Software Status Bulletin

MassHunter Quantitative Analysis     GQuantAA

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

Going from batch view and then going to open method from existing batch
you will get the QC's added as Calibration levels in the table and they are not identified as QCs.   

1. Created a new batch
2. created the method by using aquired MRM data
3. Manually inputed the conc and dilution patten
4. Now we have 5 cal levels for every compound (5 lines in conc setup)
5. He saved the method
6. He applied this method to other batch, then the cal level has 7 lines (5 Cals + 2 QCs). this is referred to as the extra lines in cal levels.

Quant has been this way always, it is not a bug.  The QC are considered to be Quality Control levels and are added to the calibration.

n/a

MolecularFormula column in dataset is missing from the database option.

n/a

N/A

the search results should change according to the RT or RI window in Library search. But it has no effect at all:

1. use the new batch file PesticidesCompounds in my D:\Data\Data_FromHarry\QuantResults folder
2. Create New Method using Scan data with Library Search
3. in Library Search Setting, change the RT window to 2min and 100 min
4. Search the library, but no p,p-DDD compound returned in the results.

The issue boils down to using the wrong RT window parameter in the Advanced Dialog. The TargetRT match tolerance window on the Compound Identification tab is only used during UA to match unknown compound candidates with target compounds. This setting does NOT affect the library match score.

In order to make the RT matching more tolerant during library search is to relax the RT range in the Library Search tab. When this is increased to 100 seconds, the desired effect is achieved.

n/a

Customers want to get the same chromatogram (scale) image in the report as Batch at a Glance screen. If customers change the scale of the chromatogram i, the updated chromatogram in scale should be appeared in the report.

The issue is that the chromatogram used in the report is not updated when changing the scale of the chromatgram.

But most cases, the customers are interested in the scale of the lower limit.

If the chromatogram that is fit y axis to lower limit of calibration is used in the report, it will satisfy the requirement, then we can close this request.

n/a

When creating New Method using Manual setup, 2D signal type has only MS to choose, no other channel like DAD to choose from. Tested both MRM and GCMS flavor, all are the same.

When doing a manual method setup, Quant does not generally have access to a sample. Therefore, there is no way to get a list of available signals from the sample, so the list is populated with the MS as the only default signal.

However, this is not an issue, since the user can type in any signal type value like GC, and the application will take it and intepret it correctly when the method is applied to a batch (assuming the signal name is present in the sample).

Resolved in Build B.02.01

Copy to Clipboard of Spectra in Qual (318) causes exception in Lib. Ed.3.1.166.0

None

Fixed in version B.03.02

creating a new batch in quant, adding new samples to this batch, but the datafile has the same name as the previous batch you will get an error message that file name already exist and brings you back to the original directory path.

Files are being processed as a batch.   Batch means all of the datafiles will exist under the existing directory so the file names need to be unique.

n/a

“Save as” library.xml format to library binary file format could cause the library editor to abort.

n/a

Fixed in B.03.02

AIA format cannot distinguish between SIM and full-scan data.  So, there is no short way to determine the data in the AIA file to whether it is full-scan data or SIM data.  So the software will continue to default the output file data type as Scan data.

n/a

n/a

When creating a quantitative analysis method using the Method-->New-->New
Method from Acquired MRM Data, one or more Time Segments may have compounds that do not have Retention Times (i.e. 0.00). All other method parameters (e.g. Compound Name, Scan Type, Transition, etc.) will be listed but not the Retention Time. Other Time Segments may have all parameters including the Retention Time listed.

The problem is caused by there not being at least 64 data points in the chromatograms extracted for the transition in those Time Segments. The default integrator for quantitative analysis method setup, the MS-MS Parameterless Integrator, requires at least 64 data points in the chromatogram in order to integrate a peak. Since no peak is found, no Retention Time is recorded for that compound. 

This problem has also been seen in MassHunter Quantitative Analysis rev. B.01.04 and the workaround described in the Solution section is the same. 

Solution/Action: 
The workarounds for this problems involve editing a file that sets quantitative analysis method setup and user interface defaults. To edit this file: 

1) Close MassHunter Quantitative Analysis. 

2) Make a copy of the file QuantAnalysis.exe.config in the C:\Program 
Files\Agilent\MassHunter\Workstation\Quant\bin folder. 

3) Open C:\Program 
Files\Agilent\MassHunter\Workstation\Quant\bin\QuantAnalysis.exe.config using the Notepad editor or an editor specific for XML files. 

Search for the line 
 
Change the "AutoMagic" to "RTE" i.e. 


The General (RTE) Integrator will now be the default integrator for creating the quantitative method using the Method-->New-->New Method from Acquired MRM Data menu item; it does not require 64 data points to integrate a peak. 

However, a superior solution from a data quality standpoint is to examine and adjust the Acquisition conditions. Often, data files that have exhibited this problem have Time Segments that are too short with too many MRM transitions. Due to the short Time Segments, some compound peaks are on the boundary and cut off, such that no integrator could successful integrate them. 

4) Save and Close the file QuantAnalysis.exe.config 

5) Restart MassHunter Quantitative Analysis.

n/a

If the user creates a Quantitative Analysis method for a compound with Area Sum turned on for its qualifiers, when a qualifier is manually integrated it does not update the quantifier area.  The correct behavior would be to update the quantifier area so that it reflects the new area of the qualifier.

n/a

For this localization issue, since we can't change any UI behavior, so the fix is in the next version of Quant (FAST). Fixed in version B.04.00

Timed events Area Sum On/Off in Genie Integrator was not working in B.03.01 unless patched

None.

Fixed in version B.04.00

A Quant method is set up which describes each transition with the associated CID.  When doing analysis Quant B.03.02 and earlier do NOT reference the CID during extraction and integration and thus reports each transition using the sum of all matching transitions.

None

Quant 04.00 has an option to extract and integrate based on CID.  User must enter a value in the new Collision Energy Delta field to activate the new feature. Fixed in version B.04.00

Instrument Name and Injection Volume were not appearing in Quant in B.3.01

none

na

When creating a 2-D UV or ADC compound, the chromatogram will not show up in the Compound Information pane until you enter something in the TS column of the Quantifier field for the new UV compound.  Until you enter something arbitrary in the TS field, the Compound Information pane will say "No Data Points".

Enter a value of 1 in the TS

n/a

for 2D GC data, Quant should separate TIC and 2D chromatogram in 2 windows, currently they overlay in one window, user has to normalize it in order to view 2 signals together.

none

n/a

Library editor crashes when undo pasted library entries into an existing library in

none

Fixed in B.03.02

1) RT in chromatogram window is not limited to RT window but shows entire run time
2) data shows up in the qualifier window (no qualifiers)
2) Spectra window shows some sort of data (no mass data)

none

n/a

Although one can asks to see peak labels for Calc Conc. in the Compound Information window you do not have the option to display its units.  Would like to see this in the form 1.234 ug/ml where 1.234 is the Calc. Conc. and not just add another column to the stack "Units = ug/ml"

none

Fixed in B.03.02

1. Install B317 Quant(released) to JPN Windows Vista SP1.
2. .NET Framework 2.0 (or higher) is already installed (Qual is already installed), but the message appears.

none

fixed in B.03.02

Sine LCMS QQQ format cannot support multiple MS signals in the same data file with DIFFERENT number of scan records. 

The GCMS file format does support same data files with different number of scan record and as a result the translator will fail in this situation by design.

None.

Fixed in B.03.02

1. Install Build 170 Quant(released) to JPN Windows Vista SP1
2. Select only "GCQQQ"
3. 4 shortcuts are created.  they are named "ShurtcutX".

in English shortcuts are removed after install

none

fixed B.30.02

In the Calibration curve window, the peak that is being viewed should have its relative concentration and relative response shown and the intersection with the calibration curve shown. I have tried to draw in the way that it should look.

when the user scrolls up and down of the sample, it would be nice to have it reflected in the calibration curve so that the user can see where does the sample reside in comparison to the levels which were taken.   This has been entered into the LCMS Quantitation Database earlier and users have been requesting this quick visualization tool.

none

Fixed in B.03.02

User just created an xml library, no problem.
Go into Quant and the software sees the file, no problem
User then tries to load the file and it will not accept the file name that was selected, it will stay open.

1 - problem is two parts, the user has a new PC and the file extensions state hide known types.   The system knows the file is an xml format because it will be displayed but the error is the open command, it will not open the file because the file program is looking for the full string to be passed and it was not.
2 - If hide file extensions is declaired to have hide known types then the user is forced to type in ".XML" to make the library work.

Configure Windows to show file extensions

Fixed in B.03.02

Can not export to Excel when he had more than 256 columns in his batch table.   When you try to export to an .xls file it tells you "Excel worksheet is limited to 256 columns, and the batch table exceeds this limit.

None

 Fixed in version B.04.00

When Time Reference Flag is checked for an ISTD compound (eg. AMP-D5 ), According to Time Reference Flag definition, it would adjust the RT of AMP but doesn’t.

Time Reference should not cause any significant shift in the reported retention times, and certainly not in the RTs specified in the method. As the Quant documentation states, Time Reference simply helps the Quantitation Engine find and identify peak groups which would otherwise not be detected due to a large shift in RTs.

