package Agilent Instrument Control Framework A.02.04. Another

application has exclusive access to the file 'C:\ProgramData\Agilent

Technologies\Instrument Control Framework\RCDriver.log'. Please shut down all other

applications, then click Retry.

To avoid this issue, stop the Instrument Controller before uninstalling

CM6-23980 Agilent 7697A: When starting a sequence while the 7697A Headspace Sampler is in an

‘Error’, ‘Running’, or ‘Not Connected’ state, the ready check does not give an error

message. After the sequence starts, the following happens:

If the sampler is in error state, the sequence starts without getting interrupted

If the sampler is running, the sequence stops with audit trail message “Sequence stopped

by user”

If the sampler is not connected, the sequence interrupts with audit trail messages “Lost

connection to Agilent 7697A Headspace Sampler", and "The instrument is offline. Check

power to all modules, cabling between modules and whether the configuration matches

the list of modules."

CM6-23992 Agilent 7697A: The 7697 Headspace Sampler has two versions; 111- and 12-vial capacity

configurations. The Chromeleon driver is written and tested with the 111 vial capacity

version. Though not tested, the driver is expected to work with the 12-vial capacity

module. The user should not use vial positions greater than 12 in this case. The rack view

always shows 111 vial positions.

CM6-23996,

CM7-19940,

CM7-21324

Agilent 7697A: The 7697 Headspace Autosampler has two options for handling missing

vials: Pause and Abort. An issue has been observed when the Abort option has been

selected. In either mode, the autosampler overlaps sample preparation, i.e.: sample 2 is

prepared while sample 1 is acquiring. If the autosampler finds that the sample 1 vial is

missing, it will Abort or Pause the sequence at the point it discovers the vial is missing.

However, if the autosampler finds that the sample 2 vial is missing, while sample 1 is

already acquiring, and the Abort option has been selected, the entire sequence will be

aborted, including the acquiring sample 1.

CM6-24004 Agilent 7697A: Using the instrument front panel, the allowed range for Transfer Line

Diameter is 200-600 microns. However, when setting this value in the Chromeleon

instrument configuration the limit is 250-530 microns.

CM6-24005 Agilent 7697A: When 7697A headspace instrument method parameters are included in a

report, the “fill pressure” parameter is rounded to the nearest integer.

CM6-24007 Agilent 7697A: Some parameters logged to the instrument audit trail are rounded to

nearest integer. However, all values are downloaded to the instrument with the proper

precision.

CM6-24008 Agilent 7697A: When editing an existing 7697A Headspace instrument method, if the

values for Purge Flow, Purge Time or Leak Flow are changed, the Save button is not

enabled until the user changes tabs.

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CM6-24009 Agilent 7697A: When configuring an Agilent 7697A, there is an option in the user

interface to “Upload Config from Instrument”. This option does not work. Instead, you

will need to manually configure the instrument settings.

5.6 Limitations with Other Third Party Instruments

ID Description

CM7-9675 Agilent 7890 GC: There is a backward compatibility issue that affects the Agilent 7890 GC

Sampler Positions. When using a 7890 GC in combination with a 7693 sampler, certain

positions in the sampler could give a misspelled value to a move command. This has now

been corrected and could in rare cases lead to Instrument Method files needing to be

updated to avoid errors.

CM7-12366 Agilent 5890 DICE Card: Please note the following when using the19257 DICE card with

the Agilent 5890 GC:

Control and acquisition using the DICE card is only supported via the serial interface. The

GPIB interface is not supported.

Digital data acquisition via the serial interface of the DICE card is only supported for a

single channel; dual channel digital acquisition is not supported.

Currently, it is possible to select certain illegal combinations in the Configuration Dialog

such as:

Digital acquisition with the 19254 card. This is not supported.

Digital acquisition on one detector and analog acquisition on the other. Acquisition needs

to be exclusively digital or exclusively analog.

