Software Status Bulletin

MassHunter Qual     

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:

Compound Identification and Spectrum Identification Results not sorted properly with m/z selected

Problem:

It is currently the case that the m/z column will sort alphabetically by first digit instead of properly sorting by considering the complete numeric value. 

Temporary Solution:

The Mass column can be used instead which does numerical sorting properly. 

Fix Information:

n/a

Keyword: 

One-line Description:

When using a *.mslibrary.xml which contains retention indices - RI values may appear in the RT(DB) column incorrectly

Problem:

When running a library search in Qual, using a *.mslibrary.xml which contains Retention Indices - it may occur that the RI value is reported in the RT(DB) column of Qual instead of the RT(Tgt) column. Though the value is correct - the value is being displayed in the wrong column.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Send to PCDL cannot handle compounds with apostrophes in the compound name

Problem:

Send to PCDL cannot handle compounds with apostrophes in the compound name

Temporary Solution:

Remove all apostrophes from your compound ID before using the Send To PCDL feature.

Fix Information:

n/a

Keyword: 

One-line Description:

Qual incorrectly reports "lib search" in ID Technique column for MS/MS data files

Problem:

When an (MS/MS) data file is searched against a .csv database, Qual incorrectly indicates that a "lib search" was executed against the data file in the "ID technique" column. This is not possible.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Initiate Quantitation feature is ignoring 'Only highlighted compounds' selection

Problem:

In Qual - you can right-click on the compound table and choose 'Initiate Quantitation'. This will automatically open Quant and create a new method using the compound details from Qual. In the initiate quantitation dialog, there is an option to only include those compounds which are highlighted (selected) in the Qual UI. This setting is being ignored with Qual 10.0. Instead - all compounds are being passed to Quant. 

Temporary Solution:

Once the Quant method has been created - you can simply delete the extra compounds from the method.

Fix Information:

n/a

Keyword: 

One-line Description:

Extra TIC's are being created upon opening a data file with results saved from Navigator B.08 SP1

Problem:

Qual 10.0 has a combined Navigator and Workflows interface. Because of the migration from Qual B.08 of saved results may include stored TICs from either view - if those results are loaded into Qual 10.0 - the UI will include multiple copies of the same TIC. 

Temporary Solution:

As a workaround - once the data files are loaded, on can simply right-click on the extra TICs and choose 'Delete' to remove them. Once the results are re-saved, the issue will not recur.

Fix Information:

n/a

Keyword: 

One-line Description:

Adding a Deuterium to negative ion species adds a "+D", should be "-D"

Problem:

Adding a Deuterium to negative ion species adds a "+D", should be "-D"

Temporary Solution:

There is currently no workaround.

Fix Information:

n/a

Keyword: 

One-line Description:

Library / DB searches not properly indicated for manually extracted spectra

Problem:

When running library / DB searches against manually extracted spectra - the Spectrum ID "Lib/DB" column is not being set if there is only a DB search hit. It should be set either by a library or database hit.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Library/Database search option - "Stop at the first match" is not being applied to database results

Problem:

In the Library/Database search configuration, there is an option to stop the search as soon as the first library or database search hit has been found. There is a known defect where this setting is being ignored for database searches (not library searches). As a result - if multiple databases are configured in the search list - all of them will be evaluated and results returned, even if only the first hit was required. 

Temporary Solution:

n/a

Fix Information:

This issue does not affect GCMS as there is no Database search run on GCMS compounds - only library searches apply.
The only consequence of this defect is that database searches make take longer to process as the software will continue to evaluate all configured databases returning all hits within their respective thresholds.

Keyword: 

One-line Description:

Print only highlighted results is ignored when printing analysis report or custom report

Problem:

The setting "Only highlighted results" is ignored while using a "custom" report or "analysis" report in Qual - instead all results are always included.

This is true for Report Builder PDF reports - not true for Excel based reports.

Temporary Solution:

n/a

Fix Information:

Fixed in a future release of Qual.

Keyword: 

One-line Description:

Error when attempting to extract signals from multiple 2D-LC split data files

Problem:

A user will encounter an error when right-clicking to extract chromatograms when multiple 2D-LC data files are selected in the Qual navigator view. The error will read:

Message: Chromatogram type not implemented

Temporary Solution:

As a workaround - make sure to only "select" or highlight one data file at a time.

Fix Information:

n/a

Keyword: 

One-line Description:

Manual correction or annotation of fragment ions in GCMS NCI data incorrectly calculates positive mode masses

Problem:

When building a PCDL from NCI QTOF data using Qual B.08 and 10 - automatic fragment formula annotation assigns correct negative formulas and corresponding theoretical masses to the observed ions.

However - if the user corrects an automatic annotation or annotates an unannotated peak - the m/z value is calculated based on a M+ ion mass, not a M- ion mass as it should. This causes a ppm error consistant with the mass of 2 electrons being incorrectly added to the fragment mass.

