Software Status Bulletin

MassHunter Quant     

Preface
-------------------------
This Software Status Bulletin (SSB) documents all known problems in the software
product designated above. The SSB is derived from Known Problem Reports (KPR)
which result from user problems that have been classified as documentation
problems or software defects. When a KPR is written, an identifying number is
assigned to it, and the KPR is added to the next edition of the SSB.

User inputs that have been classified as Enhancement Requests are not documented
in the SSB. User problems that have been submitted, but that have not been
classified by the time the SSB is generated are not included in the SSB.

How to use the SSB
-------------------------
When you experience a problem with a product, first check this SSB to see if the
problem has been reported already, and if there is a temporary workaround
available for the problem, or if the problem has already been fixed by a new
revision. If the problem is not listed in this SSB then you may wish to report
it to the Response Center or to your field support representative.

To determine if your problem is documented in this SSB, first look in the
Keyword Index section of the SSB. Under each keyword is a listing of one-line
descriptions of related KPRs. If any of these sound like yours, locate the KPR
# in the Known Problem Reports section of the SSB, and read the full KPR. The
KPRs in the Known Problem Reports section are sorted by KPR #.

There are two sections in the SSB:
Keyword Index: This index is categorized by keyword. For each KPR there is a
brief description and a KPR #. A KPR may be associated with more than one
keyword.

Known Problem Reports: This section contains KPRs, with all the available
information relevant to the problem. KPRs in this section are sorted by KPR #.

Keyword Glossary

Keyword Index

Keyword: 

One-line Description:

Message displays that error reporter could not connect to the server

Problem:

Message displays that error reporter could not connect to the server

Temporary Solution:

None

Fix Information:

Fixed in 10.0

Keyword: 

One-line Description:

 Quant B.09.647.0 doesn't validate invalid Quant DA method for checksum

Problem:

If a Quant DA method is checkout from ECM, Edited, checked back in and loaded to Quant B.09.00 or prior it is not blocked due to invalid checksum.   

Temporary Solution:

None

Fix Information:

Fixed in 10.0

Keyword: 

One-line Description:

Removing sample from batch after the sample directory (.D folder) is deleted, causes Quant to crash

Problem:

In some cases, when using SureMass data - it is possible to encounter a crash in Quant when the following occurs:

- After deleting a sample directory (.d folder) off disk in Windows explorer, user removes a sample from the Quant batch.

Temporary Solution:

Recommended workaround is to remove the sample from the batch first (or close the batch) before deleting the sample data directory (.d folder) from disk.

Fix Information:

n/a

Keyword: 

One-line Description:

 'Set Peak Filter Area Threshold' script executes when 'Cancel' or close is clicked

Problem:

 'Set Peak Filter Area Threshold' script executes when 'Cancel' or close is clicked

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

 “index out of range” message with manual integration using SureMass

Problem:

 “index out of range” message with manual integration using SureMass

Temporary Solution:

None

Fix Information:

Fixed in 10.0

Keyword: 

One-line Description:

Calibration Reference Compound does not display Average RF and Average RF RSD correctly in batch table 

Problem:

Quant 10.0 introduced Automatic semi-quant where one can define a 'Calibration Reference' compound. This allows a compound to automatically inherit the calibration curve defined in another compound without needing to copy the calibration levels. 

 There is a defect in Quant 10.0 where, in the batch table, the compound Average RF and Average RF RSD values are not being properly inherited. They are displaying the previous values used for that compounds curve fit. 

 However - the calculated concentration and final concentration are being properly calculated and displayed in the batch table. 

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Method Editor allows 'Calibration Reference Compounds' to have reference multiple levels 

Problem:

With Quant 10.0 - a new feature was introduced to permanently link a compound's calibration curve to another compound (which doesn't already have a calibration curve). This is useful when is it not possible to get calibration standards for a particular compound - and it is decided to use another similar compound's calibration curve (for which one does have standards) to quantitate it. 

For example - If CompoundA has a 4 level calibration curve, and I want to use those levels for CompoundB - I would simply set the 'Calibration Reference Compound Name' to "CompoundA" in the CompoundB row of the method. 

However - let's say I have another CompoundC. And I want CompoundC to ALSO use the same calibration curve that CompoundB is using. With Quant 10.0 - I cannot use CompoundB as its 'Reference Compound'. I cannot daisy-chain these compounds. Instead - I must set CompoundC's 'reference compound' to CompoundA.

Temporary Solution:

None

Fix Information:

Fixed in 12.1

Keyword: 

One-line Description:

Reporter name in Excel template is different between DA automation and Quant report generation 

Problem:

When generate the report in Quant directly with report template ‘QuantReport_ESTD_ResultsSummary_B_06_00’, I find that the reporter name is the same as the Quant-ECM login account, but when doing DA automation in Acq(Acquire and data automation), the report generated with reporter name which is not my LCQQQ Acq login account but my PC login account.

Temporary Solution:

None

Fix Information:

Will No Fix

Keyword: 

One-line Description:

Quant batch version is wrong in an Excel report template

Problem:

'QuantReport_ESTD_ResultsSummary_B_06_00' shows the Quant Batch version as a date rather than a number.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Setting GC signals to extract  'Deconvoluted Scan' will give error in Quant on Analyze Batch

Problem:

Setting GC signals to extract  'Deconvoluted Scan' will give error in Quant on Analyze Batch

Temporary Solution:

None - Fix method

Fix Information:

n/a

Keyword: 

One-line Description:

The matrix spike group recovery is not cleared after zero peak.

Problem:

To see this issue setup for Matrix Spike group recovery.  Perform an "analyze batch" and note the Matrix Spike group recovery contains the recovery amount.  Next zero peak one of the matrix compounds.  The Matrix Spike group recovery is not cleared but retains the original value.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Changing sample type from Blank  to TuneCheck and back causes message error

Problem:

Starting with a sample type equal blank there are missing peaks and this is reflected in the Outlier(s) message with a "Peak not found".  When you change the sample type from blank to tunecheck, the flag disappears, then change back to blank. A warning appears and the outlier flag does not display.  The expected result is the flag will display just the same as change the type before. 

Temporary Solution:

None

Fix Information:

Will Not Fix

Keyword: 

One-line Description:

Document Noise regions calculation differences for MRM/SIM data with Agile2 integrator

Problem:

Affects only MRM or SIM data when using Agile2 integrator and when users choose to re-index data files. Other data types or data using integrators different than Agile2 are not affected.

A new data indexing mechanism created in Quant 10.0 for MRM and SIM data for performance improvements with enhancements in noise regions determination can produce minor peak differences and possibly significant noise results differences compared to previous versions.

Noise regions are improved and more accurately determined with the new indexing mechanism.

The changes will only be noticeable when manually re-converting previously converted data with Quant 10.0.

Data that was previously converted using previous version of MassHunter Quant will not be automatically reconverted and will not use the new indexing mechanism and will not see any differences. Only newly acquired data (or data that is deliberately manually reconverted) will use the new indexing.

Temporary Solution:

None Required - Informational Item

Fix Information:

Change in 10.0

Keyword: 

One-line Description:

No quantitation message for qualifier not found is displayed

Problem:

There is no text in the Quantitation Message when the qualifier peak is not found. 

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Automated Quant of large worklists of LCMS runs - particularly when run from Study Manager - may fail with error

Problem:

From MassHunter Acquisition for LCMS QQQ running in ECM compliance mode - it is possible to run studies via "Study Manager" where Quant will automatically perform post-analysis quantification on that data. However - it has been observed that if a user submits a particularly long worklist (>100 samples) - an error can occur "No overload for method"

Temporary Solution:

Depending on the condition of the data file residing on the ECM - it may be possible to generate a new Quant batch manually, loading the data generated during the study. One would test this by creating a new batch in Quant (in ECM mode) and attempting to add the samples from the study. 

Fix Information:

n/a

Keyword: 

One-line Description:

Quant ECM - Method History:  Adding and removing templates in quant report method are not recorded

Problem:

When report template is added or removed in a Quant Reporting Method and  the Method History application is run the output on the change of report template is incomplete.
1) 'Inserted' or 'Deleted' is displayed but does not say what is inserted or deleted
2) Report template name that is added or deleted is not displayed

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

When excluding an Ion in Unknowns Analysis, the mass extraction window was not applied

Problem:

When excluding an Ion in Unknowns Analysis, the mass extraction window was not applied

Temporary Solution:

None

Fix Information:

Fixed in 10.0

Keyword: 

One-line Description:

Noise of Raw Signal no longer changes when zero peak done

Problem:

When a zero peak is performed the "Noise of Raw Signal" is not recalculated.  This can affect analysis where signal to noise is important factor when compound is not found.

Temporary Solution:

None

Fix Information:

Fixed in 11.1

Keyword: 

One-line Description:

 Download molfile script fails due to Chemspider site change

Problem:

Chemspider has the new portal and replaced the old API platform.  The current 'DownloadMolefilesFromChemspider' script doesn't work anymore and needs to be updated.

Temporary Solution:

Request updated script from support

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Qualifier ratio outlier remains flagged when the associated target peak is zero peaked

Problem:

If an Qualifier ratio outlier is out of limits the cell is highlighted in red or blue.  When the associated target peak is zero peaked the ratio is updated but the highlighting remains until an Analyze Batch is performed.

Temporary Solution:

None

Fix Information:

Fixed in 12.1

Keyword: 

One-line Description:

In Reporting Font size has No effect under the Quantifier/Qualifier Chromatogram settings

Problem:

In report method under Graphics settings, the Font Size under the Quantifier/Qualifier Chromatogram has no effect in the Quantifier/Qualifier overlaid graphics in the report output.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Dirty batch pegs CPU at 100% - Classic UI only

Problem:

This is an easily reproducible defect.  Note - it only occurs in the "Classic UI" interface, not the Quant-My-Way interface. 

Symptom: take a clean batch and dirty it by changing a level name without analyzing. Quant will immediately peg a processor core to 100% forever. Program still remains responsive and issue goes away once you 'analyze' batch.

Steps to reproduce:

1.) Load QQQ batch - DrugsOfAbuseDemo.batch.bin
2.) Change level name of L4 calibrator to "b". Hit enter or click into another box for Quant to accept input.
3.) Note 1 CPU will be pegged to 100% usage by Quant.

