Error with method export for SCIEX QTOF after upgrade to Analyst TF 1.8.1

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Error with method export for SCIEX QTOF after upgrade to Analyst TF 1.8.1 stephan kamrad  2021-06-03
 
Hi,
I have been using Skyline very successfully for a while to generate .dam acquisition methods for our Sciex 6600.
We recently upgraded to Analyst TF 1.8.1 and now the method export crashes Analyst and produces the following error.
I am doing this on the instrument computer with the correct hardware profile activated and I am using .sky and template .dam files which have worked before.
Can you help?

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Problem signature:
  Problem Event Name: BEX
  Application Name: Analyst.exe
  Application Version: 3.7323.0.2
  Application Timestamp: 5d69ae47
  Fault Module Name: MSVCR90.dll
  Fault Module Version: 9.0.30729.6161
  Fault Module Timestamp: 4dace5b9
  Exception Offset: 0006ccd5
  Exception Code: c0000417
  Exception Data: 00000000
  OS Version: 6.1.7601.2.1.0.256.48
  Locale ID: 1033
  Additional Information 1: 0120
  Additional Information 2: 0120e0cf538c5533ae847dad19fdbdc5
  Additional Information 3: 9694
  Additional Information 4: 969458d6bc7742c30d364858d5a7bf8e
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-System.IO.IOException: ERROR: Failure creating method file D:\Analyst Data\Projects\Stephan_June20\Acquisition Methods\20210603_K_gluC.dam. The remote procedure call failed. (Exception from HRESULT: 0x800706BE)

Command-line: Method\AbSciex\TOF\BuildAnalystFullScanMethod -s -m "D:\Analyst Data\Projects\Stephan_June20\Acquisition Methods\20min_Skiline_template_40acc.dam"
Working directory: D:\Analyst Data\Projects\Stephan_June20\Acquisition Methods
Standard input:
D:\Analyst Data\Projects\Stephan_June20\Acquisition Methods\~SKB61F.tmp
D:\Analyst Data\Projects\Stephan_June20\Acquisition Methods\20210603_K_gluC.dam
578.90178,1022.681192,0,peptides1.KYSLAPVAKE.+2y9.heavy,80,26.1,0.0578901780195,0.102268119234,peptides1.KYSLAPVAKE.heavy,,,,
578.90178,850.58767,0,peptides1.KYSLAPVAKE.+2y8.heavy,80,26.1,0.0578901780195,0.0850587669765,peptides1.KYSLAPVAKE.heavy,,,,
578.90178,760.545576,0,peptides1.KYSLAPVAKE.+2y7.heavy,80,26.1,0.0578901780195,0.076054557633,peptides1.KYSLAPVAKE.heavy,,,,
578.90178,641.441383,0,peptides1.KYSLAPVAKE.+2y6.heavy,80,26.1,0.0578901780195,0.0641441383315,peptides1.KYSLAPVAKE.heavy,,,,
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   at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 65
   at pwiz.Skyline.Util.Extensions.UtilProcess.RunProcess(ProcessStartInfo psi, String stdin, String messagePrefix, IProgressMonitor progress, IProgressStatus& status) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Util\Extensions\UtilProcess.cs:line 45
   at pwiz.Skyline.Model.MethodExporter.ExportMethod(String exeName, List`1 argv, String fileName, String templateName, Dictionary`2 dictTranLists, IProgressMonitor progressMonitor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Export.cs:line 4291
   at pwiz.Skyline.Model.AbiMethodExporter.ExportMethod(String fileName, String templateName, IProgressMonitor progressMonitor) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Export.cs:line 2447
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 254
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Util\Util.cs:line 1938
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 202
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 140
   at pwiz.Skyline.FileUI.ExportDlgProperties.PerformLongExport(Action`1 performExport) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\FileUI\ExportMethodDlg.cs:line 2116
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stephan kamrad responded:  2021-06-04
After a lot of trial and error I found out that this is because SCIEX's new Scanning SWATH acquisition software was installed on the PC. It seems like this is incompatible with Skyline method exports.
Luckily it's really easy to uninstall and reinstall, which works as a workaround.
 
Brendan MacLean responded:  2021-06-04
I have passed this along to one of our contacts at SCIEX, who is going to pass it on to the Analyst team in the hope that it will be fixed by the time Scanning SWATH is directly supported by the Analyst installer... i.e. when it will become impossible to use the workaround you came up with.

Thanks for posting to the Skyline support board where others may find your investigation helpful.

--Brendan