1) The user opened "Test1.D" file and integrated the TIC.
2) Then the user used the "AdjustPeakThreshold" to lower the line close to the xaxis so that all the peaks are labelled.
3) The user first got an exception and the exe disappeared.
4) The user again tried the same experiment and got the following error.

Date and Time: 2/7/2007  11:43 AM
Program: Agilent MassHunter Workstation Software Qualitative Analysis	B.01.02
Build Configuration: Debug
Message: Value must be a number >= 0
Stack Trace: 
Server stack trace: 
   at Agilent.MassSpectrometry.DataAnalysis.DoubleParameter.set_Value(Double value) in y:\Archer\core\CoreTypes\Parameters\parameter_double.cs:line 656
   at Agilent.MassSpectrometry.DataAnalysis.PSetChromPeakFilter.set_DisplayThreshold(Double value) in y:\Archer\core\CoreTypes\Parameters\pspl_sources\parameterset_peakfilters.cs:line 394
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.CmdSetPeakDisplayThreshold.DoSpecialized() in y:\Archer\qual\applogic\applogic\Commands\CmdSetPeakDisplayThreshold.cs:line 122
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualCommandBase.Do() in y:\Archer\qual\applogic\applogic\QualCommandBase.cs:line 717
   at Agilent.MassSpectrometry.CommandModel.CommandHistory.Invoke(ICommand cmd) in y:\Archer\core\Command\commandmodel\commandhistory.cs:line 277
   at System.Runtime.Remoting.Messaging.StackBuilderSink._PrivateProcessMessage(IntPtr md, Object[] args, Object server, Int32 methodPtr, Boolean fExecuteInContext, Object[]& outArgs)
   at System.Runtime.Remoting.Messaging.StackBuilderSink.PrivateProcessMessage(RuntimeMethodHandle md, Object[] args, Object server, Int32 methodPtr, Boolean fExecuteInContext, Object[]& outArgs)
   at System.Runtime.Remoting.Messaging.StackBuilderSink.AsyncProcessMessage(IMessage msg, IMessageSink replySink)

Exception rethrown at [0]: 
   at System.Runtime.Remoting.Proxies.RealProxy.EndInvokeHelper(Message reqMsg, Boolean bProxyCase)
   at System.Runtime.Remoting.Proxies.RemotingProxy.Invoke(Object NotUsed, MessageData& msgData)
   at Agilent.MassSpectrometry.CommandModel.CommandHistory.InvokeCommand.EndInvoke(IAsyncResult result)
   at Agilent.MassSpectrometry.CommandModel.CommandHistory.EndInvoke(IAsyncResult result) in y:\Archer\core\Command\commandmodel\commandhistory.cs:line 393
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.AppManager.EndInvoke(IAsyncResult result) in y:\Archer\qual\applogic\applogic\appdatamanager.cs:line 1192
   at Agilent.MassSpectrometry.CommandModel.CommandBase.EndExecute(IAsyncResult result) in y:\Archer\core\Command\commandmodel\commandbase.cs:line 148
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.OnAsyncCallBack(IAsyncResult asyncResult) in y:\Archer\qual\presentation\AgtQual\QualFormP1.cs:line 1953

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Resolved in B.02.00

-select the Find by Molecular Feature node in method editor
-select the Compound Filters tab
-enter "-6-9" into the "restrict retention times to" field.
The error message is:
"-6-9 is not a valid value.  Value must be range(s) with values >=0 (widths of single values must be >=0)"

The message should be:
"-6-9 is not a valid value.  Value must be range(s) with values >=0 (widths of single range must be >0)"

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Resolved in B.01.03

-Select the Find by Molecular Feature node and click on Extraction tab.
-enter an invalid range into the "restrict retention times to" field (e.g. -5-6)

The error message states that the entry must be a range with min >=0 and max >=0.  

This should be changed to max >0.

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Resolved in B.01.03

-select the Find by Molecular Feature node and click on Compound Filters tab
-enter "0" into Neutral Losses/Restrict to differences off field.  The error message is "0 is not a valid value.  Each value in the list must be a list of numbers >0"
-Enter a letter into the same field and the message is: " is not a valid value.  Value must be a list of numbers >0"

User prefers the second message, it is more consistent with other error messages in method editor.

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-load a data file
-in Method Editor, select Compounds/Find by Molecular Feature
-Highlight one or two ranges in the TIC 
-right click on the first range and select Assign Range to/Find by molecular feature.
The first range is entered into the restrict retention time to field.
-click on a second range in the TIC and select Assign Range to/Find by molecular feature.
The range in the UI does not change.  It doesn't change even after the UI is reset.  Every time you click on a different range in the TIC and try to assing it to find by molecular feature, the first range is entered into the UI.

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Resolved in B.01.03

-right-click on the integration peak list and select "export"
-in the Export dialog, deselect "Autogenerate filenames"
-click on the browse button next to the destination field.
The Save as dialog points to \Layouts\Qual.  At the same time, the default destination path is c:\temp\report.csv

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-load MS2Scan3.d
-display the Integration Peak List
-Extract and integrate a negative TIC chromatogram
-the integration peak list lists 262 as the base peak, the actual base peak should be 309.

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Resolved in B.01.03

-load MS2Scan3.d
-select Chromatograms/Extract Chromatograms
-select BPC or EIC, MS level MS, Polarity both, scan segment Any and mass range 100-400
-select "do cycle sum" and "integrate"
The extracted chromatogram consists of one big peak at 2 minutes instead of the 3 sulfa peaks.

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Resolved in B.01.03

Following tables do not support Export functionality -
1> Formula Caclculator
2> Mass calculator
3> Formula results.
4> Formula MSMS details.

The export menu on these tables are marked as advanced and is grayed out.

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Resolved in B.01.03

-load SulfamixProfile.d
-run integrate and extract peak spectra
-in Data Navigator, click on the first spectrum, press Ctrl and drag the cursor down to the last spectrum.

Not all the spectra in Data Navigator are highlighted.

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-load SuflfamixProfile.d
-run compound/MFE
-in data navigator, highlight 2 compounds
-select the walk tool and press Ctrl and click on one of the selected compounds in Chrom Results. 
Both selected compounds become unselected.
-select another two compounds
-select the walk tool hold down Ctrl key and click on a third compound in Chrom Results.
Both selected compounds become unselected.  The third compound is also unselected.

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Resolved in B.02.00

according to documentation, shift+Click when Walk tool is selected is supposed to "...display one spectrum from each analysis that has one or more currently selected chromatograms"

Currently only one spectrum is displayed.

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-load sulfamixProfile.d
-run integrate and extract peak spectra
-in data navigator, select one of the spectra
-select the walk tool
-clik on the TIC

According to documentation, the following is supposed to happen when clicking with walk tool: "If none of the chromatograms displayed in the plot are currently selected, does nothing"

When the user did it, the TIC was highlighted and a spectrum was displayed in the spectrum preview window.

The same thing happens with Ctrl+Click

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According to documentation, "the application will display one spectrum from each analysis that has one or more currently selected chromatograms" if you click on the chromatogram window when the walk tool is selected.
This didn't work for me, the user only got one spectrum in spectrum preview.

The same thing happens with Ctrl+Click

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Following problems are seen with change icons -
#1) Change icons do not get cleared on Method Explorer when changes in UI are reverted.
Following are the steps to reproduce this in Exclude Mass(es) dialog
 a)Select "Exclude masses ..." radio button
 b)Enter a valid value for m/z. As expected, change icons are seen for Exclude masses radio button, m/z textbox and MethodExplorer-Exclude Mass(es)
 c)Select "Do not exclude masses" radio button. Change icons are removed for Exclude masses radio button and m/z textbox, but not for MethodExplorer-Exclude Mass(es).

This problem is seen with almost all of dialogs where UI controls are enabled/disabled on selection of radiobutton/checkbox/combobox.
It is seen in -
 - Smooth Chrom dialog for "Gaussian width"
 - Peak Filter for "Limit to largest"
 - Integrator Tab for "General Integrator"
 - Peak Spectrum dialog for all checkbox/radio button present on this dilaog
 - Set mzData options for "MS Storage"
 - All Find Compounds UI
 - Worklist Automation-Set Retention Times dialog for retension time range.