Example workflow:
1.Extract a background subtracted spectrum
2.Add/Edit Manual Identification – insert cpd name, formula and CAS number
3.Right-click on the annotated spectrum – Edit peak annotations
4.Add M-, formula, and select “Fragment ion”
5.Right click – Send to PCDL

The resulting m/z masses in the PCDL (and displayed in Qual) are incorrectly based on a M+ ion instead of a M- ion. 

Temporary Solution:

If you choose to send the observed mass instead of the theoretical mass - the incorrect mass will not be transferred to the PCDL. This issue will not be observed in the PCDL because the fragment molecular formulas are still correct.

Fix Information:

n/a

Keyword: 

One-line Description:

Find by Formula will use negative spectral entries even when searching against only positive mode data

Problem:

Qual does not pre-filter a PCDL containing both positive mode and negative mode spectra based on polarity when searching against a single polarity data file. 

For example - if a PCDL contains an entry with negative only spectra - even when running Find by Formula on a positive only data file - one might find matches/hits for that negative only entry.

Temporary Solution:

One option would be to create a positive only or negative only subset PCDL. You can do this easily by using PCDL Manager to run a search based on ion polarity - then create a subset PCDL with the results. 

Fix Information:

n/a

Keyword: 

One-line Description:

296051 - Compound spectrum has mislabeled charge carrier in report graphics - correct in report tables and UI graphics/tables

Problem:

It has been observed in a specific data file provided by a customer that when running molecular formula generator on AutoMSMS results, a report can be generated where incorrect charge carrier labels appear in the compound spectrum. 

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

MFG not suggesting expected formulae containing halogens

Problem:

There are a number of cases where Qual's MFG formula calculator does not suggest an expected formula - particularly for formulae containing halogens. 

Temporary Solution:

In cases where expected formulae are not being suggested by MFG - it may yield better results to "zoom in" to the specific spectral peaks of interest, highlight only those peaks - then right click -> Identify. With specific peaks selected, Qual will be less likely to be "thrown" by other peaks nearby that would cause MFG to be led away from the target formula of interest. 

Fix Information:

n/a

Keyword: 

One-line Description:

300298 - Creating a MS/MS inclusions list (any kind) will not work from a MS/MS file when the results have been filtered for only highlighted compounds

Problem:

A defect has been found in the Export MS/MS Inclusion list function where exporting fails with the error "No suitable results found to export to MSMS inclusion list".

This occurs when "Only Highlighted Compounds" is selected in the Method Editor -> Export -> MS/MS Inclusion -> Results tab visible in the "compounds view" of Qualitative Analysis.

 

Temporary Solution:

Use the "All Compounds" radio button to export all compounds. 

If only a subset of compounds is desired one can delete the unwanted compounds from the compound list, then run the export.

Fix Information:

n/a

Keyword: 

One-line Description:

Qual's molecular formula generator assumes too low of a resolving power for 7250 GC QTOF - increases mass error of MFG results

Problem:

The molecular formula generator is not able to calculate isotopic distributions assuming the higher resolving power available to the 7250 GC QTOF. As such - while the instrument has a resolving power of 32000 in some cases, Qual's MFG calculator assumes a maximum of 10000. This causes isotope patterns to be miscalculated by Qual and can lead to increased mass error for specific isotopic distributions.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

 Calculating signal to noise causes Qual to re-integrate the chromatogram - which throws away manual integration

Problem:

Re-integrating a chromatogram causes Qual to discard manual integrations. This is also triggered when one clicks the "calculate Signal-to-Noise" button in the method editor or the chromatogram's "right-click" contextual menu. 

This presents a challenge when one wants to calculate signal-to-noise ratios of manually integrated peaks. 
 

Temporary Solution:

The workaround is to integrate the chromatogram, click the "calculate Signal-to-Noise" option, then perform any manual integrations. Manual integrations will immediately update the corresponding peaks' Signal-to-noise ratio without needing to click "calculate Signal-to-Noise".

Fix Information:

n/a

Keyword: 

One-line Description:

Unit Mass data shows 4 digits of mass precision instead of 2 in mass spectral labels

Problem:

A defect has been found which causes unit mass data (Tandem Quad and Single Quad) data to have mass labels with 4 digits of precision after the decimal instead of the expected 2 digits. With Qual 13 - and the removal of Excel based reporting - there is no longer a viable workaround to generating graphics with the correct number of digits. 

Temporary Solution:

As an alternative - Unknowns Analysis (a tool that installs with Quant) - may be able to accomplish your workflow needs and offer the reporting output required. Contact your Agilent support representative to see if Unknowns Analysis can work for you.

Fix Information:

n/a

Keyword: 

One-line Description:

Saturation flag on integrated TIC peak list using Agile2 is not accurate

Problem:

It is currently the case that the Agile2 integrator will flag any integrated peak whose response counts are greater than 10^6, irrespective of the instrument model, acquisition rate, or other critical factors which would impact the true saturation of the detector. 