When using the DICE card to acquire data digitally, the 5890 INET mode must be set to

“GLOBAL” not “LOCAL”. Failure to do so will result in a “No response from GC” message

following the AcqOn command in the audit trail.

Note that when performing analog acquisition, the 5890 INET mode should still be set to

“LOCAL” (as described in the online help).

CM7-15293,

CM7-18463

Agilent 1100 Obsolete Driver: Occasionally, when using a combination of older and newer

modules, the raw data was not correctly acquired.

CM7-15400,

CM7-15556,

CM7-15734,

CM7-15736

PerkinElmer LC200 Autosampler: When upgrading from earlier versions of Chromeleon 7

CDS to Chromeleon 7.2 CDS SR3, it is necessary to reload the PerkinElmer LC200

Autosampler driver and configure the loop size within the configuration. The user should

then check all instrument methods using this autosampler to ensure that they continue

to function correctly.

CM7-15716 PerkinElmer Clarus 400 GC: Some users must select Autosystem XL in configuration in

order to communicate with the PerkinElmer Clarus™ 400.

CM7-17948 Shimadzu LC: Unlike most drivers, some Shimadzu UV detectors require that you select

the Advanced filter in the Command (F8) window in order to access the Lamp On/Off

command.

CM7-20464 Varian 3800 GC: It is not possible to start a manual data acquisition if the GC is not ready

(i.e. all temperatures, pressures and so on are at their set points). Trying to do so will

generate a Ready Check message detailing what is not ready.

CM7-24724 Agilent 7890B GC: With certain firmware versions, the GC does not properly send abort

information to the software, meaning that events such as FID flame out, pressure errors,

hardware faults and so on, will not be recognized or reported by Chromeleon. The

problem is seen in FW versions B.02.01, B.02.04.2 and B.02.05, but not versions A.01.xx.x.

The 7890A GC does not seem to have this problem.

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ID Description

CM7-24840 PerkinElmer Clarus 580 GC: For the PerkinElmer Clarus 580 GC without an internal

autosampler the automatic type recognition of the PerkinElmer GC driver configuration

module fails for the 580 type. The automatic type recognition detects a 500 series

instead. Setting the GC type to 580 manually does not allow to connect to the

instrument.

Workaround: Leaving the setting on 500 (or 600) allows to connect to the instrument and

to control it properly.

CM7-24868 Shimadzu LC-2010A: If using a large injection volume, samples could remain in a running

state until interrupted manually by the user. The need to configure the loop volume in

two places was not correctly documented in the help.

CM7-25156 PerkinElmer Autosystem XL GC: Chromeleon is currently not able to control or change the

signal source of a channel. Such settings must be controlled by the user at the GC display

and it must be verified that the channels are linked to the correct detector before the

method is used for Chromeleon control.

CM7-25298 Perkin Elmer GC: Sporadically sequence interruptions are observed with an error

message "No response from the GC". The reason seems to be an unstable serial

communication. If this occurs, please contact your Chromeleon support desk for

assistance.

CM7-25300 Agilent 7890: When used with certain LAN cards that are slow to initialize, the GC will

sometimes fail to connect if the acquisition service is set to automatically start on system

start. The workaround is to start the acquisition service manually, not automatically.

CM7-25343 Instruments: Third Party GC Drivers: Instrument Configuration Manager does not report

mismatches between the hardware and the Chromeleon configuration.

CM6-23947 Shimadzu LC-10A, LC-2010: If the user cancels the keylock state of the front panel of the

instrument and then, for example, stops a manual acquisition, this is likely to lead to

unexpected effects during the next operation such as sudden abort of the sample run.

5.7 Other Limitations

ID Description

CM7-11692 Console - Instruments: When monitoring the baseline with an overlay chromatogram

added to the signal plot, the overlay disappeared after changing to a different ePanel and

back.

CM7-15455 Studio - Processing Method: Without data in the first injection, it is not possible to select

the 2nd or 3rd Detector for Dead/Delay Time.