#2) Change icons incorrectly shown in Peak filters
 a) Load default method. Go to Peak filter UI. By default Peak area is selected.
 b) Select Peak height. Change icon is shown for "Peak height" radio button and the combobox for units which has not changed. The tooltip for combobox is "This value has changed. The original value was % of largest peak".
 c) Change the units in combobox to "% of largest peak". Its change icon is not cleared and the tooltip display is still the same "This value has changed. The original value was % of largest peak".
 d) Also there is a change in the text box that lies between the "Peak height" radio button and the combobox for units, but there is no change icon shown for it.

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- Run Qual
- Goto Method explorer -> Chromatogram -> Integrate section.
- Goto Peak filters tab in method editor
- Input value as 'abc' for peak height and click on Restore button on method editor toolbar.

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Resolved in B.01.03

Open a data file SulfamixPeak.d
- Highlight TIC node in data navigator 
- Goto Chromatograms -> Integrate and Extract peak spectra
- Goto View -> Integration Peak List
- Right click on Integration Peak List and select Export option
-In export dialog, select "specified file" option
-Enter the "C:\a.txt" filename the text box and press tab

Here, even though file type combo box shows extensions as .txt and.csv, .txt extension is not accepted

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Following are the UI defects for Export dialog in Qual

- Tab order is not set correctly.Also, SHIFT + TAB  does not work properly.

- Only close button should be shown. No maximize/minimize buttons should be shown.

- Controls are not properly left alligned.
- Overwrite dialog box displayed should be same as that of displayed while saving a method that already exists

- If overwriting is discarded then error icon is displayed for a text box of file location. Here, error icon should not be displayed since, the actual path in the text box is perfectly valid. Only the file specified already exists.   

- Icon should not be displayed for export dialog to keep consistency with other dialogs shown

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Resolved in B.01.03

Currently the default for export contents in the Set Export mzData options is 'Highlighted spectra' for worklist automation.  To have useful exported data the default needs to be 'Entire Data file' especially when worklist actions are run with acquisitions.

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Resolved in B.02.00

If you have a wiff file with profile data, say A.wiff, you may want to translate it as both profile and peak.   I translated it first as profile data, creating A.d.   Then I tried to translated it with peak detection as A_Peak.d.   I specified an "at location" of ".../A_Peak.d", which gave me an error icon because the directory did not yet exist.  So I created the A_Peak.d directory and proceeded ... but the translator put the result in A_Peak.d/A.d.

User needs to be aware that the results will be placed into the same file.

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-Clear app data and run Qual
-Open sulfamixpeak.d file without results
-Select TIC node in data navigator and goto  Chromatograms -> Integrate and extract peak spectra   menu option.
- Goto View -> Integration peak list.
- Right click on Integration peak list and click on Add/remove columns
- in the dialog displayed, click on Remove all and add only "Area" column
- Make sure that peak list now displays only one column as "Area"
- Right click on peak list and select "Export" option.
- In export dialog,
   1. change file type to .xml
   2. enter the file name as "C:\rpt" 
   3. check "Include only visible columns" option
- Click on OK.

The xml file C:\rpt.xml should include the information for only "Area" column. Since, this is the only currently visible column in the peak list.

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Resolved in B.01.03

- Start the Qual application and an error occurred after double clicking Setup.exe.

The error occurred while the Windows automatic updates were being installed on the machine.  During the update process, one should not be running the system or cancel the update process.

Resolved in B.01.03

- Start Qual application and go to display options of spectra settings. (Tools -> Plot display options -- > Spectra settings)
- Change Mass values combo box to Exponential.  A change icon is displayed for the combo box.  Old value can be restored using Default value.
- Change the actual no. digits AND Mass Value combo box value.
- Press Default button, the old values are not restored.

The same problem also occurs for Retention time values in Chromatogram settings

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Resolved in B.02.00

The user was trying to create a new template that will be visible in the Choose Report Templates section of the Method Editor.  

Select the Open Report Template menu item in the Tools menu.

Select the Open menu item in the File menu in the Microsoft Excel program. The templates that are available in the Report Templates\Qual directory are listed.

To edit a report template, select it from the list. To create a new report template, select the Blank.xlt template.

(optional) If you are creating a new report from the Blank.xlt template, you need to specify which type of report template it is. Click the Advanced Properties toolbar button. Select what Report Type this template will be and then click the Close button.

Select the Save As menu item in the File menu in the Excel program.

Enter a new File name for this template. You need to put the file name within quotation marks. For example, you could enter “test.xlt” as the file name.

Select Template (*.xlt) as the Save as type. 

When you change the Save as type field, the directory automatically changes. Use the toolbar to return to the Report Templates\Qual directory.

Click the Save button to save the template to a new name.

None of the templates that the user created using these steps shows up in the Choose report templates section.

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Resolved in B.02.00

Currently, generating empirical formulas can only be interrupted "between compounds", but the generation for a single compound can't be interrupted.   The formula generator code should be modified to check for cancel requests periodically so that very time consuming requests can be aborted if the user loses patience.   Preferably, the code can be restructured to use the same cancel/progress indication used within Qual

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1) Open sulfamixPeak.d file
2) Select View-Integration Peak List.
3) Select "Calculate Signal-to-Noise" from Chromatogram node in Method Explorer
4) enter 1.600-1.800,2.300-2.700,2.800-3.100,3.300-3.500 in "Noise regions".
5) Uncheck the "Automatically compute when chromatograms are integrated" checkbox
6) Go to Tools - Plot Display options and set "Retention time" as primary and "Signal-to-Noise" as secondary peak labels and click OK.
7) Run Calculate Signal to Noise from Method Editor
8) Click on "Manual Integration" button in Chromatogram results window and while manually integrating SNR values get changed

This should not happen since "Automatically compute when chromatograms are integrated" checkbox is unchecked

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-Clear app data and run Qual
-In method explorer, goto Chromatogram -> Extract Peak Spectrum

In method editor, in TOF spectra group box, the text box for m/z range is enabled. But, this text box should be enabled only if "In m/z range(s)" option is selected.

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Resolved in Build B.01.03

Excel SP2 is the prerequisite of Qual reporting.
Following error is generated if Sp2 is not available on the machine.

Microsoft Excel encountered following error while formatting the report :
"The message filter indicated that the application is busy. (Exception from HRESULT: 0x8001010A (RPC_E_SERVERCALL_RETRYLATER))"

An error log is created at : C:\temp\AgtErrorLogs\2007-03-20.20.02.36.QualMemoryTrace.gz.  Error log atatched.

It is correct that reporting will not work if prerequisites are not available.  However an appropriate error should be generated in such case.  Also if possible, reporting should check for all prerequisites before firing the command.

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1) Go to Tools - Plot Display Options
2) Change the Retention time values i.e., Change the combo box value from "Digits after decimal" to "Exponential" 
3) Change icon appears near the drop down and the up down control
4) Change icons should not appear near the up down control

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Resolved in Build B.01.03

After uninstalling Qual software, the Qual Reporting Add-in gets uninstalled. It also removes the "Report Designer" menu from MS Excel menubar. However, the Report Designer toolbar does not get removed from Excel toolbar. 

Steps to reproduce:
- Uninstall Qual application
- Click on Agilent Report Designer toolbar
- Excel error dialog is shown up with following error description
"MassHunter Reporting Qual.xla could not be found"

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- Start Qual application
- Go to Worklist Automation à Set export mzData options in Method Explorer
- There is no restriction on entering file path or file name.  It should honor the restrictions imposed by Operating system.  An exception is thrown if you enter very long path.

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Resolved in B.02.00

- Start Qual application
- Go to Worklist Automation à Set export mzData options in Method Explorer
- Select the button to browse the destination folder
- The file type in ‘Save As’ dialog  is empty
- A default file name should be generated.

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Resolved in B.02.00

Qual help window is shown up when clicked the "Help" button on Report Designer toolbar, however this does not work when clicked the "Help" menu from "Report Design" menubar.