As such - one should ignore the "S" saturation column in the chromatogram integration peak list table when running the Agile2 integrator.

The saturation * (asterisk) which appears on peaks within MS spectra and the corresponding "S" in the "Saturation" column of the MS peak list continue to be accurate and properly reflect saturation. 

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

User defined fields not available in Qual's Report Builder

Problem:

Qual's implementation of Report Builder does not make available the User Defined fields from the Acquisition sample table.

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Exporting Graphics doesn't support plot setting

Problem:

In Chromatogram Display Options, plot parameter changed to "Pattern" as the user want to show only "monochrome" in chromatogram.
Chromatogram's display is changed to "monochrome" in the screen.
The user tries to export this screen to metafile by exporting function.
But the graphics in the exported metafile is not "monochrome" instead still a color choromatogram.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Peak Label "Resolution" null if data extracted as "profile when available otherwise centroid"

Problem:

If a file contains both profile and centroid data and the extraction data format set to "Profile when available, otherwise Centroid" and a spectrum is created it appears in profile. But the peak label Resolution is blank. If the same spectrum is created while the extraction data format set to "Profile only" the Resolution Mass Peak Label is filled in.

Temporary Solution:

Use the "Profile only" option to have resolution properly populated.

Fix Information:

n/a

Keyword: 

One-line Description:

All Ions MS/MS (AIM) - Visualization in the Compound Fragment Spectrum Results window in Compound Details View (CDV) is incorrect

Problem:

a) The default zoom range in the x-axis is currently not limited, for target compounds, to the mass of the highest selected adduct species multiplied by the charge state plus 20.
b) The red isotopic pattern boxes are incorrectly drawn with a factor of 20 too high.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

When running Find By Deconvolution on a SIM/Scan file, Qual combines both SIM and Scan data in its visualization rather than displaying SIM and Scan separately.

Problem:

When running Find By Deconvolution on a SIM/Scan file, Qual combines both SIM and Scan data in its visualization rather than displaying SIM and Scan separately.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

The pusher offset (not puller offset) value is not displayed in the MSActuals for data acquired on a 6560.

Problem:

The pusher offset (not puller offset) value is not displayed in the View -> MS Actuals panel for data acquired on a 6560.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Data files acquired with different storage settings (Profile/Centroid/Both) in different time segments confuse Qual - may not extract compounds

Problem:

Qual's detection logic for determining what kinds of data are present in the data file assumes that the storage type chosen by the user (in the acquisition method, centroid/profile/both) is the same across all time segments. When that isn't true - the "Find by" algorithms may fail to find compounds in one or more time segments.

Temporary Solution:

It is recommended to use the same storage setting across all time segments in the data file.

Fix Information:

n/a

Keyword: 

One-line Description:

The "Min m/z for matching" algorythm does not behave as intended and implemented in Quant.

Problem:

The behavior of the  "Min m/z for matching" is not working as needed for matching as implemented in Quant.  In Quant, the software looks at both the sample spectrum and the library spectrum and determines the minimum m/z in BOTH spectra which it uses to drive the matching function.  The user can increase the m/z via the interface to make it even higher but not make it lower.  In Qual, it can be set to a value in the method that is something less that the min seen in both sample and this results in a library spectra resulting in false negatives.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

"Integration Off" Event in ChemStation Integrator causes Find by Formula to fail

Problem:

If a user attempts to use the ChemStation integrator while performing any Find by Formula operation - an "Integrator Off" entry in the integrator events table will result in zero compounds found by FbF.

Temporary Solution:

Use any other integrator - or do not turn off the integrator while running FbF with the ChemStation integrator.

Fix Information:

n/a

Keyword: 

One-line Description:

Qual applies MS peak filters when manually integrating non-MS signals

Problem:

Normally - the integration of non-MS chromatograms is controlled by the Integrate (UV) or Integrate (GC) sections of the method editor. This includes things like peak filters and the maximum number of integrated peaks.

A defect has been discovered, however, that once a manual integration is applied to a non-MS chromatogram, the method parameters defined in the Integrate (MS) section of the method editor are applied. 

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Unexpected jump in area counts as manual integration is adjusted - within the General integrator

Problem:

A defect has been discovered in Qual where minuscule adjustments to the integration of a peak using the manual integration tools (comparing to General integrator results) would lead to unexpectedly large changes in the overall peak area. 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Suitability - Number of Plates - Calculations do not match Qual help definition

Problem:

When Suitability is enabled the values do not match expected values based on formula in Help. 

Temporary Solution:

None

Fix Information:

n/a

Keyword: 

One-line Description:

For GC/MS QTOF data - "Frag" refers to source ionization energy and should be in eV, not "V"

Problem:

The "Frag" label in GCMS QTOF spectra incorrectly reports a voltage rather than the electron energy actually involved in the GCMS source. The units should be in "eV" not "V".