CM7-15588 Discovery: The Discovery service failed to start if the PC name included non-standard

characters. Now, the Discovery service will not crash and will log the PC name to help

troubleshoot why it is not listed in the Console or Administration Console.

CM7-17203 Report Designer: With some date/time formatting settings in the report, the order of

month and day changes for some formats automatically. The settings in the Report

Template can change based on the windows regional settings. For example it is not

possible to set m.d.yy as format with German regional settings. The Report Template

replaces this with d.m.yyyy. The substitution occurs for report variables and non-report

variable entries.

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ID Description

CM7-17465

Client: Studio: Processing Method - MS Settings: It can happen the spectral bunching

value for Peak Dependent Correction that is displayed as an annotation on the

chromatogram plot does not match the value entered in the processing method on the

MS setting page. This is by design, because the method setting defines the maximum

number of spectra for averaging. The actual number of spectra used is determined the

number of MS spectra which fit the filter used for the chromatogram. This is not correctly

documented in the Chromeleon online help.

CM7-17841 Report Designer: If using a non-Chinese format as the regional setting in Windows, and

Chinese as the setting for Non-Unicode programs, then the header on a Chromeleon

report is not correctly displayed for variables. If the format is changed to Chinese, then

everything is correctly displayed.

CM7-17966 Online Plot: For the Vanquish CAD, some properties and two channels are recorded

where the data is transmitted as aA, and scaled to pA with 6 digits resolution. The online

plot displays these numbers for the current signal value with 2 digit precision only.

CM7-18252 Export MS Raw Data: When acquiring MS data, Chromeleon acquires MS data and all

other signal data, such as UV, FLD, and pump pressure signals, in separate formats. As a

result, when MS data is exported, non-MS data is not exported with the MS raw data file.

CM7-19336 Chromeleon 6 Import: Due to changes in Auditing between Chromeleon 6 and

Chromeleon 7, when a Chromeleon 6 Sequence is imported into Chromeleon 7, some of

the text displayed in the Instrument Audit trail will not appear exactly as it did in

Chromeleon 6. Refer to the topic "Viewing Chromeleon 6 Data" in the online help for

further information.

CM7-19836 Console - eWorkflows: The eWorkflows wizard fails with a message "Failed to retrieve the

required Data Vault" when there is more than one Data Vault with the same name in the

Chromeleon Domain.

CM7-20335 Comparison of Old Report Versions Shows Change in CmbxExportParameters: If a report

which was created in Chromeleon 7.2 SR2 or earlier, and modified in SR3, has its history

compared in SR4, the history will appear to show that the "Cmbx Export Parameters"

value has changed from True to False. This is due to a change in the default value of this

field, and does not represent any user-modification of the report.

CM7-20449 User Management: Login "Role" dropdown box becomes empty after upgrading to

Chromeleon 7.2 SR4. This is due to the fix for CM7-18178 "Roles were offered in the

Logon dialogue, even if they were not specified as Logon roles". To work around this

issue, enable the "Logon Role" property in the user database for all logon roles that users

need to be able to select.

CM7-21331 Studio – Reporting: The mass spectrum resolution report variable returns an internally

used processing value instead of the resolution setting defined in the MS instrument

method. It is recommended to discontinue use of this report variable until further

notice.

CM7-21399 Console – Data Query: Injection Variables 'Auto Dilution Ratio' and 'Retention Time

Standard': Auto Dilution Ratio and Retention Time Standard columns are not available in

the custom filter conditions for injection records (e.g., in the IRC editor or summary

report).

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ID Description

CM7-21780 Setup: NIST MS Search and Demo Library No Longer Automatically Installed:

Incompatibilities of the NIST 2008 MS Demo Library installer with Window 7 and 10 could

cause the main Chromeleon installer to hang or crash. To address this, the NIST Demo

library, and the associated AMDIS and MS Search software are no longer automatically

installed when you install Chromeleon. If desired, this package may be installed manually

using the setup program found in the /Tools/ folder of the Chromeleon DVD.