 Note: this is highly reproducible with other batch "dirtying" activities like:

Applying any manual integration

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Using 'Save As' in Quant-My-Way interface to overwrite an existing batch crashes Quant

Problem:

Using 'Save As' in Quant-My-Way interface to overwrite an existing batch crashes Quant

Temporary Solution:

None

Fix Information:

Fixed in 10.0

Keyword: 

One-line Description:

Library Editor: sort by compound name doesn't work in the same way as Quant

Problem:

Library Editor: sort by compound name doesn't work in the same way as Quant

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Link for PDF Report Index at MassHunter/Shortcuts/Quant/Supplemental not working

Problem:

Link for PDF Report Index at MassHunter/Shortcuts/Quant/Supplemental not working

Temporary Solution:

Link could be manually edited to point to file  INDEX_Quant_PDF_Reports_10.1.pdf.

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Agile/Agile2 Integration issue:  Both peaks in the extraction window get integrated as one

Problem:

A typical problem scenario for this issue involves data with multiple sharp peaks (i.e. few points per peak).   The fix involves a change in the Agile/Agile2 integrator.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Change in numeric format fails to work on certain systems

Problem:

Quant B.09.00 supports a feature where the user may select numeric format for a data field and the reports that use that field will pick up the format change.  Example: Change RT from 3 digits to 4 and print report.  The report will show 4 digits.  Some systems have been found to not work this way and the format remains the default value.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Screener issue: Index outside the bounds of array when Spectrum Qualifier Quantifier only field is checked

Problem:

Issue affects the screener workflow in Quant.  Software will crash (error message: Index outside the bounds of array) when some data files are added to the batch but not the others, and only when using screener settings but not general Quant. More specifically, when the Spectrum Qualifier Quantifier Only field is checked. 

Root cause is the ions that are very abundant in the background (and they tend to be low m/z, <80).  The workaround is to swap the Quant with Qual ion of higher m/z, this solved the problem for all the data files in the batch. 

Temporary Solution:

None.  See workaround in description.

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

SureMass mass accuracy in negative ions is poor

Problem:

SureMass analysis of negative profile data results in mass accuracy that is poorer than seen for positive ions. 

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Zero Peak Target Ion in Quant result but fails updating screening results

Problem:

Performing a Zero Peak on a target should be considered as "Compound not found" (a "red" in screener) however not all outliers and calculated values used by the screener are updated leading to misleading conclusions.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Adding 'Save Batch As' to Ribbon yields a button that doesn't work

Problem:

Use the Flavors Setup Tool to add the 'Save Batch As' button to the Quant ribbon.  Button displayed but not functional.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Batch-at-a-Glance -> Properties -> Color scheme is not persisted when app closes in Quant-My-Way mode

Problem:

The Batch-at-a-Glance -> Properties -> Color scheme setting is preserved when restarting the program in the 'Classic' Quant UI but not when using a Quant-My-Way version.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

GC-QTOF fail to create SureMass file due to corrupt MSMassCal.bin file

Problem:

When certain files, with corrupt MSMassCal.bin file, are being converted to SureMass the conversion fails with an Index out of bounds error on files that have a corrupted MSMassCal.bin file.  The reason that the MSMassCal.bin file is corrupt is usually because the GCMS Acquisition method calls for Cal gas but there is none (Example 7250).

Temporary Solution:

Remove the corrupt MSMassCal.bin file from the data file and then perform conversion.

Fix Information:

Fixed in 10.1 (no crash, error indicates file problem)

Keyword: 

One-line Description:

There is no deconvoluted spectrum in screener window for target without library match score

Problem:

This issue is seen with the screening workflow.  For target compound without library match score, there is no spectrum shown in the screener window.  But in many cases, the compound is still real and the Quant ion and another qualifier are usually found.

For those cases, if deconvolution fails finding a component for the target, quant will show raw extraction spectrum in screener window instead of leaving spectrum blank and leave library match score blank to avoid the confusion with the match score from deconvolution.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

280261 - Cannot quantitate if ISTD has no calibration rows and is the first compound in TargetCompound list

Problem:

ISTD compounds do not get quantitated using a calibration curve, therefore they do not need any entries in the calibration table. However, quantitation will not complete successfully if the TargetCompound table's first compound is an ISTD without calibration rows.

Temporary Solution:

This seems to only happen if the method is opened in the method editor then applied and analyzed. If the method is applied directly to the batch, the analysis seems to work just fine.

Fix Information:

Do Not Fix

Keyword: 

One-line Description:

Unknowns Analysis - Fragment Identification via accurate mass does not find 13C and other isotopes

Problem:

There are cases where 13C and Br isotopes are not being used in formulas and that including them in the possible isotopes will identify the fragments.  Requesting that a complete table of isotopes be used so that more ions are identified correctly

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Quant theoretical plates calculation is incorrect

Problem:

The Quant number of theoretical plates was using peak width rather than peak width using the tangent method.  

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Quant-My-Way Custom flavor - Method table columns do not show custom label in Compound Table view

Problem:

Reported that when creating a custom label for the User Annotation field that custom label appeared in the custom flavor except in Compound Table view where it appears as User Annotation.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Agile and Agile2 not integrating very sharp peaks

Problem:

In some data sets very sharp peaks of significant size where not integrated.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

When Quant-My-Way version converts files there is an error writing to log, Classic works

Problem:

When a set of untranslated data files are added to a batch in Quant-My-Way each file appears to be translated but with each file an error message appears indicating that the translation log could not be updated.  Classic does not show this issue.  Quant-My-Way doesn't when run "as administrator".

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Unknown Analysis - Graphic setting does not support Spectrum font size

Problem:

Unknown Analysis - Graphic setting does not support Spectrum font size

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Unknown Analysis  - Crash after sorting one column then selecting 'Refresh' in queries

Problem:

Steps to reproduce:
1) Open 'Target and Non-Target Analysis.uaf' (MassHunter\Data\QuantExamples\MS\RI-PEST-MATRIX from Supplemental installation)
2) Select Report > Query.  Select any of the first three queries (Batch Non-Target ..., Batch Quant Target ...).  Click Open
3) In the Query window, sort any one column by clicking the column header
4) Right-click in the query window and select 'Refresh' 
--> Crash

Temporary Solution:

None

Fix Information:

Fixed in 11.1

Keyword: 

One-line Description:

Quant displays incorrect Reference Library source after overwriting existing Reference Library file

Problem:

Steps to reproduce

1) Open VOA batch
2) select a cal file 
3) enter method editor, Create Reference library based on a cal file
3) Exit, apply, analyze 
4) name of Reference file displayed in spectra
5) enter method editor, Create Reference library based on NIST11 by overwriting existing library (i.e., Leave 'Create reference library at' as it was for the first Step 3)
6) Exit, apply, analyze
7) name in spectra is still cal file, not NIST11

Temporary Solution:

Use different file name rather than overwrite existing file.

Fix Information:

n/a

Keyword: 

One-line Description:

Library searches does not recognize updates from Library Editor

Problem:

The issue can be seen in the steps below as

1) Add library X to Qual (same seen with Unknowns Analysis) library list
2) Perform search
3) Open Library Editor and add a new compound, then save library X
4) search again, new compound not found (bad)
5) edit library to use Y and search 
6) change back to Library X, search, new compound not found (bad)
7) close application, restart application, search library X and compound is found.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

ECM Quant : Adding Quant Reporting method to existing method "save as" not possible

Problem:

Only seen in ECM quant.  This issue can be seen if the user uses the "New" button to create a Quant Reporting Method and then tries to use the "Save" option to place it into an existing >m method folder.  When this is done Quant gives an error message saying method exists when in fact there is no Quant Reporting Method in the .M folder.  This is a common workflow that works in non-ECM Quant where it works.

Temporary Solution:

Workaround is to "Edit" the existing method and then "Save".

Fix Information:

n/a

Keyword: 

One-line Description:

Level code order in ISTD causes validation error

Problem:

Randomly Quant had an error after analyzing the batch : "sample not validated :calibration level name mismatch between target & ISTD". Same results after checking/correcting/recreating the quant method. Problem found to be for ISTD, calibration level were set in the following order : 1-10-2-3-4-5-6-7-8-9 . For target, cal level were 1-2-3-4-5-6-7-8-9-10. The issue was solved after putting the calibration level for ISTD & target in the same order in the quant method."

Temporary Solution:

Manually reorder the levels in the ISTDs.

Fix Information:

n/a

Keyword: 

One-line Description:

When a PCDL is opened in Library Editor, some of the spectra cannot be correctly displayed - no m/z shown

Problem:

When a PCDL is opened in Library Editor, some of the spectra cannot be correctly displayed - no m/z shown.  Root cause is that the spectra are not stored in increasing m/z order.

Temporary Solution:

Edit in PCDL to correct ion order.

Fix Information:

n/a

Keyword: 

One-line Description:

The R2 and average response factor RSD outliers show in Flat Table (Single Compound) but not Compound Table (Single sample)

Problem:

The R2 and average response factor RSD outliers show in Flat Table (Single Compound) but not Compound Table (Single sample)

Temporary Solution:

If you are using the R2 and average response factor RSD outliers as part of your analysis, it is recommended to stay in the 'Flat Table (Single Compound) view to eliminate the possibility that you miss either outlier being flagged. You can toggle between either view at any time using the View menu.

Fix Information:

n/a

Keyword: 

One-line Description:

Matrix Type Override outlier:  Entering a negative value for outlier limit (e.g., Sample RSD) is not flagged in method validation

Problem:

Method error is flagged at batch analysis time in the batch table

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Matrix Type override outlier:  Does not use the expected outlier limits

Problem:

No method validation occurs in the Matrix Type Override window in Quant B.08.00, so the existing matrix type outlier (before Quant B.08.00) can be used in addition to the new matrix type outlier (override).