Steps to reproduce:
- Install Qual application
- Open Microsoft Excel application
- Click  menubar
- Select  menu

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Resolved in B.01.03

1) Go to Tools - Show Formula Calculator
2) change the value of any one of the UI Control i.e., change Max mass error from 9.5 to 7.5
3) Now click on Undo
4) Values do not get restored

Same things were observed for Mass Calculator

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Resolved in B.01.03

- Open a data file that contains information about instrument curves
- Generate a graph for the instrument curve, say TCC Temprature
- Y axis unit displayed in chromatogram pane is "Response"
- Appropriate unit should be displayed instead.

Note that there is a single graph displayed in chromatogram pane.

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- Start Qual application and open a data file
- Generate a spectrum by double clicking on TIC
- Select a range in spectrum and generate empirical formulae
- Note that the m/z values in EFG results are shown as per precision settings in plot display options for spectra.  For example Calc m/z in isotopic distribution table.
- Go to Plot Display options -> Spectrum settings tab.  Change the precision type to Exponential with some digits after decimal.
- The m/z values in EFG results should be formatted as per new settings. On the other hand, labels on graph control does honor the settings.

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- Run Translator 
- Select "At location" option and specify input path as "PRN"  and press tab

IO Exception occurs.
Exception is also observed in all the cases where destination path is any of the device names reserved by DOS. e.g. CON, AUX, LPT1etc. 

Note: Even though this exception is raised, UI works fine after continuing.
Also, such an input is not frequently specified. This issue gets resolved by the usage of Directory.Exists() in the code.

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Resolved in Build B.01.03

- Start Qual application. Go to Formula Calculator
- Execute the algorithm. Results are generated for the mass value 61.064
- Add an element 1H in the element and limits table
- Run the algorithm. An exception is generated.  (Detailed at the end)
- Exception is generated because of entering invalid element. UI should validate the element before adding into the table.

Date and Time: 3/27/2007  5:59 PM
Program: Agilent MassHunter Workstation Software Qualitative Analysis	B.01.02
Build Configuration: Release
Message: Illegal element
Stack Trace:    at CompositionCalculatorEngine.CompositionByMassEngine..ctor(Double neutralMass, Single massTolerance, ElementBounds[] elementBounds, ElectronState requiredElectronState, ISuperAtoms elementTable)
   at Agilent.MassSpectrometry.DataAnalysis.FormulaGenerator.GetCompositions(Double neutralMonoisotopicMass, ClusterInfo cluster, UserParameters parameters, ElectronState requiredState)
   at Agilent.MassSpectrometry.DataAnalysis.FormulaGenerator.FindCompositions(Double neutralMonoisotopicMass, UserParameters parameters)
   at Agilent.MassSpectrometry.DataAnalysis.FormulaCalculator.Calculate(PSetFormulaCalculator pset)
   at Agilent.MassSpectrometry.DataAnalysis.FormulaCalculatorUIControl.Calculate(IParameterSet parameters)
   at Agilent.MassSpectrometry.DataAnalysis.CalculatorUIControl.Agilent.MassSpectrometry.DataAnalysis.IUIToolDisplay.Calculate()
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.CalculateFormulasMenuItem_Click(Object sender, ToolClickEventArgs e)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.formulaCalculatorToolbarMgr_ToolClick(Object sender, ToolClickEventArgs e)

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Resovled in Builld B.01.03

-in Plot display options select scans for RT units
-load Promix5.d
-in MFE, select the Ion Species tab.
-toggle "Assume peptidic ion distribution"
-rum MFE

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Resolved in Build B.02.00

1. Install Qual software (I installed B117.0)
2. Install Analyst (version 1.1 along with the patch for TOF software On Build 9865)
3. Install TOF Acquisition software[A.02.02] (I installed B738.0) [Note: Installation order is important]
4. Run TOF software and close it without performing any operation.
5. Run Qual. Goto File -> Print ->Method Report.


The same error occurs while generating Analysis report.

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Update Method Explorer, Spectrum, Extract Spectrum - 
specify to subtract the Current background spectrum.

When no background spectrum exists, no error message is generated.

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Save a method in which the peak spectrum parameters have a non-default TOF exclusion m/z range specified but TOF exclusion unchecked.   Load the default method.   Then open the test method.   The status of the controls is okay (checkbox is unchecked, etc.), but the TOF exclusin radio buttons and text box are enabled and should not be.

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Resolved in build B.01.03

Export from plot control (or tables), select an export type that uses a file (ie. csv), and then place a colon in the file name.

(Use tab to leave the field and trigger validation)
The colon is an invalid character for a filename, but is not detected by the control.

This then causes an exception to be thrown.
The Exception needs to be caught and turned into a Qual error.

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Resolved in Build B.02.00

Ctrl Z on Formula table results generates an exception

-	Start Qual and go to Formula Calculator window
-	Run the algorithm and generate some results
-	Press Ctrl Z on the table for multiple times.

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Resolbved in Build B.02.00

Unlike other exports in Qual, export in Excel does not output sample information
   - Start Qual and run targeted MSMS on MRM multi 1.d
   - The compounds are displayed in Compound table
   - Export the list in XML / CSV format and then in  XLS format
  - Sample information is exported in earlier case but not in later case.  A consistency should be maintained if sample information is important to export.

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Resolved in Build B.01.03

-In Export dialog select file type as text / csv
-User can enter any delimiter.  User feels that not all delimiters should be allowed.  Delimiters like ".." or "8888" (numerical number) will result into wrong export results because it will be same as the numbers that are exported.

Most if the times users will set valid delimiter. In case user enters nuric delimiter by mistak and file is not importable, easy workaround would be to re export file with different delimiter.

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Compound plots in qual analysis report are shown in incorrect order when large number of compounds are selected for printing. This defect can seen with 43mm-BSA-20fmol-4.d and stds-4.d

Following are the steps to reproduce this problem
1) Open 43mm-BSA-20fmol-4.d in Qual
2) In Method Explorer->AutoMS/MS->Results Tab, check all options under Chromatogram and Spectra section
3) Run Find compounds by Auto MS/MS, 50 compounds are generated.
4) Highlight first 20 compounds and select File->Print->Analysis Report. Print the report to screen. It takes ~4 minutes to generate the report. 

In the report it is observed that after compound list table, EICs for compounds 7-20 are shown, followed by EIC and ECC for compounds 1-6 and then ECC for compounds 7-20.

The data files and an mdi image of the analysis report generated for 43mm-BSA-20fmol-4.d is ftped to SCS.

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Resolved in Build B.01.03

While creating Qual report, there are temporary files/folders created in temp folder of the system. After closing/printing the excel report, it is observed that these files are not deleted. 

As these files are not required after the report is closed/printed, they should be deleted.

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Resolved in Build B.02.00

- Start Qual, open a data file and go to spectrum peak list window
- Select some rows and export the results in Excel format
- You can see Resolution and Width column in the Excel sheet, whereas these columns are not available in the UI
- The columns are NOT seen if results are exported in CSV format.

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Resolved in Build B.01.03

- Start Qual, right click on TIC and select Export
- On Export dialog, click on browse folder. Windows' browse folder dialog is displayed
- Click on the '?' button on browse folder dialog and then click anywhere on the dialog
- The tool tip help of the control on browse folder dialog is expected to display. Instead Qual help is displayed AND context sensitive help of '?' button is displayed.

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- Export MS Actuals table in CSV format.  The CSV files results column name for each row. i.e. if there are 50 rows then column names are repeated 50 times.

- This is redundant.  
- Also this is inconsistent with other exports happen in CSV format where column names are exported only ones. For example integration peak list export

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Resolved in Build B.01.03

The design is that the background spectrum node can hold one each of (positive profile, negative profile, positive peak, negative peak) spectra.  However, trying to add a positive and negative ion spectrum to background results in only one appearing there.

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Resolved in Build B.01.03

There are cases where the row heights can get set wrong when there are very narrow values on the last column in a table.  This can trigger the rows to be taller than they need to be as Excel thinks wrapping is needed.  Once the row is marked as tall the rest are also tall.