The correct way to test the Time Reference feature is to use it on a data set where it actually makes a difference, namely on a sample where all RTs (for target compounds and ISTDs) have shifted relative to the values specified in the method.

Fixed in version B.04.00

Seen in B.03.01 Build 170.0 and 170.18.  

The steps to reproduce are:

1) Manually integrate the sample MN2 and compound NAD's target chromatogram.

2) Manually integrate its ISTD PIPES.

3) Go back and manually integrate the target chromatogram.  The ISTD chromatogram's manual integration disappears.  In addition, you can no longer make any changes to the manual integration of the target chromatogram.  If you try, nothing changes.

none

Fixed in B.03.02

Found in Q-TOF data Quant batches with 150 data files and 50-100 compounds.  They inspect every chromatogram and manually integrate those that they judge need to be better integrated.  About every hour they have been seeing a message:

Manual integration failed
Failed to get compound chromatogram for 
OpenDataFile is not called prior to calling this method  OpenDataFile is not called prior to calling this method  

after attempting to manually integrate a peak.  Then they are unable to save their batch unless they close Quant and reopen Quant.  As a result, they lose their results from the last save.

none

Fixed in B.03.02

A customer wanted to use the UserDefined1 through 9 parameters that they saw in the B.03.01 Quantitation Dataset.  However, they were unable to get any of these to show up in their report.  I reproduced this and found that I could transfer UserDefined from a worklist but not UserDefined1 through 9.

none

Fixed in B.03.02

Qualifier Ratio is not zero in the Qualifier Graph, but in method, it is set 0 when creating new method from Acquired MRM data.

n/a

n/a

While creating a method using TOF data.  The scan type ("Scan" column) is listed as "MS2Scan". 

This is TOF data, there is no MS2Scan.

n/a

 Fixed in version B.04.00

Seen on Q-TOF LC/MSs.  When they try to create a batch, it starts converting the Q-TOF data and takes a very long time.  It does this every time they create a batch with the data.

None

Fixed in version B.04.00

A user would like to use a zero concentration standard in the Cal Curve.  If one puts it in and the standard (actually a blank) has no response, it does not display a cal point in the Calibration Curve of Quantitative Analysis.

Can manually integrate a peak (or a background peak), then use Zero Peak.  Then a Level 0 Cal point is displayed on the curve.

The Blank Offset calibration curve fit uses the Blank Offset to calculate an offset.
That is often an acceptable answer to those who are looking to push the lower limit of the quantitation.  But, using 'Blank offset' for the calibration curve Origin does not display a zero concentration point on the curve.

n/a

Right now, when you attempt to create a TOF or Q-TOF method from Acquired Scan Data, it will "deconvolute' the data.  The data is extremely rich and it can take a very long time to deconvolute it.  I have even rebooted my PC after starting because it took so long it appeared to be locked up.

It would be helpful to have a way to "threshold" this so it only looks for the 20 top peaks or peaks above 500 abundance values.  This way the search for compounds could go much faster.

workaround is the following procedure:

1) Open the scan data batch in Quant
2) Go to the Method Editor
3) Right-click anywhere in the Sample information window and select Perceive Compound Settings. You will get the Parameters dialog.
4) Set the Spectrum peak threshold to a high-enough value to reduce the number of peaks. Click OK to apply and cache the value.
5) Run "New Method from Acquired Scan Data". The new threshold value will be used.

Fixed in version B.04.00

Version B.03.02 and below of the software uses the retention time and left and right retention times deltas as specified in the method to extract data for peak detection rather than the adjusted retention time, as currently calculated and then applied the left and right deltas from the method.  This can result in a peak outside of the method RT window but in the adjusted RT widow not being found.

none

B.04.00 uses the adjusted retention time window to extract signal and detect peaks. Fixed in version B.04.00

While running "Create MRM method from MRM data' the MRM transitions, which have same precursor and same product ion, are signed as MS1 SIM. They are coming with zero retention time. You have to change the Scan type to MRM and manually enter right ret times and then peaks are integrated. 
data file added

None

Fixed in B.03.01 (except RT = 0 when too few data points to detect peak)

When triggering Tools/Go to Qualitative Analysis... menu item,
the user see an error message,
but the user can continue

Qual opens the datafile, but does not correctly extract the ions (transitions).
Use Qual to manually extract the appropriate ions for that compound.

Fixed in B.03.02

B.03.01 Library editor was vary slow importing JCAMP files.

None

fixed in B.03.02

In B.03.01 A copy/paste into the Library Editor did not transfer the InstrumentType and acquisition mode, i.e. MS/MS and precursor ion did not get enter automatically

None

Fixed B.03.02

Feature was present in version before B.03.01 release where it was lost.

none

Fixed in B.03.02

B.03.01 version - When setting up(or change the existing Times events) the Timed Events (in Universal/Genie Integrator) and applied it to all, error message pops up.  Quant could hang after message.

none

Fixed in B.03.02

When accurate mass spectra are copied from Qual or Quant into the Library editor the masses are rounded to a tenth AMU.

none

Fixed in version B.04.00

Library Editor does not read Retention Index data when importing JCAM files

none

 Fixed in version B.04.00

Seen in version B.03.02

Curve fit type, origin, weight for ISTDs are modified when saving batch. Steps to reproduce:

1. Open Quant batch
2. Apply a method. Make sure Curve fit, origin, weight are 'NULL' for ISTD compounds
3. Analyze batch and Save batch (not method)
4. Close batch and open this batch again
5. Curve fit, origin, weight for ISTDs are filled by default values while those value should be NULL.

None

Issue does not impact results as ISTD do not have calibration curves. Fixed in version B.04.00

The Injection Volume field can be blank in Quant and thus Quant reports when a valid Injection Volume is in the sample_info.xml field.

Seen in B.03.01

None

Fixed in B.03.02

When creating a Quant method from MRM data using the “New method from Acquired MRM Data” feature Quant looks in the AcqData/*.m directory of the selected data file and take the first file that fits the pattern *qqqacqmethod*.xml as the acquisition method file.   It then uses this file to determine which transitions to load into the method not the data in the data file selected by the user.  When multiple files fit the pattern, as would potentially occur when the acquisition method is edited and saved under a slightly different name, the possibility exists that the software will select an acquisition method file other than the one used to collect the data.  If this happens the method may not reflect the transitions in the data file.

Delete or rename (to avoid the *qqqacqmethod*.xml format) all undesired method files that are not the desired one.

Fixed in B.03.02

When asked to display the Curve Fit assistant on some data sets the software displays no suggested calibration curves (rows) in the Curve Fit table.  Problem seen in B.03.02

None

Resolved in B.04.00 Fixed in version B.04.00

The “Use same parameters as the parent compound” in the Universal integration dialog box associated with Qualifiers does not properly copy or track the parent compounds events to the Qualifiers.  Problem could be seen after editing the method, applying to batch and returning to the method to find expected changes to events. Problem found in version B.03.01 and B.03.02.

None

Resolved in B.04.00 Fixed in version B.04.00

At times the MS-MS or MS-MS(GC) integrators will integrate a peak erroneously such that the peak variables have undefined or illogical values.  An example of this is when the integrated area appears to be completely above the peak and stretch upward forever.  When this happens to any peak in a graphics window the program encounters an error and crashes producing no report.   Usually it is not the peak that corresponds to the compound of interest but a poorly defined peak near the edge of the graphical window.  Problem seen in B.03.01 and B.03.02.

Review the data looking for bad peak integrations and manually integrate the peak.  Then generate the desired reports.

 Fixed in version B.04.00

When attempting to manually integrate a peak under the Universal integrator the integration fails and gives the error dialog that reads “ Manual Integration Failed  The method or operation is not implemented.”  Seen in B.03.02.

None

 Fixed in version B.04.00

In Quantitative Analysis rev. B.03.02 Build 170.21, manual integration of a peak in a batch that has a Cal Curve with disabled points can result in an incorrect Calculated Concentration. The problem does not occur with every batch. The problem also does not occur with the older rev. B.03.01 Build 170.0 software. To reproduce the problem: 1) Load or create a batch. 2) Disable one or more points in the Calibration Curve. 3) Manually integrate a chromatogram peak. The change in value of the Calculated Concentration will be different than it should be if the points were not disabled. A fix is currently under investigation.

None

 Fixed in version B.04.00

With Quantitative Analysis rev. B.03.02 Build 170.21, it is not possible to change the extraction window for TOF or Q-TOF Scan data. For example, if the user were to load a batch with TOF Scan data, go to edit the method (Method--Edit Method menu item or F10 button), then make a change to the Extract Left m/z or Extract Right m/z in Mass Extraction Setup, it would not be reflected in the method. The mass extraction will remain as the default value 20 ppm. The problem does not occur in version B.01.04 Build 126.0 nor B.03.01 Build 170.0 of Quantitative Analysis. The problem also does not occur with other types of data (i.e. LC/QQQ, GC/QQQ, translated single quad data).

None

 Fixed in version B.04.00

This issue involves the Area Sum function for quantitating with the addition of the qualifier ions.  This function does not work at all in the shipping Quantitative Analysis, rev. B.03.02 Build 170.21.