If an outlier is set up with both the old (previously-existing) way AND the new way, outliers may not display or flag correctly.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Matrix Type Override outlier:  Can add the same matrix type in the Matrix Override table with a different limit

Problem:

Matrix Type Override outlier:  Can add the same matrix type in the Matrix Override table with a different limit

Temporary Solution:

User needs to check that there are not multiple rows with the same matrix type

Fix Information:

n/a

Keyword: 

One-line Description:

Method validation fails to flag surrogate recovery limits for non-surrogate compounds

Problem:

Method validation fails to flag surrogate recovery limits for non-surrogate compounds

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Changing Integration Parameters does not quantitate

Problem:

Changing the integration parameters from the Compound Information window will update response but clears the concentration values .  This is inconsistent with manual integration which automatically determines concentration.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Undefined cal level gives misleading results

Problem:

User assigned a level code to an existing calibrator and this new level was not defined in the method. When they analyze the batch there is no error message appears warning that the level is not defined and the table shows old expected concentration of the old calibrator level and gives an accuracy value.

Temporary Solution:

This defect manifests only when the calibrator levels in your batch table differ from the calibration levels defined in your Quant method. It's very important that the user never do such a thing. It should never be the case that the calibrator levels present in the batch differ from the levels defined in the method editor.

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

2 - 3 second delay when changing sample type or level

Problem:

Changes in sample type or level in a small batch (5 samples, ~20 compounds) takes 2 to 3 seconds delay in response even on high-end laptop (i7, 16GB, SSD).

Temporary Solution:

None

Fix Information:

Fixed in 12.0

Keyword: 

One-line Description:

Unknowns Analysis ECM:  Commands displayed in the audit trail are not displayed in ATM Configuration

Problem:

Because they are not displayed, cannot configure user validation and/or reason for these commands and reasons cannot be displayed in Method History Report

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Unknowns Analysis ECM:  Method History Report and Comparison Results do not show which library changed in library method

Problem:

When a Library is changed there is a delete library and insert library event placed in the audit trail but the name of the Library being removed and the name of the library being added are not shown.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Unknowns Analysis ECM:  Actions not recorded in the audit trail

Problem:

The following actions are not recorded in the audit trail:
1) Report generation
2) Unknowns report template used
3) Library change in the method

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Negative outlier limits/associated values are not flagged by method validation

Problem:

Plates, Capacity Factor - Negative values not flagged (new outliers in Quant B.08.00)
Peak Resolution - Negative values flagged prior to B.08.00 but no longer flagged in Quant B.08.00

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

ATM Configuration shows only Quant commands

Problem:

No place to specify command groups, User Roles, User Validation/Reason associated for Unknowns Analysis commands

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Quant ECM:  Convert Accurate Mass Samples is not active

Problem:

If opening a Q-TOF batch without any converted files, the menu item Tools > Convert Accurate Mass Samples is not active

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

QuantECM:  Method History does not show all report method changes

Problem:

1) In Quantitative Analysis Report Method, Method 1 Value and Method 2 Value for 'Formatting[0]'/'Formatting[2]' display blank instead of report template path when report template changed
2) In Unknowns Method report, Method 1 Value and Method 2 Value for 'DeconvolutionMethod' are blank when LeftMZDelta/RightMZDelta and MZDeltaUnits are changed

Temporary Solution:

None

Fix Information:

Will not be fixed.

Keyword: 

One-line Description:

Overlapping dMRM windows of identical adjacent transitions cause signal artifacts and aberrations

Problem:

In the case where two dMRM compounds (as defined in the acquisition method) have identical transitions (Precursor -> Product m/z, collision energy, fragmentor voltage, etc.) and have overlapping acquisition windows (as defined by the RT and RT delta), it is possible for those signals to be summed together when extracted in Quant. This has the effect of producing aberrations in the signal at the boundaries of the acquisition dMRM RT windows.

Temporary Solution:

Modify the acquisition method to ensure that no two identical transitions are overlapping in RT. 

Two approaches can be used. 

1.) Setting the CE of one transition to be 0.1 V away from the other transition is enough to resolve the two signals when they are extracted in Quant. For example - have compound A's CE = 14.0 and B's CE = 14.2. In the Quant method, define a CE Delta of 0.1. 

2.) Adjust all compounds RT delta's in the acquisition method to ensure that no two identical transitions overlap.

Fix Information:

n/a

Keyword: 

One-line Description:

Action not displayed in User Validation and Reason box

Problem:

Steps to reproduce:
1) Setup ATM Configuration
a) Each Required User Role is assigned to its corresponding Command Group
b) Batch Analysis requires command reason and Method Development requires command reason and user validation
c) One user is in the following groups:  QuantBatchAnalyzer, QuantBatchReviewer, and QuantMethodDeveloper.
2) Open an audit-trailed batch in QQQ flavor
3) Attempt to manually-integrate a peak > User Validation and Reason window does not display "Manually integrate compound ..." for Action

*'CmdManuallyIntegratePeak' does display in the audit trail for the command name*

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

When a different concentration for ISTD is used for a calibration sample, that concentration is not used when calculating Concentration

Problem:

B.08.00 behavior:
Can change a level ISTD concentration in method editor (Concentration Setup), but it does not stay changed.  It reverts back to the ISTD conc entered for all levels (ISTD Setup).
The batch table calculates concentrations using the ISTD Conc entered for all levels.  Batch table displays the ISTD Conc used.

B.09.00 behavior:
Can change a level ISTD concentration in method editor, and it stays changed.
The batch table calculates concentrations using the ISTD Conc entered for all levels, not the changed ISTD Conc level.  Batch table displays the ISTD Conc entered for all levels (i.e., the changed level is not displayed).

Temporary Solution:

None

Fix Information:

Fixed in 11.1

Keyword: 

One-line Description:

Incorrect ISTD Concentrations displayed in the batch table

Problem:

Sometimes ISTD concentrations of other samples are changed when entering different ISTD Concentrations for Cals/QCs in the calibration table of method editor.  Software was designed to use same ISTD on all samples and if a sample needs to be given a different level in a given sample then the ISTD Dilution should be used, not editing the concentration in Method Editor.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Area Percent Report does not show path to data file

Problem:

Area Percent Report does not show path to data file.

Temporary Solution:

None

Fix Information:

Fixed in 11.1

Keyword: 

One-line Description:

Quant crash during method creation from RI based library with incomplete RT calibration file

Problem:

When using "Create New Method from Acquired Scan data with Library Search" if the library method contains an RI library and the RT Calibration file as an entry which lacks an RT the Quant Application will crash.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Peak Filter's 'Limit to the largest' toggle is stuck filtering even when unchecked

Problem:

Steps to reproduce:
1.) Load the batch and analyze.
2.) Method -> Edit. Click on a compound.
3.) Integration Parameters Setup -> Int. -> Peak Filter
4.) Limit to the largest is set to 1 peak. Set this to 100 - > apply all. See many peaks integrated in compound.
5.) Set limit to the largest to 1 peak -> apply all. See that only 1 peak is integrated.
6.) Uncheck 'limit to the largest' -> apply all. See that only 1 peak is still integrated. All peaks should be integrated because the limiter was turned off.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Quant ECM 3.X:  Message displays that files failed to convert yet Convert Samples windows shows as converted to TDA

Problem:

Quant ECM 3.X:  Message displays that files failed to convert yet Convert Samples windows shows as converted to TDA.  Seen on LCMS samples but maybe possible on GCMS.

Temporary Solution:

None

Fix Information:

ECM 3.X does not support TOF data, Use ECM XT.

Keyword: 

One-line Description:

QuantECM: Batch path on Method History Report shows local drive secure folder

Problem:

QuantECM: Batch path on Method History Report shows local drive secure folder

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Matrix Spike Group Recovery outlier requires analyze batch to clear outlier values when zero peak is done

Problem:

Matrix Spike Group Recovery outlier requires analyze batch to clear outlier values when zero peak is done

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Full Width Half Maximum (FWHM) outlier, Symmetry outlier, and Sample RSD outlier remain flagged when peak is zero peaked

Problem:

Behavior is different in Quant B.08.00.

Temporary Solution:

None

Fix Information:

Fixed in 12.1

Keyword: 

One-line Description:

Quant-My-Way: Outliers marked as "not visible"  are shown in the Method Editor

Problem:

Quant-My-Way: Outliers marked as "not visible"  are shown in the Method Editor

Temporary Solution:

None

Fix Information:

Do Not Fix

Keyword: 

One-line Description:

Exported query results as csv display the infinity symbol in Quant as an '8' in Excel

Problem:

If the query 'Replicate RSDs.linq.qry' finds an "infinity" value in the output .in .CSV file format the value that will appear as an "8" when loaded into excel.  Problem is likely found in other queries.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Crash when 'Quantitate Compound' with TPH

Problem:

If a TPH compound is selected and then a 'Quantitate Compound'  is performed Quant will crash.  

Workaround is to use 'Quantitate Batch' or 'Integrate Batch

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Peak purity value remains and outlier flag remains when target compound is zero-peaked

Problem:

Behavior is different from B.08.00.

Temporary Solution:

None

Fix Information:

Fixed in 12.1

Keyword: 

One-line Description:

Resolution values are still displayed for peak resolution outlier when zero peak is done

Problem:

Resolution values are still displayed for peak resolution outlier when zero peak is done.

Temporary Solution:

None

Fix Information:

Fixed in 12.1

Keyword: 

One-line Description:

Compound Information - Spectrum in Method Editor shows centroid data when Global Use Profile Data is checked

Problem:

Compound Information - Spectrum in Method Editor shows centroid data when Global Use Profile Data is checked.  Compound Information - Spectrum in Batch-at-a-Glance shows profile.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

When Zero Peak of target compound peak is done followed by Quantitate Batch, null values are displayed which were zero in the previous release

Problem:

Calc Conc, Final Conc, and Accuracy are null in Quant B.09.00.  In Quant B.08.00, zeros are displayed.