Alternatively, one may install AMDIS and MS Search using the full (licensed) NIST library

installer.

Note that MS library searching within the Chromatography Studio is not affected by this

issue.

CM7-21783 Studio – Processing Method: Performance When Importing Fixed Calibration Standards

for MS Sequences: When working with sequences of MS data, importing injections for

use in a fixed calibration can take 1-2 minutes to complete, depending on the data.

CM7-22111 Discovery: Mixed Installations with Chromeleon 7.2 SR5 Domain Controller: If you have

an existing installation of Chromeleon < 7.2 SR1, the following limitations apply during an

upgrade:

• Stations that have Chromeleon 7.2 or below installed will not see any data vaults

or instruments that have been created with Chromeleon 7.2 SR5, until after

those stations are upgraded to 7.2 SR5.

• It is not possible for a Chromeleon 7.2 (and below) station to join a Chromeleon

7.2 SR5 domain.

• Stations that have Chromeleon 7.2 or below will not receive any updates from

the Discovery Service after the Chromeleon domain controller has been

upgraded to 7.2 SR5, and will only see resources that were already in existence

and cached.

• Please refer to the Enterprise Documentation for guidance on upgrading an

older installation of Chromeleon 7 to Chromeleon 7.2 SR5.

CM7-22145 Reporting: Discrepancy in “Last Modified” Time: Owing to differing rounding methods

used, it is possible that the value of the "last modified" time for an object in a sequence

has a difference of 1 second between the client display and the value shown in a report.

For more details, please see the on-line help.

CM7-22738 Client: Console: Empty Inject Time and GUID fields have been seen in a few single

injections. Raw data have been successfully acquired and stored on the local Instrument

PC. The Injection Audit Trail on the Instrument PC contains complete information,

including the missing details. Too few instances have been reported to identify the root

cause of this problem.

Note: If you are affected by this problem, please contact your local Thermo Fisher

representative for assistance with recovery of the missing injection details.

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ID Description

CM7-22986 During stress tests with multiple, very long sequences with more than 1000 injections,

the queue was aborted with an unexpected error:

"Queue End 24.12.2016 16:27:22 +01:00 Stopped the sequence queue run.

Sequence End 24.12.2016 16:27:22 +01:00 End of sequence "Simple Vanquish Test 2016-

12-21 19_37".

Abort Error 24.12.2016 16:27:21 +01:00 The injection audit trail cannot be saved. Error

detail: Die Transaktion wurde abgebrochen. The transaction commit operation failed. The

save operation failed for data item(s) "'chrom://c-germoefelein/XVault/Vanquish-

H/6/Simple Vanquish Test 2016-12-21 19_37.seq/277.smp/Audit.audit'". Execution of txp

[05f69eb4-c9ed-11e6-9598-005056c00008] failed. Error message : The command

'UPDATE CJ_VERSION SET VERSION_LAST_SIBLINGS_TXN_NO = @P0 WHERE

CJ_VERSION.VERSION_INVALIDATE_TXN_NO > @P1 AND CJ_VERSION.PARENT_ID IN

(@P2)' failed."

So far the issue could not be resolved. As a workaround Thermo Fisher recommends

disabling automatic upload when running very large sequences and uploading manually

instead.

CM7-23033 Legacy Upload: With replication framework disabled, when trying to modify a sequence

while the automatic upload is already in progress the upload may fail in very rare cases

and it is not possible to remove the sequence from the instrument queue by retry of the

upload. To recover the sequence a copy of the sequence has to be stored manually.

Chromeleon 7.2 SR5 adds an audit trail entry to the manually uploaded sequence that

refers to the original sequence so that traceability is ensured.

Thermo Fisher Scientific recommends to enable the replication framework with

Chromeleon 7.2 SR5 to avoid the problem.