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Peak Status no longer shows in the drop-down list of Peak Labels shown in Tools | Plot Display Options dialog box, Chromatogram tab.

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Open 3 datafiles,
File | Export as mzData,
Highlight all 3 files, 
select radio button Entire data file

The progress bar shows the task progress moving from 0-100 three times, but no Data file progress bar is shown.

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Open Qual application. 
Open two data files and integrate and extract spectrums for each. Highlight all the extracted spectrum and select File-Export mzData.
In the export dialog select Specified file and  click the dialog.

Open the exported file. The description section/node contains information of the first selected file only

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Resolved in Build B.02.00

Open a file in Qual and run any operation that takes longer time to complete. I tried Compound Automation. 

On the progress bar select Alt+F4, it disappears and gives an impression to the user that the operation is stopped. However, the operation is still continuing and user cannot perform any other operation in Qual, untill the running operation is completed.

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Analysis report printed has ## in the abundance column for peak list tables.

This behavior is seen only with 120 DPI setting with 96 DPI it works correctly

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- Ensure that a data file does not contain any results. Open a data file in Qual.
- Right click on file node in data navigator and select "Open This Method" menu item.

Following exception is reported:

Date and Time: 10/12/2007  3:32 PM
Program: Agilent MassHunter Workstation Software Qualitative Analysis	B.01.03
Build Configuration: Release
Message: Object reference not set to an instance of an object.
Stack Trace:    at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualDAMethod.LoadMethod(String methodDirPath)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.CmdOpenDAMethod.DoSpecialized()
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualCommandBase.Do()
   at Agilent.MassSpectrometry.CommandModel.CommandHistory.Invoke(ICommand cmd)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.AppManager.Invoke(ICommand cmd)
   at Agilent.MassSpectrometry.CommandModel.CommandBase.Execute()
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.SendSynchronouslyToAppLayer(QualCommandBase command, Boolean showOutstandingMsgBox)

This happens since data file does not conatin any method. In such cases, "Open This Method" menu item should be disabled and even if it is enabled, proper message should be shown instead of exception.

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Resolved in Build B.03.00

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If a user has installed the Microsoft .NET framework security update 922770, Qual B.01.03 reportedly runs very slowly (even the program startup takes a long time).

This seems to be an interaction with Infragistics 7.1 components used in B.01.03, and does not affect B.01.02 or earlier versions, which used a different version of the Infragistics components.

Installing the later update 928635 fixes the problem.

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Resolved in Build B.02.00

- Run Qual and Open hilow225_40.d file
- Extract TWC, integrate it and extract peak spectra
- Highlight first UV spectrum (1.306 - 1.409 min) in data navigator 
- Generate EWC from this spectrum by double clicking at any wavelength < 190 nm.

Following exception is reported:

Date and Time: 10/19/2007  5:27 PM
Program: Agilent MassHunter Workstation Software Qualitative Analysis	B.01.03
Build Configuration: Debug
Message: Value must be a range with a center >= 190 and <= 600 and width >= 2 and <= 600
Stack Trace:    at Agilent.MassSpectrometry.DataAnalysis.RangeParameter.set_Value(IRange value) in z:\Archer\core\CoreTypes\Parameters\parameter_range.cs:line 823
   at Agilent.MassSpectrometry.DataAnalysis.PSetExtractChrom.set_SignalWavelength(IRange value) in z:\Archer\core\CoreTypes\Parameters\pspl_sources\parameterset_extract.cs:line 3984
   at Agilent.MassSpectrometry.DataAnalysis.FilterPropagator.CreateChromatogramRequest(IRange signalWavelength, ISpectrum[] sourceSpectra) in z:\Archer\core\CoreTypes\Algorithms\filterpropagator.cs:line 1171
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.ExtractChromOverRanges_Click(ChromType chromatogramType, RangeCollection ranges, IDataItem item, String description) in z:\Archer\qual\presentation\AgtQual\QualFormP3ProcessMenus.cs:line 604
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.UIComponent_ExtractDefaultEvent(Object sender, UIGraphicsExtractDefaultEventArgs e) in z:\Archer\qual\presentation\AgtQual\QualFormP7UIComponentEvents.cs:line 236

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Resolved in Build B.02.00

- Clear app settings and run Qual
- Open 4000-200-BSA.d file.  Goto Chromatograms -> Integrate and Deconvolute Peak Spectra. Verify that Deconvoluted spectrum is visible in Deconvolution Results window.
- Select User Spectra node in data navigator. Set custom plot limits for Deconvoluted Spectra as 5000- 10000 in Common Reporting Options UI and generate Analysis report.

Generated report contains two pages. Attached is the first page of the report. It can be seen that Deconvoluted spectrum plot shows limts as (00 - 100) instead of those set in UI (5000 -  10000). Hence, limits get cut in the report.

(This is a problem with the plot control itself, the same behavior is seen in the UI when the tick mark is very near the edge of the plot.)

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Resolved in Build B.02.00

- Clear app settings and run Qual
- Open sulfamix_peak.d  data file. Ensure that no node is highlighted in the data navigator.
- Delete all the contents of \reports\temp i.e. intermediate data location.
- Goto File -> Print -> Analysis Report. In the print dialog, check Print Preview checkbox and click 

Report is not generated since nothing was highlighted in the treeview and message appears indicating the same. This is correct. Goto intermediate data location. Temporary report data files created are not cleared. This is incorrect and inconsistent with "Keep intermediate report directories" option setting. Because, even if this check box is unchecked in UI, intermediate directories are not cleared.  This problem occurs since; intermediate files get generated even though actual report is not created since, not data was found for report generation.

When reports are successful, then the intermediate files are generated (or not) according to the checkbox accessed via the Tools -> Intermediate Report Files menu item.  

When a report is NOT successful, then the intermediate file is not deleted because it DOES help in debugging potential problems, and should have a pretty low impact as it will be relatively rare.

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1. Run Qual and open a data file. Goto File -> Print 
   -> Analysis Report.
2. Select any non-default printer, check Print Preview checkbox and click .
3. Goto Windows Explorer and delete/remove the selected Printer.
4. Switch back to Qual and repeat step <1>. Verify that deleted printer is still selected in the combo box. Without changing any of the values, click 

The user must configure a printer before attempting to print reports.

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When you use the Run button in the Method Editor to search database for compounds the Search DB window is not displayed.

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Resolved in Build B.02.00

If you use the EIC "at maxima in ranges" option, you have no way of controlling the single m/z expansion width that is applied to the m/z of the maximum (and the default value of +/- 0.5 amu is used, even for TOF data).

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The default sort order is on Category and Name.  If you click on the header for Category (sort only by that), then use the context menu to restore the sort order, it changes the Category to the original direction but does not add back in Name as a sort criterion.

You can still add the Name with (Shift + Click on the header), but you have to know what the original criteria were to get back to where you started.

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- Clear app settings and run Qual.
- Open sulfamix_profile.d file without results. Ensure that C:\temp\report folder already exists. Export extracted TIC by 

right clicking on Chromatogram Results window at specified default location. This displays warning message asking whether to 

overwrite c:\temp\report folder. Click .

New folder named "c:\temp\report.1" is created with .emf file in it. 

This is incorrect behavior which is not consistent to UI since; if overwriting is allowed in UI, existing "c:\temp\report" should be overwritten completely with only exported files (.xml and .emf) present in it as a result of export operation. The same behavior is observed in case of export to .csv OR .txt where, already existing file is not overwritten.

Also, with this behavior data is not exported at user specified location. Exporting should happen at specified location only and folder name should not be altered.

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Resolved in Build B.02.00

Open the data file, extract 2nd tic w/o cycle sum enabled. overlay the tics. scale to largest in each. zoom in on one peak (so you can see cycle sum and non-cycle sumed peaks. press walk chrom toolbar button.