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Qual system suitability calculating peaks with negative resolution

Problem:

In some specific cases - Qual may (when calculating the resolution of chromatographic peaks using the USP method) produce resolution values which are negative. This has been observed only in data files with particularly jagged chromatograms. 

The issue is caused by the integrator being confused by the jagged peaks which causes the software to incorrectly calculate the peak width as a negative number. Then the resulting resolution is also negative.

Temporary Solution:

A simple workaround is to apply gaussian smoothing to the chromatogram. Once smoothed - the integrator has no issue calculating the correct values for resolution.

Fix Information:

n/a

Keyword: 

One-line Description:

Initiate Quant launches Classic Quant UI

Problem:

The "Initiate Quant" feature is launching the "Classic" Quant interface instead of the newer Quant-My-Way interface. 

Temporary Solution:

After Quant's "Classic" interface is launched, and the batch automatically created, simply close Quant and save the batch. Next - launch Quant's "Quant-My-Way" interface and re-open the saved batch.

Fix Information:

This has been fixed in Qual 13.0. Qual will now trigger Quant's "Quant My Way" interface going forward.

Keyword: 

One-line Description:

MFE will not find compounds in Profile Only 6546 (10 GHz) data - centroid required

Problem:

MFE requires centroid data to operate. If only profile data is available - MFE would normally re-calculate the centroid data on the fly without any user interaction. 

However - a defect exists where MFE will not do this on-the-fly calculation for 10 GHz data (e.g. data acquired on a 6546 QTOF).

Temporary Solution:

As a temporary solution - one can use the AgtTofReprocessUi.exe tool to manually centroid the data before opening it in Qual. This tool can be found in this folder:

C:\Program Files\Agilent\MassHunter\Workstation\Qual\xx.x\Bin

Fix Information:

n/a

Keyword: 

One-line Description:

Retention Index (Lib) values incorrect

Problem:

A defect has been found in Qual which caused the retention index values displayed in the RI (Lib) column incorrectly. Expected values such as 1564 would appear as "2", for example.

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

GCMS - RT values populated in Qual's compound list even when library does not contain RT values

Problem:

A defect was discovered which caused Qual to display RT values populated into the RT (Lib/DB) column even when the library itself contained no RT values (and no RI to RT calibration file is provided). 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Some UV signal containing data files are not recognized by Qual as containing UV data

Problem:

In some cases - Qual will fail to recognize that a data file contains a UV signal - and will therefore not display UV signal related method sections like "Integrate (UV)". 

Temporary Solution:

As a workaround - one can force Qual to display the UV signal method sections by checking the "UV" box in the "Configuration" -> "User Interface Configuration..." dialog. This can be seen once "Configuration" -> "Show Advanced Settings" option is checked.

Fix Information:

n/a

Keyword: 

One-line Description:

Qual's saved results can take a very long time to load, a lot of space on disk

Problem:

Users have observed that running a library search on some data and saving those results to the data file can cause the data file to grow in size dramatically (on the order of 500% larger). In addition - loading these saved results can take longer than rerunning the library search workflow. 

Temporary Solution:

The issue appears only to be impacting GCMS SQ users. It has been determined that a few method adjustments can greatly improve loading times and data file sizes. 

1.) The default GCMS SQ acquisition method uses "0" for the acquisition threshold. This is too low and generally collects too much noise for efficient library searching. The recommendation is to set an appropriate non-zero value consistent with the noise level for your detector. 50 is a reasonable starting point for most cases. 
2.) Re-creating the Qual method from the default-GCMS-SQ.m method (while keeping the same workflow and parameter settings), particularly when using methods "upgraded" from earlier versions of Qual - has been shown to greatly improve the loading time issue.

Fix Information:

n/a

Keyword: 

One-line Description:

Qual crash when generating an overlaid chromatogram graphic using report builder

Problem:

In Qual - it is possible to overlay two chromatograms from two different data files. However - if you attempt to print that overlay (by right-clicking on the chromatogram and selecting Print) - and you have the Report Builder set in the method - Qual will crash with an error "Exception: Unbalanced save/restore state operators."

Temporary Solution:

If one switches to Excel based reporting - the overlaid chromatogram graphic will work without error.

Fix Information:

This has been fixed in Qual 12 - and overlaid reports from multiple files can be generated.

Keyword: 

One-line Description:

Defined chromatograms are modified when loading different data file types

Problem:

If the user has positive and negative chromatograms defined in the "additional chromatograms" section of the method editor, and the user loads a data file containing only positive data, Qual will change the defined chromatograms to include only positive polarity signals. 

Temporary Solution:

One should use a method only for the specific type of data that method should process. Use a method for only Positive data, another method for negative data, and a third method for mixed data.