CM7-23051 In a few cases Sequences have been reported to abort with messages in the audit trail

that were not conclusive, such as:

• “The audit trail was unavailable for some time. Several audit trail messages are

lost. They have been logged to the file

"Dionex\Chromeleon\Log\AuditTrailMessages.log" in the (common) application

data folder.”

• “The injection audit trail / signal "…" cannot be saved. Error detail: The

transaction has aborted. The transaction commit operation failed.”

However, the SQL Server ERRORLOG files of the affected Instrument Controller PCs

revealed errors due to slow file operations on the local hard drive. Thus it is assumed that

these failures were caused by poor disk drive performance. Chromeleon 7.2 SR5

introduced additional internal error reporting so that similar errors can be identified

more easily in the future.

CM7-23099 Third Party Drivers - Setup: The Microsoft Visual C++ 2005 Run Time component is no

longer supported by Microsoft. However, this component is required for the Shimadzu

LC-2010A and Shimadzu LC-10A/20A/30A drivers and is therefore installed by

Chromeleon.

If you don’t use these drivers, it is possible to uninstall the Visual C++ 2005 Run Time

component from the ‘Programs and Features’ page of the Windows Control Panel.

Alternatively, during the installation of Chromeleon, it is possible to suppress the

installation of the Visual C++ 2005 Run Time component by using a response file and

excluding the "__MicrosoftVisualC2005_SP1__" package. Please refer to the Installation

Guide for details.

Several of the Shimadzu devices can be controlled by obtaining an updated driver directly

from Shimadzu (see the “List of Supported Instruments” for details).

CM7-23484 Reporting: In order to display the last updated date and time for a locked injection it is

necessary to use the Chromeleon report formula procMeth.version.time.

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ID Description

CM7-23740 Query: When searching for injections by date using the operator “Is Not During

Previous”, the query result would also return injections created/modified during the

current day.

CM7-24042 Instrument Configuration Manager: The .NET 4.7 framework is installed by Windows

Update. For Windows 7 it is a recommended update, but for Windows 10 it is a

mandatory update. This release of Chromeleon has been validated against .NET 4.7.

However, under rare circumstances, the installation of .NET 4.7 could lead to

malfunctioning or crashes of the instrument configuration manager or configuration

plug-ins. If this occurs, please contact your Chromeleon support desk for assistance in

correcting the problem.

CM7-24058 Client: Console: The new eWorkflow option "Preserve Layout", introduced in Chromeleon

7.2.6 is not backwards compatible with older versions of Chromeleon. If a client with an

earlier version attempts to open an eWorkflow for which this option is enabled, the error

message "Cannot load, as the data was created with a newer Chromeleon version.” Is

displayed.

CM7-24706,

CM7-25325

Installation of KB4041083 “Security and Quality Rollup for the .NET Framework 3.5.1,

4.5.2, 4.6, 4.6.1, 4.6.2, and 4.7 for Windows 7 SP1 and Windows Server 2008 R2 SP1:

September 12, 2017” on a PC with the Agilent ICF framework will cause the Chromeleon

Instrument Configuration Manager to crash.

To resolve this issue, uninstall KB4041083. This may require reinstallation o one or more

of the following KBs, depending on what .NET versions were originally installed on the PC:

-KB4040973 for .NET Framework 4.6 or newer

-KB4040977 for .NET Framework 4.5.2

-KB4040980 for .NET Framework 3.5.1

If .NET Framework 4.7 was originally installed, please uninstall both KB4041083 and .NET

4.7, reboot, then install .NET 4.7 from the Windows updates and reboot again.

Note that the same issue can be caused by installing KB4043766 "Quality Rollup for .NET

Framework 3.5.1, 4.5.2, 4.6, 4.6.1, 4.6.2, and 4.7 updates for Windows 7 SP1 and

Windows Server 2008 R2 SP1: October 17, 2017) and any .NET Security and Quality

Rollup released since September 2017.