Install point patch. The implementation in this patch is different than previous MassHunter implementations.  The previous implementation involved summing the chromatograms of quantifier and all qualifiers, then integrating and using the area.  The implementation in the patch and future MassHunter  Quantitative Analysis versions involves integrating each individual quantifier and qualifiers, then summing the areas.  This patch implementation matches the way the area sum function has worked in the MSD ChemStation G1034xx and G1701xx since its first release.

 Fixed in version B.04.00

Seen in B.03.01 and B.03.02.  When one attempts multiple manual integrations by making fairly small changes in the start and stop points such that the area appears visually to fluctuate by 50% to 100% results in much larger variance in the area up to 10 fold.  The problem seems to happen when the start integration is placed near the start of the peak and the stop integration point is placed in a region from peak half height to and past the peak apex.

Install Patch

Fixed in version B.04.00

Issue reported in B.03.01.  While creating a method in Quant from an acquired TOF data file Quant gives the following error:

"Failed to create method from scan data
 Deconvolution failed: FindPeakMS: Missing required input parameter set of type PSetTofPeakFinder"

The data was acquired on a 6230A instrument with AJS, FPS disabled.

None

Resolved in B.03.02

When user saved their Quant method and apply it to batch, the DA method and DA method Path columns are empty when viewed in Batch-at-a-glance.  Correct operation would be to display the method name and path where the method was previously saved.  Reported in B.03.01.

None

Resolved in B.03.02

Occasionally Quant will crash when the user attempt to add a column via the add columns feature.  Problem seen in Quant B.03.01.

None

Resolved in B.03.02

Problem can be seen when viewing a spectrum.  If one zooms into a region of the spectrum  where there appear to be no masses they will observe spurious peaks at every m/z with a step of 0.1 AMU.

None

Resolved in B.03.02

In outlier setup, limits for CC Response Ratio are "CC Relative Response Limit Low" and "CC Relative Response Limit High" are not accurate and have been changed to "CC Response Ratio Low " and "CC Response Ratio High".

None

Fixed in version B.04.00

When manually integrating, the retention time is sometimes moved also indicating the area response is incorrect.

None

Fixed in version B.04.00

When Quant has UseIndexDataAccess active (the default) some data files can produce very jagged peak shapes that do not match the same peak when viewed in Qual.  This problem was seen in B.03.02.

Disable IndexDataAccess

Resolved in B.04.00. Fixed in version B.04.00

This defect can be seen in B.03.02 when a Calibration sample is changed to Continuing Calibration and then the batch is reanalyzed.  After this the sample type cannot be set back to Calibration and successfully reanalyzed.  If this is attempted an error message “Batch analysis failed  Sample not validated : Continuing Calibration level (some level name) does not match any existing calibration levels”.

None

Resolved in B.04.00. Fixed in version B.04.00

After turning on Area Sum for qualifiers, if a qualifier is manually integrated the quantifiers area is not updated.  Seen in B.03.01 and B.03.02.

None

 Fixed in version B.04.00

After installing .Net Framework 3.5 custom calculation feature does not work.  The on the fly compiler fails because a new parameter required in .net 3.5 is not supplied.

Uninstall .net 3.5 framework

 Fixed in version B.04.00

When one manually integrates a symmetrical peak measuring the area on the right half (drop from apex) vs. the left half the area ratio is approximately 2:1 when it should be about 1:1.  He sum of the left and right areas are essentially equal to the peak when it is manually integrated as a whole.

None

Fixed in version B.04.00

If a sample without Sample Name info is added to a batch the batch analysis fails since Sample Name is a required field and edits are not allowed.

None

Fixed in 4.00

The sample type "ConCal" in worklist should be "CC" in Quant but it shows up as "Sample".  Seen in B.03.01 and B.03.02.

None

Fixed in version B.04.00

The problem can be seen when running “New Method from Acquired MRM Data” in B.03.02 and there are mixed polarities.  The method is created but not all transitions get the name assigned that has been used in the acquisition method.  Instead they get names like “Compound_##” where ## is a number. Another symptom is for some qualifiers ions to become separated from the target compound and form new compounds

none

 Fixed in version B.04.00

If a batch, created in B.01.04, is opened in B.03.02 and a new sample is added to the batch Quant immediately crashes.

None

Fixed in version B.04.00

While running “Create new method from acquired MRM data “ in B.03.02 a limited number of cases have created methods where negative MRM data was assigned a positive polarity.

None

 Fixed in version B.04.00

Two sets of standards with replicate injections are in the same quant method.  The Enable check box is used to disable some compounds in some levels (where the compound is not present in that standard) and enabled in some levels (where the compound is present in that standard).  Quant can handle this case when no replicates are present but not when replicates are present.   Method becomes corrupted during the Analyze Batch step.

Split the method in two, one for each standard set.

 Fixed in version B.04.00

Each time the batch is opened Quant will indicating it is converting the data files when in fact it has already done this in previous batch use.  Seen in  B.03.02 Build 170.21.

None

 Fixed in version B.04.00

When the user loads a batch and makes either the ISTD Response Ratio or the ISTD Concentration Ratio visible, then presses Analyze Batch, these ratios are set to 0.0, regardless of what the true values should be.  Seen in B.03.02.

None

 Fixed in version B.04.00

The problem is seen B.03.02 and prior versions when a peak is found and integrated automatically and then a manual integration is made which very slightly changes the baseline.  The change in area from the automated integration will change more than would be expected and may in fact change in the wrong direction (reported area increases when peak area is actually being slightly reduced).  Attempting to recreate the automated peak area via manually integration by returning the baseline to the original position will not give the same area.  The difference seen is area cannot be explained in terms of slight differences in cursor position.

None

Fixed in version B.04.00 when using Agile integrator.  Very small variance still seen in other integrators.

In a MRM data file where the right RT Delta is too short to display the entire chromatographic peak the peak gives a jagged appearance.  If the right RT Delta is increased the jagged appearance goes away.

Disable index file use

 Fixed in version B.04.00

MassHunter Quant B.03.02 and prior shows 10 times higher results for the areas in the Universal Integrator than with other integrators.  When manual integration is enabled and a manual integration is performed the factor 10 times goes away.

None

 Fixed in version B.04.00

In version B.03.02 and prior the copy calibration level function duplicates the level identifier and concentration but does not copy response information from the current batch.

None.

Fixed in version B.04.00

Export of the batch table in CSV file creates garbled file.  Problem not seen in other localizations.

Export in .XLS format then use Excel to save file as CSV.

 Fixed in version B.04.00

Quant 3,02 attempts to open a batch file created under a previous version and an error containing "[ERROR] AppCommand.BatchFile Agilent.MassSpectrometry.DataAnalysis.Quantitative.ApplicationCommandException: Failed to read binary batch file ---> Agilent.MassSpectrometry.DataAnalysis.Quantitative.ApplicationCommandException: Hashcode does not match value stored in batch" appears.

None

Fixed in version B.04.00

When attempting to open a method from an existing batch and all of the samples files associated with the existing batch are no longer in the batch folder then Quant will fail to load the method and report an error “Failed to import method from batch.  Failed to load compounds from batch sample  Data Access failed for sample path {file path and name} : File not found {file path and name}”.  The error may also been seen if the only some of the sample files are missing and the software selects one of the missing files to open for information.

Restore missing sample files.

This defect is not planed to be fixed.

Quant and Qual are reporting different Acquisition times.  Both Qual and Quant are consistent in terms of screen and reports within its own software but they differ between the packages by 1 or more minutes.  Quant and Qual are reading different event times and thus reporting different values.

None

Future release of Qual with become consistent with Quant.

When using Universal Integrator, MI is disabled and Quant gives error message saying "method or operation is not implemented" when manual integration is attempted.

Disable Indexed Data Access.  This is done by editing the “QuantAnalysis.exe.config” file in the in the \Program Files\Agilent\MassHunter\Workstation\Quant\bin directory and changing  to .  Note that this will greatly slow data processing in the application.

Fixed in Quant B.04.00 SP1

When Isotopic dilution is activated (Rx and Ry supplied) the calibration curve is corrected but the calculated concentrations appear to be off as indicated by significantly larger accuracy figures than is justified by the data.  The problem appears to be the order in which the correction and quant are applied.  The accuracy figures are changed to the correct values if, after you analyze the batch, you perform a manual integration (zero peak) and restore the original area with a “clear manual integration”.  It appears that the quant is being calculated before the curve is corrected.

None

Fixed in B.04.00 SP1

When the area correction m/z and area correction factor are entered in the single quad quant method there is no affect  on the target response even when a peak at the m/z is found.   The area of the m/z peak multiplied by the area correction factor should have been subtracted from the target area thus reducing the target response.

None.

Fixed in B.04.00 SP1

When one attempts to create a new method from scan data Quant reports an error :
Failed to create method from scan data  
Deconvolution failed : Index was outside the bounds of the array.

Disable Indexed Data Access.  This is done by editing the “QuantAnalysis.exe.config” file in the in the \Program Files\Agilent\MassHunter\Workstation\Quant\bin directory and changing  to .  Note that this will greatly slow data processing in the application.