Fix Information:

n/a

Keyword: 

One-line Description:

Find by Formula method setting causing match tolerance values to change on data file load

Problem:

In Qual's Find by Formula method editor, under "Formula Matching" (only visible when Configuration -> Show Advanced Settings is selected), one can choose a match tolerance setting for "Masses" as +/- X in mDa or in ppm. 

If the user selects ppm - AND chooses "Symmetric (m/z)" in the "Possible m/z" section of the same method page - the mDa setting will revert to ppm when an accurate mass data file is loaded. 

Temporary Solution:

To prevent this from happening - make sure to set the "Possible m/z" value to Symmetric (ppm) instead of Symmetric (m/z).

Fix Information:

n/a

Keyword: 

One-line Description:

Saving MFG results of 6546 data leads to error "Results set exceeds operating system limits. Please reduce the result set and try again."

Problem:

Some users have reported that when using 6546 data with Qual's molecular formula generator algorithm - if one does not apply a limit to the "maximum number of hits per charge carrier" - Qual may throw an error when attempting to save those results.

Temporary Solution:

One can reduce the likelihood of this error by applying a reasonable limit to the number of formulas generated for each compound. The default method has this limit set to 5. 

Fix Information:

n/a

Keyword: 

One-line Description:

Qual generates MSMS inclusion list in an unacceptable format for MassHunter QTOF Acquisition

Problem:

A defect has been discovered in the way QTOF Acquisition parses the MS/MS inclusion list generated by Qual. The defect is such that the imported CSV will produce nonsense precursors masses as displayed in Acquisition which at first glance appear as though too many digits are being displayed in the precursor mass box. This is not the case - the values are simply incorrect.

Temporary Solution:

As a workaround - one can manually edit the exported CSV file in notepad and simply delete the first row which reads "TargetedMSMSTable". Once deleted such that the first row contains the proper headers for the table, the file will be properly imported in Acquisition. 

Fix Information:

n/a

Keyword: 

One-line Description:

Export all integration results to CSV is skipping ELSD signals

Problem:

The feature to export all integration results to CSV is skipping ELSD signal types. This feature is available under Actions -> Export all integration results to CSV.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Find by Formula returns only one polarity when feature finding in Fast Polarity Switching data.

Problem:

With Fast Polarity Switching data, MFE followed by a database search returns compound results for both polarities. FBF shows only one result per compound for only one polarity. 

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Cannot calculae both Signal-to-Noise and System Suitability at the same time

Problem:

A defect was found which caused Qual to clear the system suitability calculations (plates, resolution, tailing factor) whenever signal-to-noise was calculated - making it impossible to calculate both at the same time.

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Only report qualified compounds setting of Find by Formula missing from FBF section of the method editor

Problem:

The "Only report qualified compounds" setting - which is a feature of Find by Formula - controls if a compound not found is included in the Compound List.

This important setting is visible ONLY when the "Method Automation" -> "Workflow" -> setting is set to "Target/Suspect Screening", and NOT when set to "Custom" even though the "Custom" workflow might have "Find by Formula" included in the actions list.  

Temporary Solution:

As a workaround - the user can toggle this setting with "Target/Suspect Screening" selected in the Workflow drop down - then revert the dropdown to "Custom" after making the desired choice. It will have effect even when Find by Formula is triggered as part of a custom workflow.

Fix Information:

n/a

Keyword: 

One-line Description:

Correlate UV Chromatograms with Compounds crashes when FBF is run with a compound not found

Problem:

When running Find by Formula - and you have the setting "Only report qualified compounds" unchecked, then Qual will include in the Compound List ALL compounds searched, not just those found. If the action "Correlate UV Chromatograms with Compounds" is run on compounds which have not been found - it will crash with error "object reference not set to an instance of an object".

Temporary Solution:

Either do not attempt to correlated UV chromatograms with compounds not found - or do not include compounds not found in the compound list by checking the option "Report only qualified compounds".

Fix Information:

n/a

Keyword: 

One-line Description:

While TQ Acquisition allows ELSD signals to be acquired - Qual cannot yet extract them

Problem:

We are slowly introducing support for ELSD with MassHunter. The first step is to enable data acquisition to acquire said detector signals. The second step will be enabling the data analysis software to extract these signals from said data. Qual has not yet implemented ELSD signal extraction support. 

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Workaround for missing DAD2 signal name in Qual's method editor - allows routine processing of 2D-LC data files

Problem:

In Qual – once you have the 2D data files loaded, use the “Actions -> Extract All Non-MS chromatograms” feature. This will extract all possible signals from the data files. 

Next, right-click on one extracted chromatogram and choose -> “Use Highlighted Chromatogram” -> “Copy definitions to method”. This will add the signal definitions to the “additional chromatograms” section of the method. 

One might encounter an error when clicking in the “Additional chromatograms” window – but if you ignore the error, save the method, you can routinely extract these signals from all data files as part of a method workflow. 