CM7-24722 Print/Export: With the "Export report" option enabled for the Queue, export for each

injection sometimes fails.

CM7-24972 Nest

ed Autorepeat: When applying a two level Autorepeat rule with double grouping to a

plot object, if the sequence contains a large number of injections and a large number of

components, it is possible that software performance will degrade significantly. This has

been observed when applying Autorepeat to an MS Components plot for a sequence with

27 injections and 292 components.

CM7-25321 eWorkflow Editor: Under some scenarios, an eWorkflow is immediately marked as

"changed" after opening (i.e., the "Save" button is enabled). These changes are internal

updates related to metadata like injection volume range, available positions, and

available methods. If these changes result in invalid values for the user-editable fields

volume, position, or instrument/processing method, they are also updated.

CM7-25334 Client: Console: Data: Using the Merge option when re-importing a cmbx file can result in

the deletion of Sequences which were created since the cmbx was created.

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ID Description

CM7-25392 eWorkflow - import (*.ewfx) file: After importing an eWorkflow, the audit trail may

contain an additional "changed" entry, although the user didn't make any changes.

This is due to Tags in the eWorkflow that are not present in the destination domain being

removed.

Note that the user can also edit the tags during import; these changes would be included

in the same audit trail entry.

CM7-25463 Upload: In very rare cases, an upload may hang. The issue has been seen under high load

when using IRC to create additional channels.

Workaround: Cancel the upload and use the "Manual Move" command

CM7-25480 Client: Console: Data: If a Data Vault is unavailable, it is not shown as collapsed in the

data explorer tree despite its sub-folders and items being inaccessible.

CM7-25508 Upload: In very rare cases, an upload may succeed, however the sequence remains

locked (redirected to the Xvault).

CM7-25551 Import/Export: If two (or more) users simultaneously attempt to export a Sequence to

the same location, a "Cannot export <sequence_name>" error is displayed for all.

CM7-25586 Client: Studio: Reporting: In Chromeleon 7.2.8, reporting is now performed by a separate

'background' process on the Chromeleon Client or IPC where the Sequence was added to

the queue. The Windows session on this computer must remained logged-in until

reporting has completed. If the user logs out of the Windows session, the background

process will be exited and reports will not be generated for any queued or acquiring

Sequences. The user needs to be aware of this, especially when running a Chromeleon

Client on a Windows Terminal Server session, as no warning is given if the user logs out of

Windows with Sequences configured for post-injection or post-sequence reporting still in

the Instrument Queue.

CM7-25590 Client: Studio: Chromatogram Plot: When creating a Virtual Channel, the Power Factor

only increments in steps of 0.5, which does not provide sufficient flexibility for controlling

the scale of the extracted data.

CM7-25633 Services: In very rare cases if the Oracle database disk is running out of disk space and in

addition an IPC cannot be connected properly, it may happen that that a sequence

cannot be uploaded automatically. When trying to reboot the IPC a retry of the upload

may result in an error message "A transaction package is missing on the hard disk. The

order of transaction packages which should be sent to the network data vault can't be

accomplished." The sequence can't be removed from queue automatically. It needs to be

removed manually.

SWFR-248 The following limitations apply to the import of data from Waters Empower:

1. Time zone information is not supplied by the Waters toolkit API, so dates and times

will be imported as if they were local.

2. Empower allows injections that are not contained in sample sets. These are not visible

to the importer and cannot be imported unless added to a sample set.

3. Some peak results fields show incorrect units in Chromeleon since there is currently no

mechanism to change the units on 'core' fields. They are included correctly in custom

fields that by default are hidden.

SWFR-2543 Sampling Devices That Do Not Use uL As Units for Volume: Although most liquid injection

devices expect volumes to be entered in uL, there are a few devices (e.g. Thermo AS-HV

and PerkinElmer GC Autosampler) which do not use µL as their default volume unit. If

one of these devices is configured in the same instrument that also includes an injection

device that uses µL, problems may be observed with volume validation in the sequence

table as well as units associated with volumes in reports.