Fixed in B.04.00 SP1

When a batch is opened or created, Quant scans the data files in the associated directory and forms the Mstree2.bin files if they are not already present.  If the directory contains a data file into which data is being acquired, Quant attempts to create an MSTree2.bin file which is not correctly formatted.  If the file with the corrupt MSTree2.bin file is later added to a batch, the chromatogram graphic is blank and labeled “***NO DATA POINTS***”.  Deleting  the corrupt MSTree2.bin file and reopening the batch corrects the problem.  The core issue is that Quant does not check the status of the file to see if it is being collected and skip the conversion if it is.

Delete the corrupt MSTree2.bin file then reopen the batch to correct the problem.

Fixed in B.04.00 SP1

An attempt to search the MPW2007.L library  will cause Quant to crash.  This can been seen when a spectra is extracted using “Extract Spectrum” and the MPW2007.L library is searched.  The MPW2007.L library contains only condensed spectra (no full).

None

Fixed in B.04.00 SP1

When attempting to create new method from MRM data, from the example data file, a large number of compounds are created with names like “Compound_##”.  The problem disappears and all compounds are correctly created when the "UseIndexedDataAccess" value="true" is changed to false.  An error like this was seen B.03.01 and fixed in B.03.02 but appears again in B.04.00 for some but not all files.

The problem disappears and all compounds are correctly created when you 
disable Indexed Data Access.  This is done by editing the “QuantAnalysis.exe.config” file in the in the \Program Files\Agilent\MassHunter\Workstation\Quant\bin directory and changing  to .  Note that this will greatly slow data processing in the application.

Fixed in B.04.00 SP1

When samples that have a blank name field are selected using the Advanced reporting option, Quant crashes.

None

Fixed in B.05.00

When no peak is found for the target compound on a given sample the CurveFitStatus and CurveFitR2 are left blank.  The curve data should be present and the same on a given compound in all samples.  This defect can leave some fields in reports blank if that sample did not find the target.

Seen in B.03.02, B.04.00 and B.04.00 SP1

None

Fixed in B.05.00

When exporting a table, if the number of columns exceed Excel 2007 column “XZ” the result file will be corrupted and after the recovery the Excel column from “ZA” to “ZZ” are without values, data restart correctly from Excel column “AAA”.

Export in CSV format then open in Excel.  The data will transfer although some the Excel label formatting information is lost.

n/a

Create a new batch and add calibration standard and some samples.
Copy a method from a previous batch or method which contains calibration curve information. Method validates without errors.  
Exit and apply.
Analyze batch (no errors)
Compounds where no peaks were found in the current calibration standard  but were found in the old calibration retain the original calibration curve and give quantitation on samples.   Analyze batch (fails with error)
Edit method and validate ( errors appear – Calibration STD Path mismatch between target and ISTD)

Clear the old file names from the old batch.  Method should validate without error.

Fixed in B.05.00

"Not Found" is displayed in the qualifier signal window when using MS-MS integrator and the Normalize option in the Qualifiers section of the properties window is checked. Seen in B.04.00.

Three workarounds:
1) Use the Agile integrator.
2) Turn off ‘normalization’ in the qualifier window. (Right-click in the Compound Information window, select ‘Properties’.  Under Qualifiers, uncheck the box for ‘Normalize’.)
3) Manually integrate a peak in the target window.

Moving forward, the Agile integrator is the integrator of choice.  There are no plans to change the MS-MS integrator.

Method information is lost when doing the following.

1)	Create a new batch
2)	Do NOT add any samples
3)	Open a method from existing method or batch
4)	Exit the method editor and apply
5)	Now add samples
6)	Go to method editor – no method info

Add samples before adding method

n/a

If a method file is saved in the root of a directory, Quant is not able to find the file even if the correct location or path is specified in the sequence editor.  No batch is created during the sequence run.

Do not save method files that are to be used by Quant Console in a root directory.

n/a

The method displays Ms2SIM instead of Ms1SIM for scan type.

In Method Edit, use the pulldown menu under "Scan" to change the type.

Fixed in B.05.00

The surrogate outlier is based on Final Concentration.  Global setup should have “Apply Multiplier to Surrogate” checked to see this issue. When the final concentration is changed through manual integration the surrogate indicates high or low recovery properly.  But when the multiplier is changed via dilution, amount or total amount the final concentration will change but the surrogate outlier is not updated.

Perform an Analyze Batch after changes to dilution,  amount or total amount to update surrogate outlier status.

Fixed in B.05.00

If Integration Parameters Modified (IPM) is done, then the integrator for the compound cannot be changed in Method Edit even though it appears that it is being changed.

The workaround is to Restore Integration Parameters first, then change the integrator for the compound in the method.

n/a

Sample Information Window's properties don't affect reporting graphics

None

Fixed in B.05.00

While in Method Edit

Go to method editor on a file containing Precursor Scan data and extract a spectrum.  In the extracted spectrum, select an ion and right click the mouse to select New Compound.  A new compound entry is created but the product Ion contains the m/z value of the precursor ion and precursor ion contains the m/z value of the product ion.

Resolved in B.05.00

When creating a new method from MRM data under certain circumstances the Relative Response in the method does not match the value shown in the compound information panel.  The issue is caused by the largest peak in the qualifier EIC not being the same as the peak that is ultimately selected as the qualifier.

Update qualifiers for all compounds after creating a new method from MRM data.

n/a

When a file containing only GC data is displayed in the Sample Information window a trace of the GC data can be seen but the display of TIC data is annotated with ***NO DATA POINTS***.

None

n/a

In the nested Horizontal view if and there are no visible columns in a table, such as the Qualifier Method or ISTD Compound method, the program crashes.

Have at least one visible column for each table displayed.

Fixed in B.05.00

If the user attempts to add a sample to a batch using the “Add Samples” feature and there is a file that data acquisition is collecting into that file appears in the list of files and can be added to the batch.  Once added any operation in quant will result in incorrect operation with regard to the sample and possibly the batch as a whole (the sample might be a calibrator).

Avoid adding samples that are being acquired by checking the status of the file in the data acquisition software.

n/a

In Quant rev. B.03.02 and B.04.00, when the batch has a surrogate, the Surrogate % Recovery is not reported in the Batch Table if the Type is set to QC or Cal.  It will be reported for Samples.  This function worked for QC and Cal Types in B.01.04

None

Fixed in B.05.00

If user try to create a batch with DAD UV spectral data, it may constantly convert.  The error message in the conversion log is:

ERROR: Failed to parse spectrum file D:\MassHunter\Data\1290DADTest\test008.d\AcqData/DAD1.sd
04/05/2010 10:40:40.125  Stack trace:    at Agilent.MassSpectrometry.DataAnalysis.Quantitative.SpectrumDirFileReader.Read()
   at Agilent.MassSpectrometry.DataAnalysis.Quantitative.SignalConverter.ConvertNonMSSpectrumData(DeviceInfo deviceInfo)
   at Agilent.MassSpectrometry.DataAnalysis.Quantitative.QuantDataAccess.ConvertToIndexedData(Boolean overwrite)
   at Agilent.MassSpectrometry.DataAnalysis.Quantitative.IndexedData.IndexedDataConverter.ConvertSample(String path)
04/05/2010 10:40:40.125  Inner Exception: Invalid number of values per data point: expected 2, got 1

n/a

Fixed in B.05.00.

When a user deletes a sample injection from a batch that is set as Standard Addition and then presses Analyze Batch, an error message appears that says

Batch Analysis failed:  the value for column 'CompoundName' in table 'TargetCompound' is DBNull.  Unable to cast object of the type 'System.DBNull' to type 'System.String'

None

Fixed in B.05.00

The Standard Deviation bars in the Cal Curve will not appear until after running the Curve Fit Assistant.

None

Fixed in B.05.00

When the user tries to create a “New Method from Acquired Scan Data” with an LC/MS TOF data set, they will get an error “Deconvolution failed: Deconvolution requires sample data acquired in Scan, Product Ion scan, or Neutral Loss scan mode; found Unspecified”.

n/a

Fixed in B.05.00

An MRM chromatograms extracts with no problem in Qual.  However, when in Quant same MRM signal  does not give me a chromatogram.  Instead, it says “Failed to access sample data” and “Object reference not set to an instance of an object”.

None.

Fixed in B.05.00

Load a method from quantmethod.xml file, the parameters in file don't show correctly on UI. However, when method is applied to the batch then return to the method editor the correct values are shown.

None

Fixed in B.05.00

When setting up a method the ADC data does not appear in the menus for signal type so the method cannot be configured to use ADC

None

Fixed in B.05

When there is no variation in baseline (flat line) in the MRM, the graphic in Quant initially shows a baseline at ~40 counts.  If the scale is changed, example to the lowest Cal level, it will show the baseline at zero counts.  Once the scale is corrected cannot change the scale to produce a baseline of ~40 again, until the batch is re-opened.

None

Fixed in B.05.00

Zero peak does not work when the quantitation is based on height.  Height is not set to zero.

None

Fixed in B.05.00

In Compounds-at-a-Glance there is the possibility to overlay sample groups. 
Feature is broken in Quant B.04.00 Build 4.0.225.0 and, instead of the compound name itself, the label in the top right corner of the chromatographic windows becomes “$(CompoundName)”:

None

Fixed in B.05.00

An error message is obtained if 'Acq Date-Time' is null and Add Calibration, Average Calibration, or Replace Calibration is attempted.