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

non-MS chromatograms missing noise region display in chromatogram graphics

Problem:

A defect was discovered which causes the noise region to not be displayed in chromatograms for non-MS signals (UV and GC). 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Export destination path selection not honoring folders created during folder browsing operation

Problem:

In Qual's Method Editor: Export area, under "Export Destination" - the user can define a path for where the exports will be written. The "..." elipses file browser allows you to create new folders on the local file system. If the user creates a new folder within the browser, and then selects the new folder in the browser, and then clicks "OK" to close the browser - even though the new folder's path is displayed in the Export destination field - it will be ignored, and the previously defined path will be used. 

Temporary Solution:

After creating the new folder in the browse dialog - close the dialog. Then re-enter the browse dialog by hitting the ellipses button "..." and select the newly created folder again. The limitation is only that you cannot select a folder created in the same browser session.

Fix Information:

n/a

Keyword: 

One-line Description:

 Calculating signal to noise causes Qual to re-integrate the chromatogram - which throws away manual integration

Problem:

Re-integrating a chromatogram causes Qual to discard manual integrations. This is also triggered when one clicks the "calculate Signal-to-Noise" button in the method editor or the chromatogram's "right-click" contextual menu. 

This presents a challenge when one wants to calculate signal-to-noise ratios of manually integrated peaks. 
 

Temporary Solution:

The workaround is to integrate the chromatogram, click the "calculate Signal-to-Noise" option, then perform any manual integrations. Manual integrations will immediately update the corresponding peaks' Signal-to-noise ratio without needing to click "calculate Signal-to-Noise".

Fix Information:

n/a

Keyword: 

One-line Description:

Extracted spectra saved with Qual results are modified from original when restored

Problem:

A defect has been discovered which causes extracted spectra saved with the data file to be modified when those saved results are then reloaded. Specifically - restored spectra would be reconstructed without regard to if the spectrum was originally extracted as an average spectrum or apex spectrum. Also saturation excluded TOF spectra were ignored during the spectrum reconstruction. 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Find by Formula will use negative spectral entries even when searching against only positive mode data

Problem:

Qual does not pre-filter a PCDL containing both positive mode and negative mode spectra based on polarity when searching against a single polarity data file. 

For example - if a PCDL contains an entry with negative only spectra - even when running Find by Formula on a positive only data file - one might find matches/hits for that negative only entry.

Temporary Solution:

One option would be to create a positive only or negative only subset PCDL. You can do this easily by using PCDL Manager to run a search based on ion polarity - then create a subset PCDL with the results. 

Fix Information:

n/a

Keyword: 

One-line Description:

Unit mass data EIC extraction can produce slightly different chromatograms depending on the number of chromatograms being extracted at a time

Problem:

A defect was discovered impacting all versions of Qual prior to 13 which can impact the content of EIC (extracted ion chromatograms) extracted from unit mass data acquired and extracted in "Profile" format. "Centroid" data is not impacted. Also, accurate mass (QTOF/TOF) data is not impacted. 

The defect causes the abundances of the EIC extracted to be dependent on the set of extracted ion chromatograms being extracted at a given time. In such cases, if an EIC of, say, mass 1430.9 is extracted alone - that EIC may have a different integrated area than if the same EIC is extracted while other EICs are being extracted at the same time. 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Find by Fragment (GCQTOF) RT(Score) value not necessarily calculated based on the closest peak in RT

Problem:

In the event where two or more isomers are being evaluated as candidates by the Find by Fragment routine - when the method setting "Assign components with the same formula and RT to a single compound" is checked (enabled) - the RT (Score) will be calculated based on the difference in RT between the Target and the peak closest in RT - not the peak chosen as "best" by the Find by Fragment spectral evaluation. If the isomer peak farther away in RT from RT (Target) is selected as "best" - the RT (Score) value will have been based on the incorrect peak.

Temporary Solution:

Disable the option "Assign components with the same formula and RT to a single compound". Doing so will cause Qual to not group isomers together as a single compound and thereby not lead to the misleading RT(Score) value.

Fix Information:

n/a

Keyword: 

One-line Description:

Error when attempting to extract signals from multiple 2D-LC split data files

Problem:

A user will encounter an error when right-clicking to extract chromatograms when multiple 2D-LC data files are selected in the Qual navigator view. The error will read:

Message: Chromatogram type not implemented

Temporary Solution:

As a workaround - make sure to only "select" or highlight one data file at a time.

Fix Information:

n/a

Keyword: 

One-line Description:

TQ 12's tMRM spectrum window real-time plot is labelled as "dMRM" even while acquiring tMRM compounds

Problem:

In MassHunter Acq 12 for LC/MS TQ - the realtime plot which displays live data from the MS - labels the tMRM spectrum as dMRM. This does not impact the quality of the tMRM data. 