When mouse down in chrom results plot either 
a) plot rescales so walk chrom indicator arrow is visible and the data is scaled to extremly small or
b) data remains visible, but the indicator arrow is no longer visible within the plot window

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Resolved in Build B.02.00

Load more than one data file. In chromatogram results pane, select either normalized to the largest peak in any of the chromatograms or normalized to the largest peak in itself options. Now select the Walk Chromatogram option, there is no annotation (downward pointing triangle symbol) shown on the chromatogram.

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Resolved in Build B.02.00

Running a find compounds algorithm may fail if the MS device delay time is a non-zero value and the current chromatogram x-units are "scan numbers".   For MFE, the result will be a message saying no compounds were found.   For other algorithms, the result will be an exception complaining that "x values must be unique".

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Run find compounds Targeted MS/MS on a data file in units of minutes and with no delay adjustment.
Record the RT of a compound (e.g. 1.999)
Apply a delay of 0.2 minutes (cpd was now 1.799)
Change units to scans (cpd was now 242)
Turn off the delay (cpd was now 265)
Change back to minutes (cpd was now 2.199, NOT the original value of 1.999)

This was using sulfas-targeted.d

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When generating a window report from any peak window (chromatogram or spectrum peaks), you can set the option for Report Contents to "Limited peaks".

If you have done so, then trying to print any other table window (e.g., formula results, sample information, MS actuals) will result in the message:
"Print was canceled because no rows met the selected print options. Select different print options and try again."

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Resolved in Builld B.02.00

It used to be that you could have a Quant template open and then open a Qual template and the add-in switched to the Qual one.  Switching between the different template types would load the different add-ins correctly.  Now the first loaded add-in remains the active one which means the user will have access to the wrong toolset.  I have also seen cases where the wrong add-in was loaded and I had to explicitly select the add-in in the Add-ins dialog and restart Excel.

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Observed on a system being run by a user.  He had something like 7-8 files open and was running Find by Compounds.   When the dialog popped up for him to choose which files it should be run on, the files were listed in an order that did not match the order in the tree view (nor did they seem to be alphabetically sorted; they looked random).   The files should be listed in the tree-view order (i.e., the order in which they were opened).

This seems to happen when using the Run button, but not when using the main menu!

Resolved in Build B.02.00

The user opens a data file and runs Find Compounds by Auto MS/MS.  Then, they select the first 10 compounds or so and generate formulas.   Some work, others throw exceptions.

Traced to computing impossible fragment formulas (with more H atoms than the precursor formula) then trying to subtract to get the neutral loss.

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Resolved in Build B.01.03

Loaded sulfas-ms-only.d.  Using “Find compounds by formula” to find compounds.  Then “search database for compounds” command.  
It was observed that “acetaminophen” had multiple results in the DB Search Results window.  
Changing to the “Best” hit and this column in the compound list wasn’t changed. Using the “Generate Formulas from Compound” and changing the best result in the MS Formula Results window and the Modified column is still not changed

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In the compound list, the "Match Diff (ppm)" is displayed out to 2 decimal places.  Since our mass accuracy is a few ppm at best, the second digit after the decimal place is unnecessary.  This column should show only 1 digit after the decimal at most.

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The error can be reproduced by doing the following:

1) Create a new link in the data dictionary called "Custom Link 1".  Assign the amino acid specificity to alanine.

2) Import the serotransferrin.psq sequence.

3) Apply the Custom Link 1 to the Alanines at positions 4 and 10 in the sequence.

4) Open the Chemical Data Dictionary and change the amino acid from alanine to leucine.  Close the data dictionary to save the change.

The alanines will still be shown as being linked, even though the Custom Link 1 modification is no longer specific for alanine.  This link should be removed from the sequence when the data dictionary changes.

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Resolved in Build B.02.00

This can be reproduced in the following manner:

1) Create a custom link specific for leucine.
2) Apply it to positions 16 and 46 in the serotransferrin.psq sequence.
3) Delete the link from the data dictionary.

The bold, underlined leucines still remain in the serotransferrin sequence.  These should be deleted from the sequence when deleted from the data dictionary.

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Resolved in Build B.02.00

To turn UseOptions to FALSE.  The side effect of that is the Qual Method report will not be printed in landscape even when the user has selected Landscape in the Common Reporting Options section.

Or... the other option is to remove the HideEmptyColumns options from the template so it will ignore that setting from the Qual UI.

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Bring up the mass calculator.   
Enter a formula of "CF3CO2".   
Set species to negative ions and check "Neutral" and "-H".   
Set Number of charges to 2 and press the calculate button.

You (correctly) get the error message <>.
By changing unchecking the "-H" species.   Try again, and you get the same error message.

Fix the problem by changing the base formula to "CF3COO"

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Plot window report ( chrom / spectrum -window ->print)
If you select "One plot per page" checkbox, all pe options on "options" tab (landscape/portrait, include header / footer) have no effect.

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Chrom window -> print ... menu
Check "One plot per page" checkbox
print.
One blank page is printed at end.

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Resolved in build B.02.00

1. Change the Chromatogram Acquisition time to be Scan Number
2. Integrate a UV chromatogram with ChemStation integrator.
3. The result is an empty peaklist.

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When adding links to a sequence, the link that was just added does not show up in the list in the Applied tab in the Links dialog.  These links should be added to the Applied list as soon as the user selects a link

If the dialog is closed and reopened, the links show up.

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When MFE uses an exclusion list it should use the exact mass generated from the formula.  
Which mass is getting used if a .csv file is referenced which was exported with a Mass column.  Most likely that Mass column will have the measured mass instead of the calculated mass.  Even if there is a Mass (DB) column, the Mass column would be the one used as the reference mass, although with a Formula column there it might overlay the ReferenceMass value as the calculated mass from the Formula.

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While running a worklist on DA Reprocessor - using Ser....m and Ser...d there was an observed an error message while generating the report. Removing 'Generate Compound Report' from worklist actions this problem goes away. When running the worklist actions from Qual (with the 'Generate Compound Report' action present) I once again noticed this problem.

Remote Desktop Connection should only be used to troubleshoot the equipment.

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Doing a compound automation (Find by Formula + MFG for all compounds; show only identified results) on a series of 5 data files.  The compound was found in the first four, but not the fifth.   MFG was successful for the 1st four.  

Got an error message "Cannot generate formulas for any of the selected compounds . . ."   The message is correct if it applies only to the last data file; it is misleading because there WERE formulas generated.

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Loaded a method specifying a database at a nonexistent path.   The red error icon shows correctly in the method explorer.   However, there is no icon on either the Mass Filters tab nor on the UI control itself where the database path is shown.

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Resolved in build B.02.00

Trying to print a chromatogram window report (which succeeded in US English) after switching to French (Canada).   This generated an exception.   Portion of the log file follows:

08-11-2008 1325:38.066  Clear FirstZoomInfo, ThreadID=3
08-11-2008 13:25:38.066  Method InitializeReportEngine: Entered, ThreadID=3
08-11-2008 13:25:38.082 ExcelReportEngine::Function GetExcelObjectHandler Entered Agilent.MassSpectrometry.DataAnalysis.ExcelReportEngine, ThreadID=4
08-11-2008 13:25:38.691 ExcelReportEngine::Function GetExcelObjectHandler Exit Agilent.MassSpectrometry.DataAnalysis.ExcelReportEngine, ThreadID=4
08-11-2008 13:25:38.847 ReportingWorkerClass:DoReport, Other exception from reporting Agilent.MassSpectrometry.DataAnalysis.ReportingWorkerClass, ThreadID=6
08-11-2008 13:25:38.847 Old format or invalid type library. (Exception from HRESULT: 0x80028018 (TYPE_E_INVDATAREAD)) Agilent.MassSpectrometry.DataAnalysis.ReportingWorkerClass, ThreadID=6
08-11-2008 13:25:38.847  Recovering from Old format or invalid type library. (Exception from HRESULT: 0x80028018 (TYPE_E_INVDATAREAD)), ThreadID=4
08-11-2008 13:25:38.972  Exception Location - App: AgtQual.exe, FileVersion: 2.0.0.0
.....................Module: System.RuntimeType

Exception 1: System.Runtime.InteropServices.COMException
Message:  Old format or invalid type library. (Exception from HRESULT: 0x80028018 (TYPE_E_INVDATAREAD))
Source:   mscorlib
Site:     System.Object ForwardCallToInvokeMember(System.String, System.Reflection.BindingFlags, System.Object, Int32[], System.Runtime.Remoting.Proxies.MessageData ByRef)
   *** Stack Trace ***
   at System.RuntimeType.ForwardCallToInvokeMember(String memberName, BindingFlags flags, Object target, Int32[] aWrapperTypes, MessageData& msgData)
   at Microsoft.Office.Interop.Excel.AddIn.set_Installed(Boolean )
   at Agilent.MassSpectrometry.DataAnalysis.ReportingWorkerClass.DoReport() in r:\Archer\core\ReportEngine\ReportEngine\ReportEngine.cs:line 741

WorkStations have been tested and verified using US English as the regional settings.