Be sure the 'Acq Date-Time' field has an appropriate value.

All data files should have a value in the 'Acq Date-Time' field unless the data files are old or unusual.

The Sample Group pulldown menu in the Filtering toolbar, and the Sample/Compound Group pulldown menu in the Group Navigation toolbar do not default to "All" when a new batch is opened.  Sample Group retains the last value, and Sample/Compound Group is blank.  (If Quant is closed, then opened, Filtering and Group Navigation pulldown menus default to “All”.)
This defect is observed in B.04.00 SP2.

None

Fixed in B.05.00

Software does not calculate and display Accuracy for calibrators when compound type is MatrixSpike.

None

Fixed in B.05.00

If an attempt is made to modify "Integration Parameters" from the Compound Information window, a message is displayed saying that you don't have permission to execute that command.

None

Fixed in B.05.00

1)  The “Action” for “CmdSetMethodTargetCompoundAttribute” is blank when assigning ISTD compounds to targets and assigning ISTD concentrations.
2)  The “Action” for “CmdSetQualifierIntegrationParameters” is blank.
3)  When the integrator is changed from General to Universal and one Universal parameter is changed, the integration parameters listed don’t reflect the parameters entered.

Apply SP2

Fixed in Quant B.04.00 Sp2

Under some conditions the points displayed in the calibration curve and the calculated conc in the BAG table do not agree. The values in the calibration curve are correct while the BAG table is wrong.

None

Apply SP2 to Quant B.04, fixed in B.05.00

Method created using Method --> New --> New Method from Acquired Scan Data with Library Search.  Attempt to use 'Method --> Append --> Append Method from Acquired Scan Data with Library Search' results in error message.

None

Apply SP2 to Quant B.04.00

Analyze Batch after Zero Peak performed shows non zero calculated concentration for the zero-peaked sample.

none

Apply SP2 to Quant B.04.00

When editing a method, the customer notices that if he changed an expected retention time (e.g. 14.482 to 14.3) it makes significant changes to the chromatogram, where new peaks emerge in the middle of the chromatogram.  It appears that there is also a change to either the accurate mass extracted for the EIC (this is Q-TOF data) or the extraction window.

Issue on B.04.00 (Build 225.0) and B.04.00 SP1 Build 225.2.

None

Apply SP2 to Quant B.04, Fixed in Quant B.05.00

Compound name displayed in the Compound pulldown menu in the Batch Table toolbar is from the previously opened batch when changing between MRM batches.

None

Fixed in B.05.00

Perceive compounds setting for Sample Information window of batch mode is using LC defaults and user changes on deconvolution parameters in the Scan Analysis Parameters dialog box, 'perceive compounds' is always using LC default parameters for deconvolution.

None

Fixed in B.05.00

When running Update -> Average Qualifier Ratio in the method editor the calculated ratio is always the same (and wrong) with or without manual  integration.  The same value is reported with or without manual integrations even when this significantly alters the ratios seen in the cal samples.  It also does not appear to be the correct average ratio.

None

Fixed in B.05.00

When "Update Qualifier Ratio" is attempted using "Select All", error message is displayed, "QuantAnalysis has encountered a problem and needs to close ...".

None

Fixed in B.05.00

Previous and current information for response and x, y coordinates are not displayed in the 'Action' field of the audit trail after manual integration is performed.

None

Fixed in B.05.00

From Quant, use the Tool > Start Qual Application menu item.  Error message appears "Cannot find Qualitative application file './AgtQual.exe' Would you like to specify?".

Manually navigate to the file system to the Qual B.04.00 application AqtQual.exe.
or
Launch Qual from desktop or start menu and then navigate to desired file

Resolved in B.05.01.  Use Tools --> Actions --> Go To Qualitative Application.

Chromatogram is not centered around the expected RT.  The problem is due to Quant method having a RT window that extends beyond the data acquisition window for the MRM being plotted.  When data collection stops before the Quant method expects (RT +  Right RT delta) the software takes the latest data point found in the method window and uses this to assign the right side.  The same process is used on the left side of the chromatogram (using RT – left RT delta) and the earliest data point in the window to set the left side graphics limit.

None

Fixed in B.05.00 

When RT Reference display is ON, software will center the chromatogram by Reference RT

When B.01.03 batches are opened with B.04.00 all of the compounds had "NO DATA POINTS" in the Compound Information pane.

B.04.00 was creating an MSTree2.bin file of only 45 bytes which is far too small and indicates a failed conversion.

Disable Indexed Data Access.  This is done by editing the “QuantAnalysis.exe.config” file in the in the \Program Files\Agilent\MassHunter\Workstation\Quant\bin directory and changing  to .  Note that this will greatly slow data processing in the application.

Fixed in B.05.00

Seen on LC/QQQ with pos / neg switching and give a Quant crash when trying  to change the quantifier in the method. Go to qualifier setup in the method  and click on the product ion and Quant crashes.

None

Fixed in B.05.00

For an instance of 'CmdSetQualifierIntegrationParameters', the “previous value’ is null in the audit trail when the previous values should be the default Universal integrator parameters.

Observed in B225.19 (Quant SP2 build)

None

Since the most common setting is for the qualifier to use the same integration parameters as parent target ion, and the qualifier IPM is not as important as the target ion IPM, this issue will not be fixed.

This problem is seen when SIM & SCAN are acquired in the same run.  Quant failed to create method from scan data and gives an error message "Deconvolution failed: Source array was not long enough.  Check srcIndes and length, and the array's lower bounds."

None

Fixed in B.05.00

Help says that Average Response Factor is calculated for "enabled calibration points".  But the Avg Resp Factor is being calculated for calibration and QC points.

None

Fixed in B.05.00

The RRT outlier only works correctly when the current batch contains calibrators. If Calibration curve is loaded from a previous batch the RRT outlier fails. This problem may be seen with the DOA batch.  

1)	Create new batch
2)	Add only Samples and blanks
3)	Open method from existing batch (with full cal curve)
4)	Analyze batch
5)	RRT fails
6)	Add QCs
7)	Analyze batch
8)	RRT fails (but should work as Help says it uses QC or Cal)
9)	Add Calibrators
10)	Analyze batch
11)	RRT works

The calibration table stores only the response not the RT of the calibration standards so the calculation must fail (see image) when there are no Calibrators (or QC) samples in the batch which can supply the RT.

None

Fixed in B.05.00

If a sample’s response is higher than the highest cal level when using a Quadratic calibration curve, Quant could give the following 3 conditions:

1) Conc is calculated with Red Background—Flag conc. is outside of calibration range. 
2) Conc = Infinity with Red Background--- Flag conc. is outside of calibration range.
3) Conc is not calculated (empty in Calc Conc column) with pink background over all cells --- Quantitation message displays “Response is beyond the range of calibration curve”

Case 1 is the expected situation where the response of the sample falls somewhere on the calibration curve, but Case 2 and 3 occur when the response of the sample is above the top of the parabolic curve fit.  Case 2 occurs when the peak is found by automatic integration (no manual integration).  Case 3 occurs when manual integration is performed .

Seen in B.04.00 including service packs (SP1 and SP2)

None

Fixed in B.05.00

B.04.00 version Help says 'ignore non-target peaks', but this feature is actually for target peaks.

None

Fixed in B.05.00

Should read RRFcc < MinimumCCRelativeResponseFactor

None

Fixed in B.05.00

If the RT calibration file path referenced in the Library Search tab is invalid and a reference library is setup in the method, applying the method and analyzing the batch causes a Quantitation method ("Cannot find RT calibration file " to be displayed for all samples.

Remove the RT calibration file path:
Select Method --> New --> New Method from Acquired Scan Data with Library Search.  Select any library and sample for the Library and Sample paths, respectively.  Click 'Advanced'.  Select the Library Search tab.  Delete the RT calibration file path reference.  Click OK.  Click Cancel.  Press F5 or click Analyze Batch.  Results are displayed and Quantitation message about not finding RT Cal file disappears.

Fixed in B.05.01

Attempting 'New Method from Acquired Scan Data with Library Search' sometimes results in error with message “Failed to create method from scan data  Deconvolution failed: Arithmetic operation resulted in an overflow.”  

Problem seen in B.04.00

None

Fixed in B.04.00 SP2

When setting up the fixed graphic range for X, compound extracted window doesn't re-plot using the new fixed range, it just re-scaled in the new range.  This can result in missing (blank) signal when the scale extends beyond the RT window of the method.

None

Fixed in B.05.00

The "DA. Date-Time" field/column in the batch Sample Information is always blank.  'DA. Date-Time' field should store the date and time that the sample’s data was last processed.

None

Fixed in B.05.00

Display a TIC or EIC.  Zoom in to show small peaks, letting large peaks go off scale on the top.  Copy image to clipboard.  Paste into PowerPoint as metafile or enhanced.  Ungroup a few levels.  Zoomed TIC or EIC goes off the top of the slide rendering it useless for presentation.  The copy to clipboard is copying all the data in the y-scale, not just the zoomed data.  The x-scale seems to be okay.

None

Fixed in B.05.00

Unable to change the Universal "Threshold" parameter after initial change using "Integration Parameters" feature.