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

Find by Formula ion annotations in CEF export occasionally incorrect

Problem:

It has been observed that some ion annotations (adduct type and isotopologue notation) are incorrect in CEF files exported by Qual following Find by Formula results.

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Report builder x-axis misalignment between observed and library spectrum

Problem:

A defect was discovered in Qual 12 which caused Report Builder to generate MS(1) and MS(2) spectra using different x-axis scaling from the corresponding library spectra making it difficult to compare the two. 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Find by Formula method setting causing match tolerance values to change on data file load

Problem:

In Qual's Find by Formula method editor, under "Formula Matching" (only visible when Configuration -> Show Advanced Settings is selected), one can choose a match tolerance setting for "Masses" as +/- X in mDa or in ppm. 

If the user selects ppm - AND chooses "Symmetric (m/z)" in the "Possible m/z" section of the same method page - the mDa setting will revert to ppm when an accurate mass data file is loaded. 

Temporary Solution:

To prevent this from happening - make sure to set the "Possible m/z" value to Symmetric (ppm) instead of Symmetric (m/z).

Fix Information:

n/a

Keyword: 

One-line Description:

"Amino acid" caliper tool is non-functional in Qual B.08 through 12.0. Throws error "chemical data dictionary not found". 

Problem:

"Amino acid" caliper tool is non-functional in Qual B.08 through 12.0. Throws error "chemical data dictionary not found". 

Temporary Solution:

Copy datadictionarypreset_peptide.xml from the installation binary folder of BioConfirm 12.0 or 12.1 into the installation binary folder of Qual 12.0.  This will require Windows Administrator privileges.

BioConfirm 12.1's installation home binary folder is fixed to the following:
(just replace "12.1" with "12.0" for BC 12.0)

C:\Program Files\Agilent\MassHunter\Workstation\Bioconfirm\12.1\Bin

Qual 12.0's binary installation folder is by default the following, but can be changed in the installer:

C:\Program Files\Agilent\MassHunter\Workstation\Qual\12.0\Bin

If you have trouble locating the installation home folder for Qual 12.0, check the following registry key:

HKEY_LOCAL_MACHINE\SOFTWARE\Agilent\MassHunter\Workstation\Qual\12.0

The "Home" value contains the installation home folder; the binary folder is a subfolder of that called "bin".

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

MGF exports not working in Mascot software

Problem:

A defect was discovered in the MGF export which prevented its use within the Mascot software. 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0 with the addition of a new "Use Mascot format" option in the Export MGF Options dialog. 

Keyword: 

One-line Description:

Identify Selected Spectra performing MS2-type library searches on MS(1) spectra

Problem:

A defect was discovered where MS(2)-type product ion library searches were being performed on MS(1) spectra. 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0 so that for Library Searches can be performed on any level of GC-MS data - but can only be performed on MS(2) LCMS data. 

Keyword: 

One-line Description:

CAS Numbers not imported from .d data file into Compound Table when running Find by MRM

Problem:

A defect has been discovered which causes the CAS values recorded with the Acquisition method to not be parsed and displayed in Qual's Compound Table when running Find by MRM. 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Report Builder crash: CpdFragSpec DataItem unexpectedly null

Problem:

A crash has been observed in Report Builder when running Find by Auto MS/MS with library search results included. The crash seen includes the error "Exception: CpdFragSpec DataItem unexpectedly null". 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Running a database search on Find by formula results causes all identifications to be removed from the compound list

Problem:

A defect was introduced in Qual 12.0 Update 1 which causes identification information applied by the Find by Formula algorithm to be removed when performing a database search on those results. 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 13.0.

Keyword: 

One-line Description:

Manual Integration always uses "General" integrator - leads to unexpected changes in integration

Problem:

Whenever a peak's integration is adjusted via manual integration - the software will switch to the "General" integrator for that peak. Because each integrator performs integration differently - this change may lead to significant and unexpected changes in peak area, width, or other integrated values if the automatic integration was performed by any other integrator (like Agile2). 

Additionally - a defect has been found which causes the widths of other peaks in the same chromatogram to be set to zero.

Temporary Solution:

If all integrations are performed using the "General" integrator - the integrated results will not be unexpectedly different when comparing automatic integrations versus manual integrations.

Fix Information:

n/a

Keyword: 

One-line Description:

Manual Integration always uses "General" integrator - leads to unexpected changes in integration

Problem:

Whenever a peak's integration is adjusted via manual integration - the software will switch to the "General" integrator for that peak. Because each integrator performs integration differently - this change may lead to significant and unexpected changes in peak area, width, or other integrated values if the automatic integration was performed by any other integrator (like Agile2). 

Additionally - a defect has been found which causes the widths of other peaks in the same chromatogram to be set to zero.

Temporary Solution:

If all integrations are performed using the "General" integrator - the integrated results will not be unexpectedly different when comparing automatic integrations versus manual integrations.