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Control Panel -> Regional and language options -> switch to French (Canada).   Start Qual.   Default method has error icons wherever a csv database is specified. Message is "Input string was not in a correct forma"

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There’s a problem when running QualAutomation.exe on a data file where it’s CombinedReportOutputFile(inside .d/Reprocessing/sample_info.xml) value is empty. 

Upon investigating this problem -- it’s due to (item.DataObj as IAnalysis).FilePath not returning the full path.  It returns the file name only.

In the case where CombinedReportOutputFile is empty, the AsrExport code tried to set the output file name to be the sample data file name with ASR extension.  

When running QualAutomation and pass in the full path of the data file, then this error doesn’t occur.

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Following are the steps to reproduce
1.	Start Qual
2.	Go to Tools | UI Configuration 
3.	Make any change in the dialog and click ’
4.	Select undo. 
5.	Select undo again, exception occurs.  click it
6.	Go to Tools | UI Configuration again, make any change in the UI and  click the dialog
7.	In Method Explorer, all sections – Chromatogram, Spectrum etc are seen twice. Refer the attached image

Following are the details of the exception seen in step #5.

Program: Agilent MassHunter Workstation Software Qualitative Analysis	B.02.00
Build Configuration: Release
Message: Object reference not set to an instance of an object.
Stack Trace:    at Agilent.MassSpectrometry.DataAnalysis.Qualitative.AppManager.ChangeFeatureConfiguration(IPSetQualFeatureConfiguration iPSetQualFeatureConfiguration, QualCommandBase cmd, ActionItemCollection actions)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.AppManager.ApplyAppSettings(IParameterSet psetToApply, QualCommandBase cmd, ActionItemCollection actions)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.AppManager.SetParameterSet(IParameterSet psetToset, Boolean updateSettingsItemsPset, ActionItemCollection actions)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualCommandBase.UndoQualAppActionItem(QualAppActionItem actionItem, ActionItemCollection undoActions)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualCommandBase.UndoActionItem(Object actionItem, ActionItemCollection undoActions)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualCommandBase.UndoActionList(List`1 actionsToUndo)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualCommandBase.Undo()
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.AppManager.Undo(Int32 numOfCommandsToUndo)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.SendUndoToAppLayer(Boolean undo, Int32 count)

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MassHunter B.02.00 TOF B124
Running a worklist with DA processing enabled and with
"Stop worklist on DA error" unchecked.
For method IntactCytochromeC.m which has worklist automation action:
Integrate and Deconvolute
Match Sequences
Generate Compound Report

Excel pops up a message box with an OK button, but the only information is "unable to read file". If OK is cllicked it proceeeds and a compound report is generated

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Resolved in Build B.02.00

MassHunter B.02.00 TOF B1124 for 1 GHz TOF
Using IntactCytochromeC.m for DA method in worklist automation.
Deconvolution will fail to find compounds in a blank or matrix sample. Thus there are no compounds in the compound list. 
If "Stop worklist on DA error" is checked which is the default it will stop the worklist. It should simply generate a report that says no compunds were found.

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Attached with this defect are two data files containing non-ms data. 
Open them in Qual, bring up the Extract Chromatogram dialog.
Select the first data file, then select the second data file. 
Following error occurs, it takes ~1-2 seconds for this defect to come up. This exception does NOT affect the Extract chrom functionality.  OK clicking the exception and the extract chrom dialog, extracts the required chromatogram successfully.

=======================================
Message: Object reference not set to an instance of an object.
Stack Trace:    at Agilent.MassSpectrometry.DataAnalysis.BDAMSScanFileInformation.CombineScanFileInformation(IBDAMSScanFileInformation[] inArray) in Z:\Archer\core\BaseDataAccess\DataAccessors\BDAMSScanFileInfo.cs:line 943
   at Agilent.MassSpectrometry.DataAnalysis.BDAFileInformation.CombineFileInformation(IBDAFileInformation[] inArray) in Z:\Archer\core\BaseDataAccess\DataAccessors\BDAFileInformation.cs:line 658
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.DataItem.CombinedFileInformation(IDataItem[] sources) in z:\Archer\qual\applogic\applogic\dataitem.cs:line 1526
   at Agilent.MassSpectrometry.DataAnalysis.ExtractChromFromAnalysisDlg.SetAppropriateFileInformation() in z:\Archer\core\CoreUI\FileDialog\ExtractChromDialog\ExtractChromAnalysisDialog.cs:line 232
   at Agilent.MassSpectrometry.DataAnalysis.ExtractChromFromAnalysisDlg.m_selectAnalysisListControl_SelectionChangeEvent(Object sender, SelectionChangedEventArgs e) in z:\Archer\core\CoreUI\FileDialog\ExtractChromDialog\ExtractChromAnalysisDialog.cs:line 199
   at Agilent.MassSpectrometry.DataAnalysis.SelectAnalysisListControl.DataItemListBox_SelectedIndexChanged(Object sender, EventArgs e) in z:\Archer\core\CoreUI\FileDialog\SelectAnalysisListControl\SelectAnalysisListControl.cs:line 213
   at System.Windows.Forms.ListBox.OnSelectedIndexChanged(EventArgs e)
   at System.Windows.Forms.ListBox.WmReflectCommand(Message& m)
   at System.Windows.Forms.ListBox.WndProc(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.OnMessage(Message& m)
   at System.Windows.Forms.Control.ControlNativeWindow.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
=======================================

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Resolved in Revision B.02.00

This problem occurs only when a data file contains dual mode data and has user calibration saved (recalibration done), and the very first spectrum extracted is used in adding or subtraction with another spectrum.

The very first time a spectrum subtraction or addition is performed (can be triggered by doing peak spectrum extraction with background subtraction or manual subtraction/addition of spectra), an unhandled exception message will show up indicating spectra with different XSampling types cannot be combined.  This is due to the two spectra not having the same mode (one is profile and one is peak)

Workaround: 
If you are doing peak spectrum extraction:
execute the operation again.  The consequent operations will go through without running into this problem.

If you are doing manual subtraction/addition of spectra:
1. First deselect the addition/subtraction operation (go to Spectrum menu and uncheck the subtraction or addition menu items) so that you are in the "normal" mode.
2. Extract the first spectrum again.  This is the very first spectrum you've extracted since opening the data file.
3. Then you can go ahead and do addition or subtraction of spectra.  Notice that now both spectra should have the same format (either both peak or both profile).