None

Fixed in B.05.00

Some JCAMP files will cause the Library Editor to crash during import.

None

Fixed in B.05.00

The 'Average Retention Time' feature does not involve sample-averaging.  Also, the setup dialog that displays when the feature is selected does not contain checkboxes that allow the selection of Cal or QC samples.

None

Fixed in B.05.00

Use ATM Configuration to require User Validation and reason for generating reports.  No reason is asked, no password required and the task does not appear in the Audit Trail.

None

Fixed in B.05.00

In Integration Parameters Setup, select integration parameters for qualifier ion, check the box "Use same parameters as Parent compound". Smoothing is performed but "Smoothing" checkbox is not checked as in target ion parameters.

none

Fixed in B.05.00

If the Response is null for any Cal samples and "Average Calibration replicates" is performed, Quant crashes.

Seen in B.04.00

None

Fixed in B.05.00

The use of  Tangent Skim and Baseline Hold events in Universal integrator have resulted in inaccurate peak area calculations.

Avoid use of Tangent Skim and Baseline Hold events.

n/a

When a QQQ method has the same product ion but different precursor ions an unnecessary warning message is given.  The message would be reasonable on a MS method and indicate a duplicate signal but in QQQ it is reasonable to select the same product M/Z if the precursor ions are different.  This logic could be extended to allow the same transition to be used in the qualifier if they have different collision energy and collection energy delta is such that they are different signals.

Ignore warning.

Fixed in B.05.00

Performing a “Replace Calibration” on a single level causes the method to become corrupt.  The problem is that when the replace calibration is performed on  a compound (A) that shares an internal standard (IS1) with some other compound (B) then the software will add an additional level to IS1.  At that point you cannot enter the method editor and edit the method without having validation problems due the mismatch in levels between compound (B) and the ISTD.

None

Fixed in B.05.00

The new behavior block updates unless the update is made to ALL compounds that shares an internal standard.  This avoids the corruption of the method but limits the functionality to replacing sets of compounds rather than to single compound or subset of compounds.

Problem occurs when the method editor is entered while the sample and compound in the batch table has no peaks integrated.  This is frequently true of blanks and samples that do not contain the chemical in question.  Once this is done if the method is applied to the batch, even if no changes to the method are made, manual integrations will lost.

User must insure that there is an integrated peak.

Fixed in B.05.00

Relative Retention Time and Average Relative Retention Time is incorrect as the Help says “enabled calibration points”.  Calculations indicate that it uses QCs and calibration points.

None

Fixed in B.05.00

If a new method is created in B.05.00 using the pre B.05.00 Drugs of Abuse data files from previous Quant media some compounds will not be found.  Methods created by versions of Quant before B.05.00 give results are as expected. This issue is due to a change in the default mass extraction window to plus and minus 0.05 for MRM data.  Drugs of Abuse data files on the B.05.00 media were manually-edited so peaks are found.

None

Fixed in B.05.00

No Concentration units are displayed when "Display units for Conc. and RT" is checked in Peak annotations for Compounds-at-a-Glance.

Seen in B.04.00 and all service packs

None

Fixed in B.05.00

After checking batch in Check Batch Files (Quant SP3), the Hash Code and Audit Trail boxes are not checked for batch files.  Audit Trail box is not checked for sample files.

None

Fixed in B.05.00

If the user has installed Qual B.04 and B.03.01 and they use the main menu (Tool > Start Qual Application) to lauch Qual and open the current file Quant launches Qual B.03.01 rather than the current release.

If Qual B.04 is installed but B.03.01 is not installed the Quant brings up a message 

"Cannot find Qualitative application file: './AqtQual.exe'
Would you like to specify?

If the user knows where the application is loaded they may select "Yes" and navigate through multiple directory levels to complete the launch.

Navigate file system to complete the launch or launch Qual B.04.00 from desktop and then load desired data file.

Resolved in B.05.01.  Use Tools --> Actions --> Go To Qualitative Application.

View, Compounds at a glance, Layout, Setup, Organize tab ………then use the following step :

Organize Rows by; Compound

Overlay; None – Target only

Review Mode; Compound by Compound

Display options; Baselines, Uncertainty, Fill peaks

Using the above - Compounds at a Glance will be OK. But it only fills the top row of the grid. 

When Wrap rows feature is checked, applied then select "Link Y axis" the system crashes. This happens with different batches of data. 

Seen in B.04.00 SP2

None

Fixed in B.05.00

If the user goes to the Index and selects "Qualifier Outliers" in online Help, they get Help for the Queue Viewer.

Seen in B.04.00 and all B.04.00 service packs

None

Fixed in B.05.00

Agile integrator finds peaks in the data file when non reference window type is percent but does not when set to minutes.  This issue is observed when the window is set very wide by either minutes or percent so that the peak should never be rejected by being outside of the window. 

Seen in B.04.00 SP2

None

Fixed in B.05.00

When Qualifier Uncertainty is Relative, the graphic representation of the band in the Compound Information is correct.  But when Qualifier Uncertainty is Absolute, it is unchanged from Relative.

None

Fixed in B.05.00

If a batch has the Global Standard Addition checked then the manual integration feature fail to operate properly.  

1) Attempt a manual integration of one of the calibrator target compounds.  The peak will get an * placed by it and the MI in the batch table will be checked, but the graphic for the area will snap back to its original position and the area will not change.

2) Uncheck Standard Addition , then manually integrate a target peak, manual integration works and the concentration is calculated.  Check Standard Addition, apply the method to the batch and analyze the batch.  No concentration is calculated.

Observed with MS/MS and Agile as integrators.

Observed in B.04.00 SP2

None

Fixed in B.05.00

When using Fit to Highest Calibration Level, the top of the peak can become truncated or clipped in the Compound Information area.

None

Fixed in B.05.00

MassHunter Quantitative Analysis B.04.00 SP2 is unable to open a batch or create a new batch for specific users. For some users, when they try to either open a batch or create a new batch in MassHunter Quantitative Analysis B.04.00 Service Pack 2 (SP2), they will see an error message:

'QuantAnalysis has encountered a problem and needs to close. We are sorry for the inconvenience.'

However, when other Windows users log onto the PC, they are able to successfully open a batch or create a new batch.

The problem is caused by corrupt user-specific files that control the UI display in
MassHunter Quantitative Analysis rev. B.04.00 SP2. Reinstalling MassHunter
Qualitative Analysis will not fix the problem.
To fix the problem:
1) Select the "Restore Default Layout" button in the Batch Table view which appears when MassHunter Quantitative Analysis starts up. Then try to open a batch or create a new batch.

If 1) above does not fix the problem
2) Delete the corrupt files so they can be recreated with default values
a) Shutdown MassHunter Quantitative Analysis
b) Delete the files in the folder
C:\Documents and Settings\\Application Data\Agilent Technologies_Inc\QuantAnalysis.exe\4.0.225.19
(where "user name" is the name of the user currently logged into Windows, e.g.
Administrator.)
c) Restart MassHunter Quantitative Analysis. The files will have been recreated and the user should now be able to open batches and create new batches.

Resolved in B.05.00

In Quant, select Help --> Contents.  Under the 'Getting Started' section (purple), click 'Read the Familiarization Guide'.  Quant closes and an error message is displayed.

Go to the 'Manuals' folder on the Quant DVD and open the Familiarization Guide file from there.  Alternatively, if Internet Explorer 9 is installed, change to Internet Explorer 8.

Resolved in B.05.01

Crash occurs with these steps:
1) Enter Method Edit
2) Have levels exist in the Calibration table for any target compound
3) Select Tools-->Actions-->Custom Action
4) Select the DummyCalibrationSetup script from MassHunter/Scripts/Quant/Actions
5) Click Open
6) Application crashes

Delete any existing calibration levels from the Calibration table in Concentration Setup prior to running the DummyCalibrationSetup script.

This script is designed to be run when no levels exist in the Calibration table.

Message displayed saying that a Quant command could not be performed because the right permissions were not in place, even though ATM Configuration was in default (should be able to do perform all commands).  Turns out the command is missing from the Command Group in ATM Configuration.

Re-enter permission settings in ATM Configuration after installing the new Quant version.

Resolved in Quant version B.05.01.

1) Copy the ComplianceConfiguration.xml file from the Program Files/Agilent/MassHunter/Workstation/Quant/bin folder, then copy it back after installing the new Quant version.
2) ‘Export’ the compliance file from ATM Configuration, then ‘Import’ the saved file from the MassHunter/log/quant folder.

Retention Time method validation errors are not flagged the first time that the method is applied after 'Append Method from Acquired Scan Data' or 'Append Method from Acquired Scan Data with Library Search' is used.  Upon entering Method Edit and applying the method a second time, the Retention Time errors are flagged.

After appending a method from a scan data file, data access is switched to the scan data that was used to do deconvolution/library search.  In order to catch the error, need to switch back to the original data.

n/a

The workaround is to exit Method Edit applying the method, then re-enter Method Edit and apply the method again.

The signal-to-noise calculation gives infinity for the S/N calculation and the Noise calculation when the Universal integrator is selected.

None.