Temporary Solution:

None

Fix Information:

Fixed in 11.1 - Change in behavior in B.09.00

Keyword: 

One-line Description:

Quant Method report give error message when run in Chinese

Problem:

Quant Method report give error message when run in Chinese

Temporary Solution:

Corrected report available on request

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Reporting speed for single sample mode in ECM Compliance mode much slower than in non ECM or Batch mode in ECM

Problem:

When a batch of samples is printed using single sample mode in ECM reporting speed is much slower that seen for the same sample batch mode (same ECM configuration) on single sample mode in no-ECM configuration.  The root cause is that the data file is being download from ECM for each single sample report and this overhead is the cause of the slowness.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Library Editor - Melting point and Boiling point are not export to Jcamp file in MH Library Editor

Problem:

Library Editor - Melting point and Boiling point are not export to Jcamp file in MH Library Editor

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Script - SetPeakThreshold.quant.script - Qualifier peak filters not set to area but forced to Area Pct = 5

Problem:

The problem is that after setting the target peak to the calculated absolute area it sets all qualifiers to 5% relative (overwriting the manual values).  What it should do is set the qualifier to absolute area threshold (as was the target).  Now the value should be the target area multiplied by the expected qualifier ratio.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Unknowns Analysis - MS1 scan data creates sample spectra that fail to match any library spectrum

Problem:

MS1 Scan data files can be run in Unknowns Analysis and using either TIC Analysis or Deconvolution will find components with nice spectra.  However even when you lower the min match factor to 1 none of the spectrum match any spectra in the NIST17.L library.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Unknowns Analysis - Un checking Additional target hit match field Use CAS # does not affect matching as expected

Problem:

This issue is driven by a complaint from a user that notes that when Use Cas# is unchecked that Unknowns Analysis still uses CAS# as a match. As an  example both Use compound name and Use CAS# is unchecked and the expectation is that it will be linked as a Quant target compound by the other criteria (Within target RT window, Hit ion match criteria Target ion checked, Target Requirement Qualifier ion(s) checked).

Temporary Solution:

None

Fix Information:

Fixed in 12.0

Keyword: 

One-line Description:

ECM mode: Quant Automation from GCMS and LCMS Acq to Quant B.08.00 and B.09.00 requires 'Method Development' privileges

Problem:

In Quant B.08 and B.09 - the current Quant automation scripts require that a user have 'Method Development' privileges for automated batch creation and subsequent report generation to occur from GCMS Acquisition. Specifically (CmdStartMethodEditing) is being used in all cases,  and (CmdImportMethodFromFile) may be a better substitute for cases where method editing is not required.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Audit Trail Report marks as succeeded a cancelled operation, Audit trail in Tools menu is correct

Problem:

This issue was seen in UMAT mode with the Manual Integration requiring a reason.  When a manual integration was started but canceled out of inputting a reason the problem was seen.  The Audit Trail Report shows a check in the success box and a program exception in the reason.  The  Audit trail in Tools menu correctly shows unchecked success box and noted as "This command requires a reason".

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Go to NIST Program give "The calling thread cannot access this object because a different thread owns it." in QMY only

Problem:

When you run the Actions script "Go to NIST Program" it gives a "The calling thread cannot access this object because a different thread owns it." error message but only in Quant-My-Way, Classic runs fine and gives search results.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

PDF Report Builder - Expression fails when the column is moved

Problem:

A case was reported where moving an expression field within a table using the "Columns" dialog box.  Once it was moved and a preview report was attempted an error of  was reporting an error ""Failed to build Preview "Float object has no attribute :ToString".

Temporary Solution:

Workaround : Remove expression, move filed, replace expression.

Fix Information:

Do Not Fix

Keyword: 

One-line Description:

Do not configure a compound math compound to be based on the results of another compound math compound

Problem:

With Quant 10.0 - a compound can be configured to reflect the results of a ratio calculation based on other compounds defined in the method. For example, we can now calculate the ratio of CompoundA to CompoundB and display the results as CompoundC. However - CompoundC may not be used in another compound math calculation. 

This entry will be marked as fixed once method validation includes a check for this. Currently - method validation does not detect if a user has configured a compound as described above.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

ECM Quant - File with too long path loads on 2nd try

Problem:

I created a file with long file path to test new improved file name message in Quant 10.0 and that works well.  However if I hit OK and then try Add Samples to the same sample it loads without error message.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

GC-QTOF fail to create SureMass file due to corrupt MSMassCal.bin file

Problem:

GC-QTOF fail to create SureMass file due to corrupt MSMassCal.bin file.  This file contains the mass adjustment information.  If this file is invalid SureMass conversion will fail.  The file can be invalid if re-calibration is specified but not possible (example: no calibration gas).

Temporary Solution:

None

Fix Information:

Fixed in 10.1 - Error message given

Keyword: 

One-line Description:

Unknown Analysis - Show Alternative Hits - Library RI not displayed when using RI based library search in Unknown Analysis

Problem:

If the Unknown Analysis method is set to use RI as part of the library search and a Show Alternative Hits is preformed then the library RI is show as "zero" rather than the actual RI from the library.

Temporary Solution:

None

Fix Information:

Fixed in 11.1

Keyword: 

One-line Description:

Selecting "Monoisotopic" in "New Method from PCDL" dialog will create compounds based only on MS(1) data - MS/MS fragmentation is ignored

Problem:

When using the 'New Method from PCDL' feature - Quant will create compounds of different types depending on the type of data present in the library - and the 'Target Ion' option in the dialog box.

In the 'Target Ion' options, if 'Monoisotopic' is selected, then compounds with spectra in the PCDL are not used/ignored. Only the molecular formula is used (along with the selected adduct type) to create the compound in the Quant method. The compound's quantifier and qualifier ions will be from MS(1) level data and will be based on the calculated isotopic grouping. In other words - Monoisotopic is for creating compounds only based on MS(1) full scan data.

Temporary Solution:

In the next versions of Quant - additional information will be provided in the 'New Method from PCDL' menu to make it clear what types of compounds are going to be created.

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Create new method from acquired MRM data sets mass extraction to -0.3/+0.7 and can include unwanted signals, Qualifiers correctly set to 0.05

Problem:

When running "Create new method from acquired MRM data" the mass extraction window for the target ions is set too wide (0.3 left and 0.7 right).  In some cases this causes signal from other compounds to be erroneously merged with signals that have closely related masses.  In one case this resulted in the compound being found 3 min from the correct RT because the other compounds signal was merged and had more area.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Create new method from Library does not use calculated RT from RI in library when RT is in Library

Problem:

When a library entry has both RT and RI and the user asks to use RI and supplies the RT Calibration file the software plugs in the library RT and not the calculated RI.  This is not desirable as the point is to create a method that is adjusted to the RTs along the RI curve.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Report Builder: Report Builder 10.1 includes B.09.00 help files for Japanese

Problem:

B.09.00 version of Report Builder help files are included in build 10.1. which is included with Quant 10.0.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

ISTD Dilution causes signification miscalculation of conc

Problem:

Customer is using ISTD Dilution without problems in B.08.00. New instrument comes with B.09.00 and give extremely incorrect quantitative results. Customer uses ISTD Dilution on cals (and maybe samples) but with each Analyze Batch command the ISTD Concentration field, as seen in the Method Editor grow by large and unpredictable amounts. The net effect on the customer data set is that with each Analyze Batch command the report concentration of targets grows smaller. This is also seen in 10.0.706.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Manual integration of chromatogram can lead to case where automatic noise ranges may include an integrated peak

Problem:

In normal operation - where the user has not explicitly defined a noise region in the Quant method - Quant will attempt to automatically determine a noise region in the extracted chromatogram. However - if a user manually integrates a peak, or adjusts the automatic integration with any manual integration tool - it may become the case where the automatically determined noise region might include some or all of the area of a non-target but otherwise integrated peak. For example - a nearby peak which, though found by the integrator, is not the target for quantitation. This will cause an artificially high noise value for the signal to noise calculation.

Temporary Solution:

This issue only occurs when a manual integration is done to certain chromatograms. One can easily observe this behavior by choosing an obvious color for the "Noise Regions" setting in the chromatogram Properties window. 

To prevent this behavior - one can set a fixed noise region in the method (on a per compound basis). This fixed noise region will not change after the manual integration is performed.

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Spectrum extraction done in Sample Information gives too many ions poor LMS vs B.09.00

Problem:

Quant 10.0 give many small ions in very small m/z steps (0.05) resulting in lower LMS scores than seen in Quant B.09.00. 

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

MRM Data Access in Quant 10.0 and greater requires synchronized Acquisition and Quant methods 

Problem:

MRM Data Access introduced in Quant 10.0 and used in subsequent versions require that the Acquisition method  and Quant Method have synchronized data, specifically compound names.  MRM Data Access links signals created in Acquisition to compounds in Quant method using the compound names.  When a Quant method is created from the Acquisition method and afterword, a change to either which results in a compound name mismatch is made, the resulting chromatograms will be in error.  

Temporary Solution:

None

Fix Information:

Informational for 10.0 and greater

Keyword: 

One-line Description:

Quant ECM:  GCMS Translator must be installed in the default folder

Problem:

'If the GCMS Translator is not installed in the default folder “C:\Program Files (x86)\Agilent\MassHunter\GCMS Translator”, MH Quant cannot find it and won’t use it."

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Using Percent in Reference/Non Reference Window Type fails, minutes used

Problem:

If the units in the Reference/Non Reference Window Type are specified as Percent (the default) the window used is actually based on minutes.  Visually the Reference/Non Reference windows in the Compound Information display are shown correctly (based on percent) but the code that decides to ignore peaks is working with minutes.  The typical result will be that the peaks are integrated and used when outside the window and customer will believe the feature is not working.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Library Editor / ECM:  Can edit a library opened in Library Editor as read-only

Problem:

Library Editor / ECM:  Can edit a library opened in Library Editor as read-only

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Quant asks user to save batch after load then generate report

Problem:

Quant asks user to save batch after load then generate report.  This is unexpected as no change to the batch has taken place.  The root cause is that the batch lacks any calibration levels in the method which is not a supported workflow.

Temporary Solution:

Add a single level to the method.

Fix Information:

Do Not Fix

Keyword: 

One-line Description:

Append method from Library doesn't work properly

Problem:

Appending the method kept all the initial parameters in the method from Library but it overwrote all the original targets in the method.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Quant Method report fails on some systems

Problem:

The Quant method report fails with "Error: Common Language Runtime detected an invalid program" when run from menu or when generating report.  Other reports run fine.  Only seen in some systems, appears to by OS/Configuration dependent.