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ID Description

CM6-23886 Exception Error When Removing USB->COM Port Adapter: If a USB-to-RS232 adapter is

used to provide COM communication between an Instrument PC or 247 Instrument

Controller and an instrument, and the USB connection is unplugged, Chromeleon reports

a Fatal Error in the Instrument Audit trail. The USB-to-RS232 adapter should not be

disconnected from the Instrument PC or 247 Instrument Controller while it is powered-

on.

5.8 Obsolete Drivers

Chromeleon includes a number of obsolete drivers in order to provide backward compatibility of

existing installations:

• Agilent/HP 1200 HPLC System

• AI 1310/3000 GC Sampler - 10ul

• AI 1310/3000 GC Sampler - 5ul

• AI 1310/3000 GC Sampler - 5ul - 155 Vials

• AI 1310/3000 GC Sampler - 5ul - 105 Vials

• AI 1310/3000 GC Sampler - 10ul - 155 Vials

• AI 1310/3000 GC Sampler - 10ul - 105 Vials

• PAL Sampler for GC

• PAL Sampler for LC

• TRACE 1300 Series GC (First generation driver that has been superseded by TRACE 1300 Series GC

II driver)

Please note that issues reported for any of these drivers will no longer be addressed. If you are using

one of these drivers Thermo Fisher Scientific recommends migrating to a supported driver as soon as

possible.

5.9 Functional Differences between Chromeleon 7.2 and Chromeleon

6.8

Chromeleon 7.2.8 implements the vast majority of Chromeleon 6.8 features, and in general, has a

richer feature set than Chromeleon 6.8. However, a few Chromeleon 6.8 features remain to be

implemented on the Chromeleon 7 platform and a few will never be implemented, since they are

now obsolete or no longer relevant. If a particular missing feature is important to you, please

contact your local Thermo Fisher Scientific representative to find out if that feature is in the product

development plans.

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6 Backward/Forward Compatibility Issues

6.1 Thermo Scientific Vanquish Charged Aerosol Detector [CM6-23499]

Any Instrument Methods created for the Vanquish Charged Aerosol detector with Chromeleon 7.2

SR2 MUa and earlier may need to be updated due to changes in the driver introduced in Chromeleon

7.2 SR2 MUb.

6.2 Thermo Scientific Vanquish Autosampler [CM6-23405]

Any Instrument Methods created for the Vanquish Autosampler containing the WashSpeed property

will need to be updated. The WashSpeed value needs to be divided by 0.06 in order for the

Instrument Method to work correctly.

6.3 Thermo Scientific TriPlus RSH

The current driver for this instrument is incompatible with firmware older than version 2.4.

6.4 Thermo Scientific TriPlus 300 HS

The current driver for this instrument is incompatible with firmware older than 2001.9.0.

6.5 Thermo Scientific TriPlus LS-100

The current driver for this instrument is incompatible with firmware older than version 2.4.

6.6 Thermo Scientific TSQ Quantiva

The driver version 1.1 QF1 for this instrument, included in this Service Release, may not be

compatible with existing TSQ Quantiva mass spectrometers running driver version 1.0 without a

hardware update. Please contact your local MS service engineer before attempting to upgrade the

unit.

Note: New TSQ Quantiva modules from the factory are not affected by this issue.

6.7 Thermo Scientific TSQ Quantiva and Endura

The driver version 1.1 SP1 for these instruments may not be compatible with existing TSQ Quantiva

and Endura mass spectrometers running driver version 1.0 without a hardware update. Please

contact your local MS field service engineer before attempting to upgrade the unit.

Note: New TSQ Quantiva and Endura modules from the factory are not affected by this issue.

6.8 TSQ Quantiva and Endura Instrument Method [CM7-18759]

Instrument methods created with older versions of the TSQ Quantiva and Endura instrument method

editor cannot be opened with newer versions of the method editor. If a large number of instrument

methods have already been created for regular use, upgrade of the TSQ Quantiva and Endura driver

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is not recommended. Contact your local Thermo Fisher Scientific representative for additional

details.