Fixed in B.05.01

In Quant, select Help --> Contents.  Under the 'Getting Started' section (purple), click 'View demonstration videos'.  Click on any link to a demonstration video.  The message "'Loading multimedia control' is displayed and no video plays.

n/a

Install Adobe Flash Player.

The target peak is not integrated if ISTD peak is not found.  Attempting to manually integrate the target peak results in the message "Manual integration failed.  Previous integration results restored"

None

n/a

Average RF RSD outlier is flagged in Flat Table view but not Compound Table view.  RF RSD field is also blank Compound Table view.

Use Flat Table layout to check RF RSD status.

n/a

When generating a report for samples with Reference Library Match Score, the Match score is not shown in the spectrum on the report. 

Observed in B.05.00

None

Fixed in B.05.01

Quant fails to extract a SIM spectra.  This results in a blank spectrum in the Sample Information section of Quant and a crash in reporting that results in no report being generated.

None

Fixed in B.05.01

The IQT reference file for the COMPLIANCE module is not available in the QUANT B.05.00 installation

None

Resolved in B.05.00 Service Pack 01.

The audit trail displays Universal as 'Genie' and General as 'RTE'.  The method editor displays 'Universal' and 'General'.

None

Fixed in B.05.01

After altering the library information in the Advanced version of the Unknowns Analysis method editor the new path of gets overwritten with C:\MassHumter\Library

Create the directories C:\MassHunter\Library and copy the library into C:\MassHunter\Library

Fixed in B.05.01

If the same library is specified more than once in the list of libraries then Unknowns Analysis will crash during the library search.

Enter the library only once.

Fixed in B.05.01

Some blank lines  written in the audit trail, on occasion when clicking on the “apply” button after a method change (example - changing the integrator type).

None

Fixed in B.05.01

If a large number of files are loaded into Unknowns Analysis and the user scrolls down the list the application will crash.

Limit number of data files loaded.

Fixed in B.05.01

The maximum number of peaks cannot be activated or retain values.

1)	Open Method for edit
2)	Go to Integration Parameter Setup
3)	Go to Peak Filter
4)	Check “limit to the largest” in the “Maximum number of peaks” section.
5)	Edit the default number in “peaks” from 100 top 5
6)	Click Apply or Apply to All
7)	Click OK
8)	Reopen Integration dialog and check Peak filters’
9)	Values entered are gone (set back to unchecked and 100)Limit number of data files loaded.

None

Fixed in B.05.01

Timed events for integration that are being logged to the Compliance Audit Trail, are not understandable.
Customer wants to know what :MECEND-ECEND-MECALLVALLEY-ECALLVALLEY-MECBASELINE-ECBASELINE  and also  EC , MEC”, mean.
The list on the right should appear in the audit  trail instead:
ECALLVALLEYS   Baseline All Valleys ON  
ECAREAS              Area Sum ON     
ECBACKWARD   Baseline Back     
ECBASELINE        Baseline Next Valley       
ECDISABLE          Solvent Peak OFF             
ECEND  Integrator OFF  
ECHOLD                Baseline Hold ON             
ECIMMEDIATE   Baseline Now    
ECNEGATIVE      Negative Peak ON           
ECREJECT             Area Reject        
ECTANGENT       Tangent Skim     
ECTHRESHOLD   Threshold            
ECWIDTH             Peak Width         
MECALLVALLEYS               Baseline All Valleys OFF 
MECAREAS         Area Sum OFF   
MECDISABLE      Solvent Peak ON              
MECEND              Integrator ON    
MECHOLD           Baseline Hold OFF            
MECNEGATIVE  Negative Peak OFF

None

Fixed in B.05.01

Running the scrip, DownloadMolfiles.txt, will crash the library editor.

Seen in B.05.00

Fixed for B.05.01, but the workaround in B.05.00 is to have the following lines at the top of the script file:

//! 

Fixed in B.05.01

BL Draw column in the batch table is blank.  If Baseline calculation points is checked in Compound Information - Chromatogram properties, no rectangles or lines are displayed in the target chromatogram window.

Data is from the Quant shipping CD:  QTOF/QTOF_4GHz_SulfaQuantTargetedMSMS.  

Seen in B.05.00

None

Fixed in B.05.01

Schema files (.xsd) are missing from the Quant template directories.  They were installed in the B.04 version of the software and are required for some modifications of the templates.

Request .xds files

Fixed in B.05.01

Released B.05.00 (build 291) Japanese , Win 7 SP1 64bit, Excel 2010

1. Generate report
2. select "PDF" as format 
3. PDF report is created. but "\" on batch data path is misprinted. Excel has no problem, so direct printed report has no problem.
4. when I print out "PDF" report,  can see misprinted "\", too.

Print from Excel
Use CuteWriter as PDF driver

Fixed in B.05.01

When selecting Setup/Organize/Overlay None - target Only, the "Fit to Lowest Calibration Level" and "Fit to Highest Calibration Level" functions are not active.
When selecting other Organize options, such as target and qualifier, both functions are ON.

None

Fixed in B.05.01

The noise field is left blank if the integrator fails to detect a peak.  The noise is not even calculated when the method specifies a noise region.

None

n/a

When noise regions are manually designated in the method, the baseline calculation points that designate noise regions for the parameterless integrators remain the same.  In this case, the graphic in the chromatogram window is not correct.

None

n/a

Example of this issue can be seen in the DOA data set in the Blank and Sample1 for Amp.  When no Qualifier peak is found for a compound the report fails to properly VLOOKUP the required graphic because the SampleID, CompoundID, and PeakID fields are blank and thus the key is malformed.  See attached modified report template for one approach that works.   Seems that the key fields from PeakQualifer were used rather than TargetQualifier where the graphic is stored.

Template available on request.

Fixed in B.05.01

Steps to reproduce:
1)	Open DrugsOfAbuse batch
2)	Delete all but 3 samples
3)	Perform IPM on each of the three samples changing Agile to Universal
4)	‘Restore Int Params’ on one sample displays the message --> "Failed to find a sample with unmodified integration method for compound Amp"
 5)	Restore Int Params on the 2nd or 3rd sample --> crash

Observed in B.05.01 Build 307.1 and B.05.00.

None

Fixed in B.05.01

For 2D data only batch, Quant crashes when generating report. Not dependent on Template and can't be avoided by generating report without graphic files.

None

Fixed in B.05.01

batch.results.xsd is required to add new data fields to an existing template and customize the template.

Request file

Fixed in B.05.01

In method editor, select "Show Reference R.T" in compound information property.
Move to next compound  at method table.
Target Peak and Qualifier peak don't show in the center of the window.
Uncheck  "Show Reference R.T".
Target Peak and Qualifier peak show in the center of the window.

Seen in B.05.00

None

Fixed in B.05.01

Changing the 'Retention Time Window CC' units for 'CC Retention Time' outlier, from Percent to Minutes or vice-versa, does not change the outlier range and result after the method is applied and Analyze Batch or Quantitate Batch is done.

Also, when the 'Retention Time Window CC' outlier is clicked in the method, the 'RT Units' column should display along with the 'Retention Time Window CC' column.

Seen in B.05.00

None

Fixed in B.05.01

When the quantifier is set to a zero area with the Zero Peak function it is not treated as “not found” but as a real value of zero and the below  calibration range outlier is activated.

None

n/a

Users wish to use the User annotation field to record comments during data review.  However the data is not protected during a method edit session (edit method, apply) and the comments are lost.  Normal data review practice can easily require a method modification after some comments have been entered.  Seen in B.04.0# and B.05.00.

None

n/a

Re-analyzing a batch after manual integration of a sample does not update the calibration curve.  After clearing calibration then analyzing the batch, the calibration curve is updated.  But the calculated concentration does not agree with the calibration curve equation.  

Seen in B.05.00

None

Fixed in B.05.01

Manually integrate a sample in a batch that is using standard addition, then Analyze Batch.  After the first manual integration, the response in the Calibration Curve pop-up window is updated.  After a second manual integration, the target compound final conc is updated in the batch table, but the response in the Calibration Curve pop-up window remains unchanged.

None

Fixed in B.05.01

For profile data, the manual mass accuracy calculation does not match the mass accuracy displayed in MassHunter Quantitative Analysis.

MassHunter Quantitative Analysis does not support profile data.  Centroid data must be used.

n/a

Revised algorithm results in improved Library Match scores.  Library Match scores in Quant B.05.01 may not be the exact same as in previous versions of Quant.

n/a

Fixed in B.05.01

If a non-MS signal is selected, such as a GC-FID, and the retention time (RT) of the signal is outside the RT range of the MS signal, the method editor validation displays an error message indicating that the retention time is out of the window.

Issue observed in Quant B.04.00 and B.05.00.

Ensure that the MS signal is collected over the RT range of other signals.

Fixed in B.05.01

Prior to MassHunter Quantitative Analysis B.05.01, Report Templates would remain after uninstallation of the Quantitative Analysis Reporting application.
Beginning with MassHunter Quantitative Analysis B.05.01, Report Templates will be removed with uninstallation of the Quantitative Analysis Reporting application.  Customized report templates with file names that are different from the installed templates will remain after uninstallation.

n/a

Report templates from previous versions of MassHunter Quantitative Analysis (prior to B.05.01) will not uninstall.