Temporary Solution:

Request new report template

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Reports do not display ISTD data on target when the ISTD is not selected compound

Problem:

The problem can be seen when running the below reports and only selecting a subset of compounds:
 * Gen_Complete.report.xml
 * Gen_resultsSummary.report.xml

When run this way the ISTD data is not made available and the ISTD fields are blank.  They have date when all compounds are selected.

Issue is old and reported in B.07.01 report but I checked and the issue is in the 10.0 code (and I assume B.08.00 and B.09.00).

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Gen_BySample  or Gen_bySamplewithSN templates print in ESTD format when subset of compounds selected

Problem:

When printing the Gen_BySample  or Gen_bySamplewithSN templates and selecting a subset of compound the software thinks it is an ESTD method when in fact it is ISTD. 

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Change in Sample type from Cal to other type can change ISTD levels in method

Problem:

Problem is seen when a Cal is changed to a sample type that does not have a level and the level is left on the sample.  After an Analyze Batch is preformed the ISTD concentration levels are altered and the Calibration Type changes from Calibration to Method.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Unknowns Analysis  - MRM/Scan data displays alternating MRM and Scan data in chromatogram

Problem:

When processing MRM/Scan data in Unknowns Analysis the TIC and EIC chromatograms do not filter out the MRM data points and have a "zig zag" look.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

TPH Subtraction:  Results same as Quant 10.0 but different from Quant B.09.00

Problem:

When we try to decide whether we should deduct the area of a compound from TPH, prior to 10.0  we looked at integrationStart and integrationEnd, but in 10.0 and greater we changed it to RT,

Temporary Solution:

None

Fix Information:

Change in behavior B.09.00 ->

Keyword: 

One-line Description:

Compound Math - Concentration Sum fails with Relative ISTD

Problem:

Compound Math - Concentration Sum fails with Relative ISTD

Temporary Solution:

None

Fix Information:

Do Not Fix

Keyword: 

One-line Description:

Excess ECM license consumption by Quant 

Problem:

A single Quant session consumes multiple ECM licenses and sometimes fails to properly release them for reuse thus leading to a larger than expected number of licenses being used especially over extended use.

Temporary Solution:

Contact Agilent support for solution.

Fix Information:

Do Not Fix

Keyword: 

One-line Description:

UMAT mode - ATM Config - Check "Always enable audit trail" locks Unknowns Analysis in no audit trail mode

Problem:

When Quant is in UMAT and you configure the ATM to "Always enable audit trail" it does just the opposite in Unknowns Analysis.  When you create a new analysis the audit trail box is unchecked and grayed out thus disabling the Audit trail.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Setting outlier limits for target and ISTD changes Symmetry values

Problem:

This problem can be seen when the same peak is evaluated by a method that deferrer only in that one has no symmetry outlier limits and one does.  The calculated peak symmetry should be independent of having the symmetry outlier limits or not or for that matter what the symmetry outlier limits are.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Audit Trail report in UMAT mode lacks Reported by: info

Problem:

This issue came to light by a series of comments from sites under regulation when doing software validation testing.  Customer points out that that the name of the person printing the audit trail report is not on the report.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Quant-My-Way Flavor Editor - Adding Compound Approval tool to Ribbon causes a crash

Problem:

Adding Compound Approval tool to Ribbon causes a crash in the  Quant-My-Way Flavor Editor

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

CEF file import from Qual on GC-QTOF fails (Find by Integration and Find by Chromatogram Deconvolution)

Problem:

CEF file import from Qual on GC-QTOF fails (Find by Integration and Find by Chromatogram Deconvolution)

Temporary Solution:

None

Fix Information:

Will Not Fix

Keyword: 

One-line Description:

SureMass data give inaccurate spectrum in Update RT Tool

Problem:

In Quant versions prior to 10.1 when SureMass data is seen in the Update Retention Times Tool the spectra are created from a single scans RT.  Unless the SureMass features apexes at this time it is excluded from the spectrum and some ions will be missing.

In Quant 11 this issue is partially solved by extending the RT range from a single scan a small number of scans before and after the scan RT and displaying all SureMass features that apex in that range.  This will include most of the ions of interest however it may still miss SureMass features that begin or end in the RT range but do not apex in it.

Temporary Solution:

None

Fix Information:

Will Not Fix.

Keyword: 

One-line Description:

Go to Qual extract unit mass mz extraction for Q-TOF data

Problem:

Go to Qualification Application under Tools --> Actions will extract EIC with unit mass window in Qual even though for Q-TOF data with mass extraction window in method in ppm unit. 

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Compound Approved data in BAG is inaccurate in Compound Table mode

Problem:

The issue is seen when users Export the BAG table to Excel in Compound Table Mode and multiple compounds / sample.  The Compound Approved field appears in the Compound Method column only once but needs to appear once per compound.  As a result the exported data is incorrect.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Generate Qualifiers from Library doesn't generate the correct information for Q-RAI data

Problem:

*Generate Qualifiers from Library-LC* doesn't generate the correct information of the Qualifiers for Q-RAI workflow which includes the precursor ion, Transition, and Collision Energy Delta.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

'Alternative Peak RT Difference' displays as a default Outlier column for all flavors

Problem:

'Alternative Peak RT Difference' displays as a default Outlier column for all flavors

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Keyboard shortcuts for manual integration buttons do not exist in QMW interface

Problem:

Keyboard shortcuts for manual integration buttons in the Quant-My-Way interface do not exist / do not work.

For example - "Delete" to (Zero Peak) does not work in Quant-My-Way but does in the classic UI. This is true for all of the manual integration buttons.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

QRAI doesn't show any spectra at MSMS level in Compound Information of Method Editor

Problem:

When a QRAI compound is displayed in the Compound Information of the Method Editor the Spectrum window is blank.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Quantifier mass accuracy calculated from MS2 spectra, not MS1 when Product scan selected as Spectrum override

Problem:

When processing AutoMSMS data on a LC-QTOF, where the ‘Scan’ parameter for a quantifier has been set to ‘Scan’, but the ‘Spectrum Extraction Override’ parameter has been set to ‘Product Ion’, to enable library spectra matching, the ‘Mass Accuracy’ is be calculated on the m/z being detected in the ‘Product Ion’ spectra, rather than the ‘Scan’ spectra. 

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Unknowns Analysis - Excluded mz for SureMass doesn't work

Problem:

In Unknowns Analysis > Method > Peak Detection > Peak Filter > Excluded m/z has no effect on SureMass data.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Report Builder Calibration reports not reflecting disabled calibration level correctly

Problem:

Disabled calibration data points appear in the report to be enabled when they are not.  Problem is seen in the following report templates:
  Gen_Calibration.template.xml
  Gen_Complete_ESTD.template.xml
  Gen_Complete_ISTD.template.xml

Temporary Solution:

Request updated reports.

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Remove the diamond sign of precursor ion form product ion scan for QRAI in Compound Information

Problem:

QRAI does not have a specific precursor value as seen in MRM and other data so it should not be rendered in the Spectrum. 

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Mixed GC and MS data causes graphics issue in Report Builder sample chromatograms

Problem:

Consider a case where multiple samples are generating a batch report using Gen_Samples_ISTD .  In the 1st sample there are separate TIC-MS and GC Chromatogram which is correct , but starting in 2nd sample, there is an overlay the MS and GC signal together.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

 Compliance Mode - Queue Report - No Audit Trail entry for printing report

Problem:

When printing reports using direct print vs. Queued printing that there are two issues.

1) Direct printing of the report has an audit trail entry showing report printing and the version of the batch is 1 greater than shown on the report (normal and expected).

2) Queued reports do not add an audit trail entry for printing the report and the version of the batch file matches the version on the report (audit trail failure).

Temporary Solution:

None

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

 Unknowns Analysis - TIC Compound (mz = 0) from Quant not treated as a target compound

Problem:

When a compound is set to extract the TIC by setting mz = 0 and that batch is imported into Unknowns Analysis it is not seen as a target compound but as a Non-Target.  This is the case even when the method does *not* require the target ion be in the Hit ion match criteria (see attached screen shot). 

Note that there if the old method of picking a target ion and very wide left and right mz extraction windows is used it is seen as a target.  Also the target mz appears as blank rather than zero in UKA.

Temporary Solution:

Work around : Note that there if the old method of picking a target ion and very wide left and right mz extraction windows is used it is seen as a target.  Also the target mz appears as blank rather than zero in UKA.

Fix Information:

n/a

Keyword: 

One-line Description:

Env_CC reports use highest level not mid

Problem:

The following  reports (Env_CC_MidPoint.report.xml, Env_CC_MidPoint_RTDiff.report.xml, Env_CC_Avg.report.xml and Env_CC_Avg_RTDiff.report.xml) are reporting against the highest level rather than the mid point level.  This was the case in B.08.00 and B.09.00 but the B.07.01 version works and can be swapped in as a workaround.

Temporary Solution:

Request fixed reports.

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Audit Trail report says 'Create method ...' when 'Append Method' was done

Problem:

Audit Trail report says 'Create method ...' when 'Append Method' was done.  The Action show the correct operation only the description is inaccurate. 

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Quant ATM custom command groups do not let contents inherit role selections

Problem:

In Quant B.09 or 10 running in UMAT mode, create a custom command group called 'Manual Integration'. Move one or more Manual Integration commands from the 'Batch Analysis' group to the new 'Manual Integration' group. 

With the top level 'Manual Integration' group selected - check the box for QuantBatchReviewer. Then select any of the commands. You will see that they do not have the QuantBatchReviewer role checked.

... If you do - File -> Save in the ATM - then re-open the ATM and see if the commands are still checked for QuantBatchReviewer - I find that they are not.

Only after checking them individually - then saving everything AGAIN, do I see that they persist after reopening the ATM.

Temporary Solution:

See description.

Fix Information:

n/a

Keyword: 

One-line Description:

Cannot manual integrated TPH compound 

Problem:

Problems were seen with manual off compounds in the range of a TPH Compound.  In some cases Quant crashed, others the peak was zeroed.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Audit Trail: "Clean up calibration table" meaning is not clear

Problem:

The action "Clean up calibration table" was not clear and has been replaced with a more clear statement that calibration replicates have been averaged.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Dual Injector in batch table is ON when it is FALSE in sequence.xml

Problem:

The Dual Injector flag is checked when the “Dual Injector Acq. Date Time” is populated or the “Dual Injector Volume” is not null. 