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1 Run Qual and open sulfas_PosMS.d file
2 Extract ADC chromatogram and integrate it
3 Select any peak of ADC chromatogram  using peak select tool
4. Right click on chromatogram results window and select Extract peak spectrum menu

Following excpetion is reported:
Date and Time: 9/12/2008  6:14 PM
Program: Agilent MassHunter Workstation Software Qualitative Analysis	B.02.00
Build Configuration: Release
Message: PeakSpectrumExtract for Other
Stack Trace: 
Server stack trace: 
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualDAMethod.GetUsageKey(QualFunctionality functionality, QualDataType dataType)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualCommandBase.EnsureBackgroudPresentFromPeakExtraction(QualDataType dataType, DataItem[] selectedItems)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualCommandBase.ExtractPeakSpectra(DataItem[] selectedChromatograms, SpecType typeOfSpectrum, Boolean clearPreviousResults, Boolean useOnlyHighlightedPeaks, Boolean& unhighlightOthers, ProgressTracker progressTracker, Int32 startPercent, Int32 endPercent, ActionItemCollection actions)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.CmdExtractChromPeakSpectra.DoSpecialized()
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualCommandBase.Do()
   at Agilent.MassSpectrometry.CommandModel.CommandHistory.Invoke(ICommand cmd)
   at System.Runtime.Remoting.Messaging.StackBuilderSink._PrivateProcessMessage(IntPtr md, Object[] args, Object server, Int32 methodPtr, Boolean fExecuteInContext, Object[]& outArgs)
   at System.Runtime.Remoting.Messaging.StackBuilderSink.PrivateProcessMessage(RuntimeMethodHandle md, Object[] args, Object server, Int32 methodPtr, Boolean fExecuteInContext, Object[]& outArgs)
   at System.Runtime.Remoting.Messaging.StackBuilderSink.AsyncProcessMessage(IMessage msg, IMessageSink replySink)

Exception rethrown at [0]: 
   at System.Runtime.Remoting.Proxies.RealProxy.EndInvokeHelper(Message reqMsg, Boolean bProxyCase)
   at System.Runtime.Remoting.Proxies.RemotingProxy.Invoke(Object NotUsed, MessageData& msgData)
   at Agilent.MassSpectrometry.CommandModel.CommandHistory.InvokeCommand.EndInvoke(IAsyncResult result)
   at Agilent.MassSpectrometry.CommandModel.CommandHistory.EndInvoke(IAsyncResult result)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.AppManager.EndInvoke(IAsyncResult result)
   at Agilent.MassSpectrometry.CommandModel.CommandBase.EndExecute(IAsyncResult result)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.OnAsyncCallBack(IAsyncResult asyncResult)

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This has been fixed in B.03.00

There appears to be an off by one error in the data navigator.
Loaded 7 data files and selected all of them.  Then, clicked on the Chromatogram > Integrate command and all but the last chromatogram are integrated.  
If I select all of the chromatograms but the last one, then click the Chromatograms > Integrate command, then the second to last chromatogram isn’t integrated. This also happens for the “calculate signal to noise command.

This is not ALWAYS reproducible.
1.	Start Qual.
2.	Load six data files (I chose the MRM data files in the SulfaDrugs directory)
3.	In Data Navigator, click each “negative” icon to close it. (all data files are shown with a plus sign)
4.	Highlight all data files.
5.	Click Chromatogram > Integrate.
6.	Scroll in the Chromatogram Results window and the last TIC is not integrated.
7.	If I click the “plus” sign in the data navigator, the last TIC is not highlighted.  That appears to be the problem.

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1) If one extracts an EIC and specifies an exclude range, then copy the EIC definition to method (right click on the chromatogram plot->Use Highlighted Chromatograms->Copy Definition to Method), you will notice that the EIC definition in the Method (Chromatogram->Define Chromatograms) m/z value(s)got broken into 2 ranges.  And even if you check "Merge multiple masses into one chromatogram", there are still 2 EICs (one per mass range) being generated.


2) TIC extraction does not honor mass exclude range (has been this way since B.01)

Workarounds:
1) Set up the EIC definition in the Method (Chromatogram->Define Chroamtograms) manually, don't use "copy definition to method", then it generates the exact same EIC as when you do it through the Extract Chromatogram dialog from the menu.


2) Workaround is extract EIC instead and specify m/z over all mass range, and specify exclude range on the third tab of the Extract Chromatogram dialog

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Doing a print preview of the acquisition method report from qual and leaving the preview up, while doing a tune could cause Excel to abort while printing the tune report.

As a workaround it is suggested to wait for the tune to finish and print the acq. method report from the acquisition software. (Do not print both reports at the same time.)

Resolved in Build B.03.00

When doing an Acquisition Method Report (using File-->Print-->Acquisition Method Report), set it to Print Preview, occasionally one could get the report but instead a series of Excel errors:

Run-time error -2147417848 (810010108)
Method "Cut" of object "Range" failed
Hitting Debug takes you to this line in the Qual Add-in code:
 designList.range.Cut newWS.Cells(2, 1)

Hitting End generates this Qual error:
Microsoft Excel encountered the following error while processing the report:
Exception from HRESULT: 0x800A9C68

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While resetting the layout to default:

Message: Object reference not set to an instance of an object.
Stack Trace:    at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.LoadAllBitmaps()
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.LoadQualWindowLayoutSettings(Boolean initializingProgram, Boolean forceRegisterForToolbarEvents)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.DefaultLayoutMenuItem_Click(Object sender, ToolClickEventArgs e)
   at Agilent.MassSpectrometry.DataAnalysis.Qualitative.QualForm.UltraToolbarsManager1_ToolClick(Object sender, ToolClickEventArgs e)

and the screen layout is totally corrupted

This problem, or something highly related,  also could be related to docking a window.  The core folders had to be deleted (CoreDefinitions and QualDefinitions folders) to fix it - the folders are automatically created when the system is restarted.

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Resolved in Build B.03.01

The dialog box that is opened when you click the File > Import Compound command doesn’t have a help button (and F1 doesn’t work because it only brings up context sensitive help, rather than the QualDA help file)

The user needs to select CEF files only.

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The use of RT on spectra does not effect the search results.   The RT match is to be used with unknown compound searching where 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 when performing library matching against spectra versus compound identification.

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Resovled in Build B.03.00

The Chromatograms tabs on the Peak Survey-Chromatogram Extraction is missing some of the group box labels.  
Missing "Additional chromatograms to extract" label on 2nd group box and
"Chromatogram parameters" label on 3rd group box.

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Resolved in Build B.03.01

Extracted GC Signals in MassHunter Qual and tried to integrate the signals using each of the integrators, including the ChemStation integrator. With each integrator the message returned No peaks found. Integrators on other system do find the solvent peak, C13, C14, C15, and C15 peaks without any problems with the FID MDL sample.

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Resolved in Build B.03.01

When you take a snapshot the first time the user will see the results correctly.
If you close the datafile and reopen it during the same run you get an error: 97% Loading "matched sequences"
This only happens when you have selected "Load results" in the file load screen.

User needs to update the .NET Framework to the current service package from microsoft.

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When you do a second snapshot (just load datafile) then MassHunter will tell you that the file is already open. You first have to close the datafile before you can take the second snapshot. This is GCMS-QQQ system

The refresh is designed with the use case for this operation.  One click and you remove what you have done and reload the same file without having to select it from a list of files.

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MSMS Integrator may not work on some GC data files.

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Occasionally when users close Qual by clicking the close [X] in the upper right corner, Vista pops up a message box offering a choice of searching the Internet for solution or offering to Close the program.

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After highlighting the row for compound in compund result table found by library search having structure the respective spectrum results window & structure viewer window shows the structute for that compund. But after clicking on the spectrum for that same compound the structure viewer window do not shows structure.

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When printing the spectrum window via the printer toolbar icon on that window, or via the context "Print..." menu, any predicted isotope pattern annotations seen in the UI are not reproduced in the printed (or previewed) spectrum.

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A user had 20 data files open with processed results when he exited the application.  He was prompted to save results and said to do that.   Unfortunately, his disc was nearly full and had room for only two data files' results.  He got 18 error messages saying the disc was full -- and Qual closed in spite of having not saved the data.

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Enter a formula (e.g., C12 H26 O5) with a comparison m/z value (251.1855) and calculate while the UI is set to show 4 digits after the decimal for mass and m/z values.   The calculation is correct, but the comparison m/z text box is updated to show the comparison mass as "251.2" (and pressing the calculate button again now computes incorrect mass errors using the rounded value).

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When a user prints out Analysis Reports for a lot of data files using the option "Separate report per data file" it prints them in an arbitrary order.

If they turn off the option, "Separate report per data file", then it prints them in the order they are listed in the Data Navigator.