Fix Information:

This behavior remains as described in the problem description - but the online help was updated to describe this behavior in Qual 13.0.

Keyword: 

One-line Description:

Manual Integration always uses "General" integrator - leads to unexpected changes in integration

Problem:

Whenever a peak's integration is adjusted via manual integration - the software will switch to the "General" integrator for that peak. Because each integrator performs integration differently - this change may lead to significant and unexpected changes in peak area, width, or other integrated values if the automatic integration was performed by any other integrator (like Agile2). 

Additionally - a defect has been found which causes the widths of other peaks in the same chromatogram to be set to zero.

Temporary Solution:

If all integrations are performed using the "General" integrator - the integrated results will not be unexpectedly different when comparing automatic integrations versus manual integrations.

Fix Information:

n/a

Keyword: 

One-line Description:

Qual 13 installer does not allow user to change installation path

Problem:

The Qual 13 installer no longer allows the user to change the program's installation path. 

Temporary Solution:

One can use Symbolic Links to redirect the default installation path to the preferred location. Read more about Symbolic Links here: https://www.howtogeek.com/16226/complete-guide-to-symbolic-links-symlinks-on-windows-or-linux/ 

Fix Information:

n/a

Keyword: 

One-line Description:

Unable to select DAD1 in "additional Chromatograms" Qual 13

Problem:

In the Qual method editor -> Additional chromatograms, when certain LC data files are loaded, the "Other Chromatograms" selection boxes may become unstable, preventing the user from selecting otherwise valid signals. 

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 14.

Keyword: 

One-line Description:

The "Workflow Report" button in the Qual ribbon does not generate valid "report.xml" and EMF graphics

Problem:

The Qual feature to "generate graphics and report.xml files" at a specified location does not happen correctly when clicking the "Workflow Report" button in the Qual ribbon. This feature works properly using the "Print Workflow Report" button in the Qual method editor.

Temporary Solution:

Use the "Print Workflow Report" button in the Qual method editor (or as part of DA Automation) to "Generate graphics and report.xml files" at the specified location. 

Fix Information:

n/a

Keyword: 

One-line Description:

"Qual" tab under Acquisition "DA" method section missing if Qual installed before Acquisition

Problem:

When Qual 13 is installed before MassHunter Acquisition, the user will not be able to find the "Qual" tab in Acquisition's DA section of its method editor. It is expected that one must "Repair" Qual to resolve this issue if the software is installed in this order. However - a defect has been found in Qual 13 where simply repairing Qual does not resolve the missing DA tab. 

Temporary Solution:

The issue is resolved by reinstalling Qual 13. Do this by removing Qual 13 via Windows Control Panel and then re-running the Qual 13 installer. Only Uninstall Qual 13 proper. It is not necessary to uninstall any OpenLab Shared Services components. 

Fix Information:

n/a

Keyword: 

One-line Description:

Missing application icon in Windows Task Bar

Problem:

It has been observed that the icon for Qual will be missing and appear as a default placeholder in the Windows Task Bar. This has no impact on the functionality of the software.

Temporary Solution:

n/a

Fix Information:

n/a

Keyword: 

One-line Description:

'Manual integration' permission not being enforced in Qual 13

Problem:

The "Manual integration" permission in Qual 13 is not being enforced. The user can perform manual integrations regardless of whether the permission is granted or not.

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 14.

Keyword: 

One-line Description:

'Report options' permission not being enforced in Qual 13

Problem:

The "Report options" permission in Qual 13 is not being enforced. The user can manipulate the report option 'Generate graphics and Report.xml files' setting regardless of whether the permission is granted or not.

Temporary Solution:

n/a

Fix Information:

Fixed in Qual 14.

Keyword: 

One-line Description:

GC-only data file causes Qual to display empty Chromatogram Display Options window

Problem:

A defect has been found which will cause the Chromatogram Display Options window to appear empty when a GC-only data file is loaded (one which contains no MS data). 

Temporary Solution:

As a workaround - one can modify Qual's "User Interface Configuration" to add an MS (check the MS box) which will temporarily address the issue. The User Interface configuration is displayed only when "Advanced Settings" is checked under the "Configuration" section of the Qual 13 ribbon or Qual 12 and prior menu bar.

Fix Information:

n/a

Keyword: 

One-line Description:

Adjust Delay Time feature causes compound EIC peak integration to be shifted, incorrect

Problem:

The Adjust Delay Time feature aligns signals from different detectors within a data file so that a given peak appears at the same retention time (RT) across all signals. This is achieved by shifting each signal’s X-axis relative to the earliest signal in the flow path.

However, a defect has been identified in the integration of Extracted Ion Chromatograms (EICs) generated by feature-finding algorithms (such as Find by Molecular Feature). The integration start and stop points are calculated using the original, non-shifted data, resulting in incorrectly integrated EICs when Adjust Delay Time has been applied.

Temporary Solution:

n/a

Fix Information:

n/a