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Quant 10.0 spectrum inconsistence with B.09.00 and Qual 10.0

Problem:

Spectra taken for selected RTs are inconsistence with B.09.00 and Qual 10.0.  The root cause is the MRM Data Access code introduced in Quant 10.0.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

PDF Report Builder reports do not use Fixed Graphics setting

Problem:

When you set the fixed graphics setting of fixed x min and max they are used in Python reports but ignored in PDF Report Builder.

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

RT manual integration toolbar keyboard shortcuts do not work in Quant-My-Way UI

Problem:

RT manual integration toolbar keyboard shortcuts do not work in Quant-My-Way UI

Temporary Solution:

None

Fix Information:

Fixed in 10.1

Keyword: 

One-line Description:

Manual integration tool "merge" may not include peaks as expected

Problem:

The manual integration toolbar includes functions to merge a peak with an adjacent peak. It has been observed that the tool may occasionally not merge the adjacent peak as expected. 

Temporary Solution:

When this occurs - simply use the manual integration start/stop boxes in the chromatogram and drag the appropriate box to include the peak that failed to merge as expected.

Fix Information:

n/a

Keyword: 

One-line Description:

ECM Quant - UAF file is not Checked out when "check out " option is selected

Problem:

When in Unknown Analysis and opening a UAF.ssizip file as Checked out the UAF.ssizip is not checked out in ECM.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Create Levels from Calibration Samples doesn't work properly in an existing quant method

Problem:

To see issue with DrugsOfAbuse example.

1) Create a new batch adding all of the samples
2) Open method from existing batch, 'DrugsOfAbuse.batch.bin' --> L1 through L5 exists for calibration levels
3) Delete all calibration levels
4) Create Levels from Calibration Samples --> Only L1 Cal, L2 Cal, and L2 QC exists - Expect L1 through L5 cal levels

Seems to happen when new batch is created for Step 1 - If an existing batch is used, issue is not observed

Temporary Solution:

None

Fix Information:

Will No Fix

Keyword: 

One-line Description:

Append method from Library - LC may not function properly depending on the library

Problem:

It has been observed that certain libraries will not result in any additional compounds being appended to the Quant method when using the 'Append method from Library - LC' feature. 

Temporary Solution:

If this feature does not append any compounds to the Quant method, try using the "Append method from Library - GC" instead. It may work perfectly.

Fix Information:

Will Not Fix

Keyword: 

One-line Description:

New/Append Method from Library no longer has option for 'Sum qualifier(s) from any additional spectra'

Problem:

When running New/Append Method from Library the 'Sum qualifier(s) from any additional spectra' feature is no longer an option.

Temporary Solution:

None

Fix Information:

This feature has been removed.

Keyword: 

One-line Description:

 'New Method from Library - GC' does not create method using the compound list

Problem:

When performing a 'New Method from Library - GC' and the Targets is set to "Use compound list" with a list file selected the software fails to filter on the compounds in the list and uses the entire library.

Temporary Solution:

None, workaround is to create a small library made up of compounds that would have been in the compound list file.

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Unable to access the diagnostic information during application load

Problem:

When launching the Quant application the splash screen briefly appears before the application.  On the splash screen there is a link "Not for use in diagnostic procedures, click here for more information" but this link is broken.  The link and the information are available after the application loads, and the user brings up the splash screen via the "About" function.

Temporary Solution:

The link and the information are available after the application loads, and the user brings up the splash screen via the "About" function.

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

'New Method from Library - LC' does not add compounds to the method

Problem:

'New Method from Library - LC' does not add compounds to the method

Temporary Solution:

None - Workaround use 'New Method from Library - GC'

Fix Information:

Will Not Fix

Keyword: 

One-line Description:

Unknowns ECM:  Audit trail does not record what method was loaded

Problem:

Unknowns ECM:  Audit trail does not record what method was loaded

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Unknowns Analysis - Robust recalculation of Estimated Conc

Problem:

Unknowns Analysis will calculate an Estimated Conc using dilution however this is not robustly implemented in Quant 10.1.  Even when "Analyze All" is run it skips recalculating Estimated Conc .  In 10.1 the workaround was to explicitly run 'Target Match' but this is not obvious.   

Temporary Solution:

None - use workaround in description.

Fix Information:

Fixed in Quant 11.0

Keyword: 

One-line Description:

QMW Calibration Curves-at-a-Glance:  No curve displayed when 'Power' fit type selected

Problem:

QMW Calibration Curves-at-a-Glance:  No curve displayed when 'Power' fit type selected, Curve displays in the batch table but not in the Calibration Curves-at-a-Glance window

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Installing Quant 10.1 breaks the "Edit" template button in Qual Method Editor

Problem:

If you install Quant 10.1 it will remove Report Builder 10.1 from the system.  Qual 10.0 uses Report Builder 10.1 to edit Qual 10.0 report templates.  As a result clicking on the Edit button has no effect.

Temporary Solution:

See Service Note Number: G3335AA MassHunter Software-413 - MassHunter Quant 10.1 Removes Qual's Report Builder for details and instructions.

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

Report Builder in ECM mode - crashes when loading data 

Problem:

Report Builder in ECM mode - crashes when loading data.

Report Builder not supported in ECM mode.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Append method from Library adds duplicate Qualifiers 

Problem:

Steps to see this error.  Create a method from a library, then Append method from same library.  The compounds are not duplicated but a second set of duplicate Qualifiers are added to the existing compounds.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Compounds-At-Glance - Fit to Lowest level give bad scaling vs Batch-At-Glance

Problem:

When in Compound at a Glance if you place the interface in "Fit to Lowest Calibration Level" the graphics do not look reasonable, certainly not like those seen in Batch-at-a-glance.  In some cases they are blank and the baseline is way too high crushing the peaks.

Temporary Solution:

None

Fix Information:

Fixed in Quant 11.0

Keyword: 

One-line Description:

Custom Calculation outlier not working automatically

Problem:

When running a script and setting a Custom Calculation value even when High and Low limits are in the Quant method will not automatically set the outlier to red/blue status.  The logic to detect high/low condition and set the outlier must be coded in the script.

Temporary Solution:

Add logic to detect high/low condition and set the outlier must be coded in the script.

Fix Information:

Fixed in 12.1

Keyword: 

One-line Description:

Quant does not properly handle "Dynamic CE" data where CEs are replaced by "0"

Problem:

All verisons of Quant (including 10.0 & 10.1's MRM Data Access layer) do not properly handle the behavior of "legacy" LC QQQ's (excludes Ultivo) when it condenses multiple MRM transitions into fewer scan segments using a technique called "Dynamic CE". This behavior also occurs in some older versions of the GC QQQ driver. 
"Dynamic CE" occurs when a common precursor and more than one product ion are being collected and the collision energy (CE) is not the same over all the transitions.  In this case the CE is set to zero in the data file while the actual CE is still recorded in the acquisition method.  Unlike Qual, Quant relies only on the data file.  Thus if a specific CE, and collision energy delta are found in the Quant method, the signal will not be extracted.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

LC screener graphics blank with QRAI non-SureMass data

Problem:

The LC screener tool does not display graphics when using QRAI data that has not been SureMass converted. 

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Quant ignoring Spectrum % Saturation Threshold

Problem:

When Quant method has a value in the Spectrum % Saturation Threshold it should exclude spectra above that saturation level however it does not do so and includes all spectra.  This has a negative impact on mass accuracy. 

Temporary Solution:

None

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

SequenceFileName and SequencePathName in the Samples table are blank and not defined in the QuantDataSet

Problem:

SequenceFileName and SequencePathName in the Samples table are blank and not defined in the QuantDataSet

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Gen_ByCompound fails to print compound graphics when subset of samples selected

Problem:

Gen_ByCompound fails to print compound graphics when subset of samples selected

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

ReportBuilder does not include ISTDs when subset of compounds is selected

Problem:

Most Report Builder templates use "SelectedCompound" to provide a list of compound that the user selected when generating the report.  This list does not include the ISTDs associated with the selected compounds and as a result they do not appear in the report.  A new "SelectedCompound" that can be used in cases where ISTDs are required.  Using this new feature requires that the report Builder template be edited.

Temporary Solution:

None

Fix Information:

Fix in 11.0 (after editing template)

Keyword: 

One-line Description:

Unknowns Analysis - LSR_NonTarget_Details.template.xml - Reports Surrogates, Matrix Spike and ISTD

Problem:

In Unknowns Analysis the LSR_NonTarget_Details.template.xml Report includes Surrogates, Matrix Spike and ISTD compounds. The is also the case with the Python report version of the report. Although the report says non target no one wants to see the ISTD, Matrix Spike and surrogate compounds listed as "unknowns" when in fact they would be in every sample.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

GC/LC Screening displays absolute value in RT difference rather than plus/minus

Problem:

GC/LC Screening displays absolute value in RT difference rather than plus/minus.  

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Cannot generate audit trail report if batch cannot be saved

Problem:

Under certain circumstances a Quant batch can become invalid and can not be Analyzed or Quantitated.  If this happens, and it is not corrected, the batch can not be saved.  Saving a batch is required to run all reports including the audit trail thus no audit trail report can be generated.  

Temporary Solution:

Resolve issue making batch invalid then Analyzed or Quantitate.  If this is not possible use the audit trail viewer.

Fix Information:

Will not be fixed.

Keyword: 

One-line Description:

Smoothing + Agile2 integrator breaks RMS S/N calculation - leads to null result

Problem:

The combination of RMS Signal to Noise calculation with Agile2 integrator and smoothing has been found to lead to a null S/N value.

Temporary Solution:

Avoid the combination of Smoothing + Agile2 integrator + RMS S/N calculation

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

When selecting a set of compounds for template Gen_Samples_ISTD , the Graphics section couldn't be displayed

Problem:

When running the Gen_Samples_ISTD template the report will no display graphics when a subset of compounds are selected.  Works when ALL compounds are selected.

Temporary Solution:

Report template available on request

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Accurate mass profile data gives incorrect mass accuracy

Problem:

The logic to locate the measured mass and thus calculate mass accuracy had a defect which in some cases was returning the wrong mass and leading to incorrect mass assignment and mass accuracy.