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A user tried exporting a spectrum with about 78000 points.   Only about 65000 showed up in the .xls file.   However, export to CSV and then import that into Excel works fine.

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Qual B.03.01 (SP1,SP2 and SP3) reports an error "Cannot generate acquisition method report for , because it has no acquisition method file." when an attempt is made to print the acquisition method for a GC-QQQ data file.

None.

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When the user asks to perform a NIST search using the NIST search program (“Search Using NIST MS Program”) the software overwrites the AUTOIMP.MSD data file changing the contents to “C:\Documents and Settings\tbarrett\Local Settings\Temp\FILESPEC.TXT”.  Once this is done Chemstation/AMDIS software malfunctions because it no longer is writing spectra to the correct file.  Seen in B.03.01 SP3 and before.

Must manually restore the contents of the AUTOIMP.MSD so that the original text is restored to the file path that is expected by DRS. The AUTOIMP.MSD  file is found under \NIST08\MSSEARCH directory.   The DRS path is typically "C:\msdchem\HPNIST.TXT" but can be different depending on install.  Locate the HPONIST.TXT file on the system to confirm the correct path.  This is a temporary fix as the next time the NIST search is run from Qualitative Analysis it will once again over write the file thus recreating the problem.

Fixed in B.04.00

The MS/MS GC integrator is designed for MSMS chromatograms like MRM and cannot processes some GC data signal.  When it fails an error message box with stack trace information will appear and the integration will fail.  Problem seen in B.03.01 and B.04.

Try using any of the other integrators on GC chromatograms.

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Exported csv file does not contain complete data when csv file was exported with right click and selecting Export as CSV... context menu (Compound List pane).

1. Try with Export as .xml
    >> OK (Start Excel application, File > Open, then specify xml file, and then use 'Open as XML Table')

2. Try with Export as .txt or .csv with deliminator [space   ','] / [','] / [space   ';'] / [';'] / [TAB]
   - a. OK (Start Excel application, File > Open, then specify txt file, and follow Text File Wizard screen)

 *File must be opened with Excel Text File Wizard to be parsed correctly.

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If Excel 2007 is not already installed on a system, when MassHunter Qualitative Analysis is installed the reporting add-in for Excel 2007 will not be installed.  Instead, the reporting add-in for Excel 2010 will be installed.

1) Uninstall MassHunter Qualitative Analysis
2) Install Excel 2007
3) Install MassHunter Qualitative Analysis

The reporting add-in will then be installed.

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Old example data files do not display fragmentor or collision energy in Qualitative Analysis.  This is because the feature to write those values in the data file was not in the older Acquisition software that they were acquired with.

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When running Find by MSMS on several large data files eventually the system runs out of memory and a message appears at the bottom "Low Memory".

Workaround : Turn off all checkboxes in Find By AtuoMSMS result pane. That is do not extract spectra nor chromatograms. This works and results can be retrieved faster. User can "Extract Complete Result Set" selectively on the compounds of interests.

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Load a large data file with its results and load the results Qual method.

Sort based on Volume, and run MFG on the largest volume compound.  In some cases, Qualitative Analysis will freeze.

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The service packs for B.03.01 Qual do not install on Vista SP1 since the default is for UAC (User Access Control) to be enabled. However the script executes, logs the "Access Denied" conditions BUT reports that SP3 (for example) was successfull installed. This is not correct. The appropriate files are not copied to the bin directory and the splash screen remains unchanged which of course is correct.

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1) Run Worklist Actions using the a method.  The result is a large number of compounds found--about 5000.

2) Select alll the MFE compounds that have a BioConfirm sequence hit and Extract Complete Result Set 

3) Select 20 compounds found by Find by Auto MS/MS and Extract Complete Result Set

4) Select File--Save Results

After about ten seconds a dialog will come up that says that the computer is out of memory.

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customers would like to be able to have multiple Best hits in Find-by-Formula because often they are using isomers which have the same formula.  The current behavior is that it will arbitrarily choose one of the isomers and designate it as the Best hit, ignoring isomers at other retention times.

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Run as Administrator required to install Qual & BioConfirm on Vista & Windows 7.

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Peak width in the peak table corresponds the value at half height of the peak, however when you manually integrate any peak, we you get the width at the baseline.

This is due to the fact that manual integration uses the General integrator.  For the General integrator the definition of width is the full peak width from start to end.

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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.

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The Identification Chromatographic Peak Wizard throws an exception if TWC is checked but no DAD spectral data is available.

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Exception when Saving Results containing Universal (Genie Integrator) timed events.

Use another integrator.

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The "Import" button used for sequence browsing under "Define and Match Sequence Method editor/ Sequence tab" does not remember the last entered value/path. 
If the different path is browsed for importing sequence, then the newly browsed path is not remembered by the application while browsing the sequence next time, it again browsed to the default location.

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For high resolution data Qual shows low memory issue when "Find By Maximum Entropy" operation is performed.   If you delete all the compounds and spectra generated by the first operation and then run a secomd operation, there is high chance that it succeeds.

Upgrade to Windows 7 64-bit version.

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A user cannot delete a custom modification from Chemical Data Dictionary.

Edit the XML file.

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The current Agilent Windows 7 mage "R6C" for workstations does not include any .Net Frame 4 components. The Qual installation does detect this and installs the components as needed. However if the user attempts to load Qual B.05.00 after this installation they receive a warning that this application requires one of the following version .Net Framework v4.0.30319, etc.  What they actually need to do is just reboot the PC.

Reboot the PC and the message will go away.

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Qual does not correctly remember the last-used layout of the Compound List.

To reproduce:

1. Remove B.05 files from C:\users\\AppData\Roaming\Agilent_Technologies,_Inc
2. Start Qual
3. Configure workflow -> General
4. Open a file and run FbF or MFE/DBSearch to generate multi-level compound results.   Check the columns visible at the second level are correct [Best, ID Source, Name, Formula, Score . . .]
5. Exit Qual
6. Restart Qual.   Load the file and regenerate results
7. Check the table layout.   Second-row columns are now [Score(Acq), Precursor(Acq), Find by MRM Product Ion, . . .]

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When ‘Display level’, Level 1 is clicked on compound table, all the rows show a (+) sign in front of them irrespective of the fact whether they have sublevels or not.

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In the define chromatograms dialog in the method editor, the complete list of detector signals is not displayed.

By right clicking on the TIC of the data file in the Data Navigator window, the additional signal types can be extracted.  Doing this looks in the data file for available signals.

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The column Peak Number found in the integration peak list is not included when a report is generated in Excel.

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When a search is done on a library containing only 1 entry for a compound Qual returns three duplicate hits.   Issue seen on a customer created library.  

Seen in B.04.00

If  the library search is done with the "enable screening" box unchecked, the issue is not seen.

Fixed in B.05.00

Create an xml library.   Go into Qual and navigate to the directory containing the  libarary, software shows the file.
If one 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 extentions 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 declared to have hide known types then the user is forced to type in ".XML" to make the library work.

Alter Windows file extension to display known gile types.

Fixed in B.03.01

Data collected on CI mode on GC Triple Quad does not display the collision energy (CID) in product ion spectra.  The problem is the result of a negative CID value which is incorrectly placed in the data file by data acquisition.  Seen in B.03.01.

None.

Fixed in B.03.01 SP3.  

Also corrected in data acquisition.

Manual integration can give significantly incorrect results under some conditions.  Issue seen in B.03.01 up to SP2.

None.

Fixed in B.03.01 SP3

When data is being acquired on the same precursor but with different product / collision energy combinations and this causes Qual to display “CID=**” on some chromatograms and combine ions into a single spectrum .

None.

With the new data files generated by GC-Triple Quad B.05.01 and later

When a spectra is matched against a mslibrary.xml using Search Unit Mass Library the compound structures are not displayed in the MS Spectrum Results  window.  This defect was also confirmed to exist in B.03.01 SP3 thru B.05.01 SP1.

None

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When the adduct NH4(NH3)2 is entered it is accepted as valid but when the application attempts to generate the mass and error message is generated.

Seen in B.04.00.

Express formula without ().

Fixed B.05.00