6.9 Signed Sequences [CM7-16374]

Sequences that have been signed within Chromeleon 7.2 SR1 will fail verification after copying within

later versions of Chromeleon 7.2 CDS.

6.10 Chromeleon Enterprise Compatibility of a Chromeleon 7.2 SR5

Domain Controller with Newer Versions of Chromeleon Clients and

Instrument Controllers

In general, it is possible for a Chromeleon Enterprise with a domain controller running Chromeleon

7.2 SR5 (MUa, MUb, MUc or MUd) to work with instrument controllers and client PCs running newer

versions of Chromeleon (7.2.6, 7.2.7, 7.2.8).

For customers with a fully validated Chromeleon 7.2 SR5 system, we would not recommend

connecting clients or IPCs with a later version of Chromeleon installed.

However, should you choose to create a ‘mixed’ Chromeleon environment, the following restrictions

apply:

Opening Processing Methods Created on Newer Versions on an Older Client

These processing methods may be opened, edited and saved without losing any parameters specific

to the newer version. However, the new parameters will not be applied to data processing, will not

be accessible as report variables and will be completely ‘invisible’ on the older client. The new

parameters include:

• Peak Identification by Reference Mass Spectrum

• Time based specification of the Cobra Wizard the integration parameters ‘Smoothing Width’,

‘Baseline Noise Range’ and ‘Consider Void Volume’

• UV Spectrum Search Across Multiple Libraries

• Variable Amount ISTD quantitation Based on Ratio (Response) vs Ratio (Amount)

Enterprise Functionality Specific to Newer Chromeleon Versions

Features such as email notification, automated results export, post-sequence reporting with

Chromeleon Client closed, and Chromeleon XPS will not function, even if accessed from a client

running a newer version of Chromeleon.

Support for Instrument Control Specific to Newer Chromeleon Versions

In general, it is possible to control these instruments. However the following restrictions apply:

• The instrument controller PC must be running the newer version of Chromeleon

• Older client PCs will not be able to create, edit or view instrument methods for the new

driver

• Older client PCs will not be able to view ePanels related to the new driver

• Some instrument view toolbar items such as ‘Consumables’ and ‘Troubleshooting’ may be

disabled (or have fewer sub-options) on the older client.

• Older client PCs will not be able to perform manual tuning or do real-time scanning for

remote mass spectrometers

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Additional restrictions may also apply. If you have any questions or concerns, please contact your

local Chromeleon support channel.

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7 Appendix

This chapter contains general Information about Service Releases, Release Notes, Online Help, and

Contributed Content.

7.1 Release Notes

The Release Notes list the new features and improvements of the current release. Included in these

Release Notes are all of the functionality and bug fixes from Chromeleon 7.2 SR5 MUa, Chromeleon

7.2 SR5 MUb, Chromeleon 7.2 SR5 MUc and Chromeleon 7.2 SR5 MUd. For details about Chromeleon

7.2 SR5 and other previous releases, refer to the relevant release notes which can be found on the

Chromeleon 7.2.8 DVD.

7.2 Online Help

In general, new features, updates and drivers that are introduced with this release are described in

an updated Online Help that is distributed with the release.

7.3 Contributed Content

The Chromeleon 7 disk contains a folder titled Contributed Content. This folder contains:

• Demonstration Material

• Localized Documents

• Localized ePanels

• Localized Report Templates

• eWorkflow Templates

• User Management Example

• Charlie Mouse Pointer

Note: The files in the Contributed Content folder have not been tested and validated according to

Thermo Fisher Scientific Software Development Cycle guidelines modeled after ISO 9001:2008

standards. Thermo Fisher Scientific assumes no responsibility for any errors that may appear in

the content provided in the Contributed Content folder.

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