Temporary Solution:

None

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

Value other than default of 5 in Noise SD Multiplier give increasing signal to noise with each Analyze Batch command

Problem:

Value other than default of 5 in Noise SD Multiplier give increasing signal to noise with each Analyze Batch command.  Is related to MRM Data Access in Quant 10.0 & 10.1.

Temporary Solution:

There are two workarounds in Quant 10.0 &10.1)

1.	Change integrators from Agile2 to any other.
2.	Disable MRM Data Access (Modify the QuantAnalysis.exe.config file by setting key="UseMRMDataAccess" value="false")

Fix Information:

Fixed in 11.0.

Keyword: 

One-line Description:

ISTD Dilution not changing outcome of calibration curve regression

Problem:

The ISTD Dilution is being applied to calibrators only after the curve fit has been calculated. This means the dilution is not having an effect on the concentrations of the unknowns (samples).

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Crash when '# of Verified Ions Limit' set on opening 'Compounds-at-glance'

Problem:

When the "# of Verified Ions Limit' is set in the outlier and an attempt to open 'Compounds-at-glance' is performed the Quant app will crash.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Resolution = Valley Height/Peak Height Avg values do not match hand calculated values

Problem:

The resolution shown in Quant is not correct and the actual resolution should be about twice as much as shown.
  
The following describes the calculation as performed in Quant 11.0.
 
Although peak heights can be displayed in the batch table or peak labels, the valley height used in the calculation is not viable.  The software is using the average of the three lowest points in the peak valley to determine the height of the peak valley.  Thus a visual inspection will not match the actual peak height used and the height used will be above the valley seen in the peak graphics.  This will typically result in an overestimation of the peak valley height and an underestimate of the  resolution when comparing reported values vs what would be obtained by measuring against peak graphics.

Temporary Solution:

None

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

Manual Integration with General integrator acts bizarrely

Problem:

In some cases manual integration with General integrator is acting bizarrely.  The behavior noted is that when positioning the start/end points the point will leap to an unexpected location.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Valley Height/Peak Height resolution calculation incorrect

Problem:

In versions of Quant prior to 11.0, the "Valley Height/Peak Height" resolution calculation would not always use the correct peak for the denominator of that calculation. Beginning with Quant 11 - the primary peak (the one selected as the target - shaded in green) will always be used as the peak height. If no primary peak can be found - Quant will use the largest available in the window.

Temporary Solution:

None

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

Export Table does not retain last used format as Export Graphics does

Problem:

Export Table does not retain last used format as Export Graphics does

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

Product ion scan EIC for targeted MSMS data in TDA format is incorrect

Problem:

EIC chromatograms extracted from Product ion scan data in TDA format give zig zag data.  Root cause is a defect in the software that creates incorrect data points with zero intensity.

Temporary Solution:

None

Fix Information:

Will Not Fix.

Keyword: 

One-line Description:

Excel Reports - Peak Chromatogram Graphics -> "Fit to Peak" does not apply to ISTDs

Problem:

When printing Excel based reports if one sets the Peak Chromatogram Graphics to "Fit to Peak" the target graphics will display correctly but the ISTD will not respect the setting and be "Autoscaled".

Temporary Solution:

Use PDF Report Templates where issue is not seen

Fix Information:

Will not be fixed 

Keyword: 

One-line Description:

Quant Method report fails with error about "qualifiers" 

Problem:

Method throws an error about "qualifiers" in Quant 10.1 and Quant 11 build 750 but not in Quant 10.0.  

Temporary Solution:

Moving Quant 10.0 python code lets it run in Quant 10.1 without error.

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Report Builder - Original Compound and Qualifier Peak blank

Problem:

Both the Original Compound Peak and Original Qualifier Peak appear as blank in Quant 10.1 and Report Builder 10.2.1 

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

ECM Quant : ATM User not having System: Roles Configuration -> View causes error, default ATM configuration

Problem:

It is expected that all ECM users should have the ECM permission "System: Roles Configuration -> View" defined in the ECM server. 

There is a defect in Quant 10.1 where, if a user logs into the ATM Configuration tool without this privilege - Quant will warn the user of this condition - then load the default ATM configuration (which grants all users all permissions). 

Temporary Solution:

None

Fix Information:

Fixed in 10.2. Now - if a user does not have the "System: Roles Configuration -> View" permission - Quant will warn the user of this - then terminate the ATM configuration tool immediately.

Keyword: 

One-line Description:

Report Builder ignores subset selection of compounds in single sample mode - always includes all compounds

Problem:

A defect has been found in Quant's Report Builder engine when printing in "Single Sample" mode. This defect causes all compounds to be included in the report even if the user chose to include only a subset of the compounds defined in the method. 

Temporary Solution:

Python based PDF Reports do not exhibit this defect. Please use a Python based report template until this defect in the PDF-Report Builder engine is fixed in a future release.

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

 QMW flavor setup - Adding to Compound Information does not appear where placed

Problem:

The customer wants to add Compound Approved to Compound Information into an existing toolbar. QMW flavor setup allows customer to place this in an existing toolbar where customer wants it. But when the customer tests/deploys the app a new toolbar is created with only the Compound Approved check box. Worst still the toolbar is not displayed by default but has to be manually enabled by customer each time they start Quant.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

ECM Complince mode only - No Logo appears in default python based PDF Reports

Problem:

All Python based PDF reports, when run in ECM Compliance mode, will not display the logo file. 

Temporary Solution:

None

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

ECM Quant - Overhead in .S folder causes error due to path too long issue

Problem:

ECM Quant maintains secure local storage in the .S folder.  The storage uses a long (38 character) GUID to create unique storage allocation and this competes with user LCDF and Windows file information.  Some user have reported error caused by this overhead in the form of Windows "Path too long" problems and requested that the GUID be replaced with a smaller number of character path.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Compound Math:  Concentration Sum incorrect when compound is also TPH Subtraction

Problem:

Compound Math:  Concentration Sum incorrect when compound is also TPH Subtraction

Temporary Solution:

None

Fix Information:

Will not fix

Keyword: 

One-line Description:

Unknowns Analysis report fails when "Display legend" checked in Chromatogram properties 

Problem:

There seems to be an issue with the "Display legend" being checked in Chromatogram properties and then creating a report.  Report aborts with error.   

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Quant fails when PC has FIPS enabled

Problem:

Quant on a PC with FIPS enabled and Quant crashes when they attempt to load a batch.

Temporary Solution:

None.

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Wavelength Extraction Range Feature Ignored by Quant

Problem:

Quant allows a user to define a UV signal's wavelength extraction range to pull chromatograms out of data acquired with full spectra instead of using one of the explicit signals A, B, C, etc. However - Quant ignores the extraction range pulling out all wavelengths equivalent to a total wavelength chromatogram. 

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Scans with no ions detected treated as if no data was acquired in that region

Problem:

In some cases, example being when thresholding is set very high, there is no signal seen in one or more contiguous scans. When an EIC is extracted over this region, Quant will display this as an empty space with no baseline rather than a zero intensity point for each scan. This can effect integration of peaks and is not correct as it can be said that no signal was detected (a zero intensity point) in such scans.

Temporary Solution:

None

Fix Information:

Fixed in 11.1

Keyword: 

One-line Description:

Change in Quant noise calculation to use the MIN over noise regions

Problem:

In some cases Quant prior to 11.0 can determine that the noise value is zero and this will result in infinite signal to noise.  This is most often seen in Triple Quad systems where signals can be almost noise free but can also happen in files where noise has been removed by high threshold settings in acquisition.  Starting in Quant 11.0 when zero noise is detected it will be assigned a value of 1.

Temporary Solution:

None

Fix Information:

Change in behavior 11.0 

Keyword: 

One-line Description:

Unknowns Analysis - Show Alternate Hits - RI support missing

Problem:

When doing a Show Alternate Hits and using an RI Library the RI is not used. Specifically no penalty function is applied to the LMS.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Integrator problem - Peak width and FWHM 

Problem:

Peak width calculations in Quant 10.1 were observed to be inconsistent with manual observation and FWHM.  In some cases peak width (Start to End) were less than or equal to FWHM.  Nature of problem varied based on integrator used.  Also when peak was manually integrated with extremely minor change to peak start or end significant change in peak width was observed with manual values comparable to values calculated by inspection of the peak graphics.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Before and After Manual Integration qualifier peak graphics scale differently in y-axis on reports

Problem:

When printing before and after manual integration graphics of the qualifier peaks in reports there is a difference in appearance as far as the Y-axis goes.  In one graphic the peak is printed close to the top label and in the other there is noticeable "spacing".

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Quant does not recognize UV signals from Compact LC (models #)

Problem:

The UV signals from compact LC (model) are not recognized by Quant

Temporary Solution:

None

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

New method from CEF does not use compound names from MPP

Problem:

Some compound names created in Mass Profiler Professional (MPP) which are exported via CEF file and then imported into Quant using the "Create new method from CEF" are assigned a different name in Quant.  The affected compounds will appear in Quant as "Cnnn - RT"  where nnn is an incrementing number and RT is the retention time as seen MPP.

Temporary Solution:

None

Fix Information:

Fixed in 11.1

Keyword: 

One-line Description:

DrugsOfAbuse data files pre Quant 11.0 are not process correctly

Problem:

DrugsOfAbuse data files installed by Quant before Quant 11.0 will not be proceeded correctly in Quant 11.0 and later software.  This is know to happen in Create method from MRM data file and Analyze Batch but likely in many other places.  The DrugsOfAbuse data files are very old and required editing to make them work in Quant 11.0 thus older unedited copies will fail.

Temporary Solution:

Replace older data files with Quant 11.0 version.

Fix Information:

Informational for 11.0 and beyond

Keyword: 

One-line Description:

Compounds at a Glance crashes when batch has NumberOfVerifiedIons outlier on

Problem:

When opening Compounds at a Glance window, it immediately crashes, when Number of verified ions outlier is ON.