When 'Add Samples' is done from a particular server location, the samples are not in any particular order.  If the data files are moved to a local drive, 'Add Samples' displays the data files in the order that the files were collected.

Issue seen in B.04.00 SP2

Move files to local drive.

Fixed in B.05.01

ChemStation file was translated using the GCMS Translator.  It can be opened in Qual B.04.00 SP2 without error and all signals can be extracted (FID and SIM).  However if it is added to a Quant batch  it generates the error "There were problems with adding one or more samples: Failed to import sample from worklist"  The issue was found to be an illegal character string in the barcode field that was present in the ChemStation file.  No Barcode reader was installed and the field contained random data.

None.

The B.05.02 Build 1032 of the GCMS Translator will remove illegal characters and fixes this problem.

The Average RF value shown in the method editor does not match the calibration curve graphics (slope) when Average of Response Factors is the selected curve type.   The graphics value is correct and based only on the calibrators.  The value in the method editor includes QCs or CCs.

None.

Fixed in B.05.01

SIM data files are translated to MassHunter format and included in a Quant batch. There are two clear problems. 

1)	The Spectrum area of the Sample Information is blank and the title area reads “Spectrum: Failed to access sample data”

2)	Attempts to generate reports with graphics on fail with by either hanging or give error message.  No Graphics report is generated.

Problem is associated with spectrum graphics.

Problem seen only in B.05.00.  Problem does not exist in B.04.00 SP2.

If only non-graphical reports are required then turn off Graphics generation (uncheck "Generate graphics files" at the top of the "Report graphics files" page in Advanced reporting options).

If graphical reports are required consider down grading to Quant B.04.00 SP2.

Fixed in B.05.01

If using more than one library and using different RT Cal file for different libraries, only one RT Cal file can be chosen in the Library Search window of Method Edit.

None.

Fixed in B.05.01

The User Annotation field is not displayed In Compound Table view.  The User Annotation field is only displayed in Flat Table view.

None

n/a

When method validation is performed on the VolatileOrganics.batch.bin file from the VOA data set, warnings are displayed because some of the MZ extraction window units for the quantifiers are different from the MZ extraction window units for the qualifiers.

n/a

Fixed in B.05.01.  MZ Extraction window units set to Thomsons for all quantifiers and qualifiers.

n/a

n/a

Difference between Mustang-genie and either Qual-Genie or Quant-Genie:  Genie was changed to obtain the same area as all the other MassHunter integrators so manual integration was consistent across integrators (Agile, MS-MS, …).

Difference between Qual-Genie and Qual-Genie:  Peak areas are in the ballpark of each other.   Qual and Quant do not necessarily share the same time or mass windows (RT windows, mass extraction windows).  If those settings are different, they can easily explain the different in areas.

The units on the X axis are different for different integrators in Mustang.  Different units easily explains different values.  In MassHunter  the same X-axis units is used for all integrators.

The issue is observed when the data file contains signals other than MS such as GC or UV.  Normally, if a sample is selected from the batch before entering the method editor, the method editor displays the sample information, such as name and data file name, in the Sample row.  The Quant method editor uses this information to determine what signals are present in the data file.  If an attempt is made to define a GC or UV signal using the Compound 2D Setup menu item found in Advanced Tasks, Quant populates the drop down list under Scan Type with the GC or UV signals.  

However if an existing method is loaded into the method editor, either from a batch or method file, the data file name information in the Sample row is cleared.  This breaks the link to the data file and the drop down list under Scan Type loses the GC or UV signals.  

Problem seen in B.05.00.

Exit the method editor, apply changes, then re-enter the method editor.  The selected sample will be restored as will the drop down list.

n/a

If the selected sample in the batch table is a TuneCheck and an attempt to enter the method editor is made the program will crash.

Avoid entering the method editor on a TuneCheck sample.

Fixed in B.05.01

Setting options to display peaks scaled to lowest or highest calibrator level will be lost when switching samples or compounds in a layout which is doing review by sample or compound.  The setting is a temporary zoom that is not automatically applied each time the grid is reloaded with the next sample or compounds data.  This issue is also seen when the pre-defined or user defined layouts are used and it attempts to set the scale.  It works when initially applied but fails when the next sample or compound is displayed.

None

n/a

If no target peaks are found in all calibration samples, performing Analyze Batch does not rebuild the calibration curve.  The calibration curve that previously existed (if any) is retained.
In this situation, the status bar (lower right) displays “Processed” but the batch table does not reflect results using the current calibration curve.

None

Do Not Fix

With two different CC samples in the same batch,

CC Relative Response Factor and CC Average RF outliers
(1) do not display the expected values, and
(2) the different CC samples display the same outlier results

n/a

Resolved in Quant B.05.01:  Different CC samples in the same batch display the expected values for CC RRF and CC Average RF

MassHunter supports libraries in the .L format however many of the shipping libraries look to see if ChemStation software is installed and if it is not will refuse to install the library.  The following is a list of libraries that will install properly on aMassHunter only system as of March 2012

NIST08
NIST11
Wiley9/NIST08
Wiley9/NIST11
CWA - only available with 5975T Military Bundle
MPW2011

The following is a list of all the libraries that do NOT install with only MassHunter:

Agilent RTL Library Databases			
	G1671AA	Hazardous Chemical RTL Database 
	G1672AA	Pesticide RTL Database Library	
	G1673AA	Indoor Air Toxics RTL Database Library	
	G1674AA	Forensic Toxicology RTL Database 
	G1675AA	JPN Positive List Pesticide RTL Database 
	G1676AA	Fiehn GCMS Metabolomics RTL Library
	G1677AA	Environmental Semi-VOAs RTL Database
	G1678AA	Solvents Plus RTL Database

	G1039D (MPW - 2007 edition)


All other libraries may fail to install.  The libraries are valid and can be searched by MassHunter only the installer fails.

Install the software on a system with ChemStation software installed then locate the .L folder and copy it and its contents to the MassHunter system.  The library should then be functional in MassHunter.

Plans exist to address the install issue on all library installers.  Dates to be determined.

Qualifier ratio outlier does not work for samples of type 'Blank'

None

Fixed in B.05.01

1) Quant displays a batch with accurate mass scores.
2) The pattern reference library that is used in the Quant batch is modified in Library Editor.
3) 'Analyze Batch' in Quant still displays the original accurate mass scores and spectrum.
4) Re-selecting the library in method edit, applying the method, then analyzing batch still displays the original accurate mass scores and spectrum.

1) Save the batch
2) Close the batch
3) Open the batch
4) Analyze Batch
The accurate mass scores and spectrum based on the changed library are displayed.

The library file is cached, so it's a trade-off for performance..

Samples deleted from the original, analyzed batch so only four samples remain.  Sample type changed such that two of the four samples are 'Cal' type and the other two are 'QC' type.  Appropriate level entered for each Cal or QC.  Concentration of one or more Cal samples is not displayed when Analyze Batch is done.

Enter method edit.  Exit method edit applying the method.  Then Analyze Batch displays concentrations for all of the samples.

n/a

The sample field in the header of the batch table dose not display long sample names fully even when there is space in the tool bar.

None

n/a

Audit trail shows integrator’s development name instead of displayed names when Integration Parameters Modified (IPM) is used:
'Universal' displays in the method but 'Genie' displays in the audit trail.
'General' displays in the method but 'RTE' displays in the audit trail.

None

n/a

Audit trail needs the following corrections:
1) Action for 'CmdZeroOutQualifierPeak' says 'Zero out primary peak ...' instead of 'Zero out qualifier peak ...'
2) Name for Append method from CEF file says 'CmdCreateMethodFromCefFile' instead of 'CmdAppendMethodFromCefFile'
3) Name for Append method from library file says 'CmdCreateMethodFromLibrary' instead of 'CmdAppendMethodFromLibrary'
4) Action for Append method from CEF file says 'Create method from CEF file ...' instead of 'Append method from CEF file ...'
5) Action for Append method from library file says 'Create method from library file ...' instead of 'Append method from library file ...'

None

n/a

Average Response Factor Relative Standard Deviation is not calculated correctly if calibration samples of type 'Method' are in the method calibration table.

n/a

Fixed in B.05.01

After exporting Components from Unknowns Analysis to Excel (.csv), some CAS numbers are displayed in date format.  Changing the format of the cell in Excel does not get the original CAS number back.

n/a

Import the file in Excel instead of opening:
1) Open the .csv file in Excel.
2) Click the ‘Data’ tab
3) Under the ‘Get External Data’ section, click ‘From Text’
4) Select the .csv file and click Import.
5) Select ‘Delimited’.  Click Next
6) Select ‘Comma’.  Click Next
7) Select ‘Text’ and select the CAS# column.  Click Finish
8) Select ‘New worksheet’.  Click OK

Number of scans is not displayed in the spectrum of the batch table for DMRM data when a qualifier does not have the same precursor ion as the quantifier in Quant B.05.01

None

n/a

'Create New Method from Acquired MRM Data' does not create a method for dynamic MRM data.  Data is from a 6490 with posneg switching.

This issue is observed in MassHunter Quantitative Analysis but is actually caused by LCMS Acquisition.

Method can be created with generic compound names by removing or renaming the .m file in each data folder.

Final resolution will be in MassHunter Aquisition.