Temporary Solution:

None

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

ECM Mode - Print Method Report fails when reason/verification required

Problem:

This issue can be seen in ECM Compliance mode and likely in UMAT.  In the ATM require that the Method report require either reason or validation.  Then attempt to print the Method Report (see attached).  After supplying a location there will be an error message.  The verification/reason dialog was not displayed either before selecting a location (where I would expect it) or after with the Save button.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

 PDF Report Builder - Footer Center - > 999 pages makes number print incorrectly 

Problem:

When a PDF Report Builder template contains more than 999 pages the total number of pages will start clipping the number as if the field size is too small to hold the 4 digit number.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Report Builder version/build on splashscreen and 'About Report Builder' do not match those in the list of installed programs

Problem:

When installing Quant 10.2, Report Builder 10.2.1 is installed on the system and this is what is seen when checking the install version in Windows.  However the  "splash screen" and "About" screen in the application erroneously show 10.2 it shows.  The issue exists in the Report Builder 10.1 SR1 which installs Report Builder 10.2.1.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

UMAT mode - attempting to save as a batch which already exists, then saving again corrupts audit trail

Problem:

Prerequisite - have two saved batches with existing audit trails (UMAT mode) - I'll call them:
 * Batch A
 * Batch B

Steps to reproduce:
 # In Quant 10.1 - load a UMAT batch with an audit trail - I'll call this "Batch A".
 # From the File -> Save As, save the batch as "Batch B" (which already exists).
 # An error occurs that you cannot save this batch because the batch already exists.
 # Acknowledge the error - and now, simply save the batch (as Batch A) from the File -> Save menu.
 # Close the batch, and re-open Batch A. You should find the audit trail is now corrupted and throws an error.

Temporary Solution:

None

Fix Information:

Fixed in 10.2

Keyword: 

One-line Description:

Unknowns Analysis - Show Alternate Hits does not work on GC signals

Problem:

If you set up an UA session with TIC Analysis of a GC signal and set Library search Type to Retention Time Match you will get components identified as expected. However if there is a mistaken ID when you try to Show Alternate hits the search shows no choices even if you manual select the GC library used in the UA method. This means that there is no way to correct a misidentified component with the correct compound.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

 Unknowns Analysis - Library description not show when using GC RT only Library

Problem:

When using a GC RT only library the description field is not transferred from the library to the component as it does in a MS library.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

 ECM 3.x:  Batch path on report shows local drive

Problem:

When a batch is uploaded to ECM and a report is generated the old Windows directories are shown rather than the LCDF location.

Temporary Solution:

None 

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Quant B.08 in ECM mode appears to add two entries to batch audit trail for every save event

Problem:

It has been observed that while running ECM 3.4.1.691 with Quant B.08.00, every time they click the Save batch button - two save actions are recorded in the batch audit trail.

Temporary Solution:

None

Fix Information:

Fixed in B.09.00

Keyword: 

One-line Description:

Report Builder - Some graphic - Null parameters causes error

Problem:

When generating a report using a Report Builder template most of the graphics elements will display an error message and fail to create the report if one of the parameters have a null value.  This often is the case when there are missing ISTD peaks or a variable number of qualifiers (some compounds have 1, others have 2 or more). 

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Unknowns Analysis - Excel template only works for single samples

Problem:

When generating Excel based report templates in Unknowns Analysis selecting "All Samples" will result in an error ''Please specify a batch ID''.

Temporary Solution:

None

Fix Information:

Will not fix

Keyword: 

One-line Description:

Unknowns Analysis - QMY - Check box and labels displayed incorrectly when app width reduced

Problem:

In the "Component Filter“ section under tab Home: depending on the size of this window, different options are displayed. The options “Hit” and “Non-Hit” are hidden and it looks like the check mark belongs to the option “Manual Components”.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Unknowns Analysis - SureMass - Chromatogram Range Low/high throws errors

Problem:

When running Unknowns Analysis in SureMass mode entering Chromtogram Range Low/high causes an Index out of bounds error. 

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Unknowns Analysis - RT features not working with Accurate Mass Pattern Match

Problem:

When running Unknowns Analysis in Accurate Mass Pattern Match mode some of the RT related feature fail to work as expected.

1) Library RT is not displayed.
2) Delta RT is not displayed.
3) RT match factor is ignored.

possibly related 

4) Match Factor is not displayed.
5) Ions Peaks displayed show ions that are not part of the isotopic pattern
6) EIC peaks show saturation not seen in the Ion Peaks

Temporary Solution:

None

Fix Information:

Fixed in 12.0

Keyword: 

One-line Description:

Update -> Average Retention Times and Update -> Average Qualifier Ratios Breaks with single CAL or single QC

Problem:

When a batch contains only a single calibrator sample, or a single QC sample, the functions which update RT's and qualifier ratios based on the average of more than one CAL or QC do not function properly. Instead of taking the average of a single value - they fail and return a 0 for the RT. Because the RT is 0 - the qualifier ratio observed at that time may very well be zero or null.

Temporary Solution:

Use the "Update RT" or "Update Qualifier Ratio" feature when the batch contains only a single calibrator or QC sample.

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Average Calibration Replicates will remove calibration level from curve if a calibration standard has no response for a target compound)

Problem:

Using the "Average Calibration Replicates" feature from the Method Editor -> Calibration Curve menu, will nullify the entire level if the first replicate has no response. This can occur if a user "Analyzes" a batch containing a standard with no response for a compound with a calibration curve.

For example - if a calibration standard (marked as a "Cal" in the batch table) does not contain a given compound (such that no response is found), a level will be added to the method's calibration curve of type "Method" which does not participate in the calibration curve regression. When the "average calibration replicates" function is executed, it will average all replicates within a given level leaving only the "Method" level in place. This has the effect of removing the entire level from the calibration curve.

Temporary Solution:

It is strongly recommended to not use the "Average Calibration Replicates" feature for replicates of standard injections that do not contain all calibrated compounds. One can manually remove the "method" type levels from the calibration table before using the "average calibration replicates" feature. 

Fix Information:

Fixed in 11.1

Keyword: 

One-line Description:

Matched isotope pattern in the Screener doesn't match the mass match score in BAG

Problem:

The screener UI shows poor isotope matching while the mass match score is very good in the BAG table.  The root cause was that the screener was using different mass match score calculation code and not saturation aware spectrum as was the BAG values.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Unknowns Analysis - Crash with error indicating null height in ion peaks 

Problem:

Under certain and intermittent conditions Unknown Analysis will crash with an error about null height in ion peaks.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Quant's activity log did not reflect when new batch files were created

Problem:

The Quant activity log (viewed in the Control Panel or in Quant itself) does not reflect that a new batch file has been created until the batch is saved. 

Temporary Solution:

n/a

Fix Information:

Fixed in Quant 12.

Keyword: 

One-line Description:

Quant ISTD concentration behavior inconsistent between replace calibrator and Analyze batch

Problem:

Consider a case where a batch contains a set of calibrators.  There are two paths to make the calibration curve be based on the current set of calibrators, the most common is Analyze Batch while it is also possible to perform a Replace Calibration command and replace all calibrators and all compounds (a common EnviroQuant workflow).

What is different is that Analyze Batch retains the concentration values in the individual calibration tables rows while the Replace Calibration command reloads the concentration in the calibration tables rows with the ISTD Conc. field in the Quantifier table. 

This issue came to our attention when a customer who had a method with one concentration in the ISTD Conc. field in the Quantifier table and a different one stored in the concentration in the calibration tables rows noticed that they got different calibration curves when doing Analyze Batch vs. Replace Calibration (this was due to 1/y weighting where the difference in ISTD concentrations shifts the weighting).

 

Temporary Solution:

None

Fix Information:

Fixed in 12.0

Keyword: 

One-line Description:

Method History Tool does not track changes to globals

Problem:

Method History Tool does not track changes to globals

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description:

Editing compound name in quant method does not update extracted data

Problem:

MRM Data Access filters MRM and SIM data based on matching compound names in Quant method with compound names in the Acquisition method.   When changing a compound name in the Method Editor this might cause a match or mismatch but such edits does not update the extracted MRM or SIM signals.

Temporary Solution:

None

Fix Information:

Fixed in Quant 11.0

Keyword: 

One-line Description:

Early SubscribeNet Quant 10.2 media is incomplete -  missing PeakQualifierChromatogram crashes Supplemental installer

Problem:

Some customers report an issue installing Quant Supplemental on Quant 10.2 media downloaded from SubscribeNet immediately after Quant 10.2 was available.  An error message mentions missing PeakQualifierChromatogram.

Temporary Solution:

Redownload Quant 10,2 media from SubscribeNet or order USB media

Fix Information:

Fixed at SubscribeNet

Keyword: 

One-line Description:

RT Calibration function lacks permission control

Problem:

The RT Calibration function lacks permission control and is available to all users.

Temporary Solution:

None

Fix Information:

Fixed in 12.1.

Keyword: 

One-line Description:

Retain Filter settings when starting Quant

Problem:

Filter contents (i.e. Compound Groups, Sample Groups, ISTDs) is not retained when Quant is exited and restarted.

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

ECM Unknowns Analysis - Save As leave old .UAF checked out and does not checkout new >UAF

Problem:

When running Unknowns Analysis with a Analysis (.UAF file) "checked out" it is possible to perform a "Save As" and create a new Analysis (.UAF file) .  If this is done the original .UAF file that was checked out and the new .UAF is not checked out.

Temporary Solution:

None

Fix Information:

Fixed in 11.0 

Keyword: 

One-line Description:

ECM XT, Enterprise:  Unknowns Analysis - No way to view the unknowns method audit trail in Unknowns Analysis

Problem:

There is no interface in Unknowns Analysis to view the Unknowns Analysis method audit trail.

Temporary Solution:

View the unknowns/library method audit trail in Quant.

Fix Information:

Fixed in 12.0

Keyword: 

One-line Description:

Qual and Quant give different peak resolutions for USP

Problem:

There seems to be a significant difference in the way Qual and Quant calculate USP resolution in an example peak.  The issue does not exist in EP / BP / JP / DAB.  The difference between USP and the others is the use of peak width determine by the tangent method (USP) vs FWHM for the others.   The example peak shape is very poor and this could easily affect the tangent method peak width.  Performing a MI in Quant and reducing peak width to about 1/4 the current size makes the resolutions approximately agree.

Temporary Solution:

None

Fix Information:

Fixed in 11.0

Keyword: 

One-line Description: