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MS Amanda error dkueltz  2020-10-03 18:03
 
Hi,
I am getting the following error message after specifying the PTMS (just CAM and MetOx) for a DDA search with MS Amanda within the latest build of Skyline daily. The error pops up when clicking next after specifying PTMs. I am not sure why the algorithm is looking for heavy isotope mods since I did not specify any of these in the peptide settings or ms amanda ptm options. I did report the error using the otion in the error popup and checked to include the Skyline document (since it was small) but the error report did not seem to work (at least there was no indication that anything happened). Let me know if you need a DDA raw data file for debugging. I am using bruker .d data and can upload a BSA QC file that I used to generate this error.
Thanks,
Dietmar

Skyline version: 20.1.9.268-f970ef4c5 (64-bit)
Installation ID: 62026530-da44-466f-b8a5-1c67fe40d053
Exception type: IndexOutOfRangeException
Error message: Modification type heavy not found.

--------------------

System.IndexOutOfRangeException: Modification type heavy not found.
   at pwiz.Skyline.Model.DocSettings.PeptideModifications.ChangeModifications(IsotopeLabelType labelType, IList`1 prop) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\DocSettings\PeptideSettings.cs:line 1473
   at pwiz.Skyline.FileUI.PeptideSearch.MatchModificationsControl.AddCheckedModifications(SrmDocument document) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\FileUI\PeptideSearch\MatchModificationsControl.cs:line 179
   at pwiz.Skyline.FileUI.PeptideSearch.ImportPeptideSearchDlg.UpdateModificationSettings() in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\FileUI\PeptideSearch\ImportPeptideSearchDlg.cs:line 0
   at pwiz.Skyline.FileUI.PeptideSearch.ImportPeptideSearchDlg.NextPage() in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\FileUI\PeptideSearch\ImportPeptideSearchDlg.cs:line 523
   at System.Windows.Forms.Control.OnClick(EventArgs e)
   at System.Windows.Forms.Button.OnClick(EventArgs e)
   at System.Windows.Forms.Button.OnMouseUp(MouseEventArgs mevent)
   at System.Windows.Forms.Control.WmMouseUp(Message& m, MouseButtons button, Int32 clicks)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ButtonBase.WndProc(Message& m)
   at System.Windows.Forms.Button.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
Exception caught at:
   at System.Windows.Forms.Application.ThreadContext.OnThreadException(Exception t)
   at System.Windows.Forms.Control.WndProcException(Exception e)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Form.ShowDialog(IWin32Window owner)
   at pwiz.Skyline.SkylineWindow.ShowImportPeptideSearchDlg(Nullable`1 workflowType) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 3006
   at pwiz.Skyline.SkylineWindow.importPeptideSearchMenuItem_Click(Object sender, EventArgs e) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 2988
   at System.Windows.Forms.ToolStripItem.RaiseEvent(Object key, EventArgs e)
   at System.Windows.Forms.ToolStripMenuItem.OnClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleClick(EventArgs e)
   at System.Windows.Forms.ToolStripItem.HandleMouseUp(MouseEventArgs e)
   at System.Windows.Forms.ToolStrip.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.ToolStripDropDown.OnMouseUp(MouseEventArgs mea)
   at System.Windows.Forms.Control.WmMouseUp(Message& m, MouseButtons button, Int32 clicks)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ToolStrip.WndProc(Message& m)
   at System.Windows.Forms.ToolStripDropDown.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at pwiz.Skyline.Program.Main(String[] args) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Program.cs:line 306
 
 
Nick Shulman responded:  2020-10-03 18:40
Dietmar,

We did successfully receive your error report. Thank you for sending it.

The problem is that you have changed the name of your Isotope Label Type from "heavy" to "none", and this import peptide search code does not handle that correctly.

What you need to do to work around this problem is go to:
Settings > Peptide Settings > Modifications > Isotope Label Type > <Edit List>
and change it so that the word "heavy" appears at the top of the list.

Then, you actually need to save your Skyline document and open it again (the easiest way to reopen a Skyline document is to choose its name from the recent file list at the bottom of the File menu). There is a bug in the way that the Import DDA Search code is looking for the "heavy" modification type, and a newly renamed one, or one that is not at the top of the list, will not be found.

After you have done that, you will be able to successfully perform a DDA search.

Thank you for reporting this error. We will try to fix it soon.
-- Nick
 
dkueltz responded:  2020-10-04 14:56
Hi Nick,

Thanks for that suggestion. I did rename the "none" isotope label type to "heavy" in the peptide settings but I still get the same error. I also get the error if I do not specify any PTMs for the DDA search. Let me know what else I should try if you have another suggestion. Hopefully, this error can be fixed in one of the next daily releases.

Thanks much,
Dietmar
 
Nick Shulman responded:  2020-10-04 15:52
Hmmm. Renaming the Isotope Label Type, saving, and then reopening the Skyline document was sufficient for me to fix the problem. There might be something additional going wrong.

Can you send me your Skyline document after you have renamed that Isotope Label Type?
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms, spectral libraries, and iRT databases.
If that .zip file is less than 50MB you can attach it to this support request.
Otherwise, you can upload it here:
https://skyline.ms/files.url

This bug manifests itself even if you do not have any heavy modifications. The code is trying to add zero new modifications to the Isotope Label Type named "heavy", and if it does not find it in the correct position in the list, the error happens.
-- Nick
 
dkueltz responded:  2020-10-04 17:12
It actually does work now. I suppose that I did not close and restart Skyline after I renamed the isotope type from "none" to "heavy". I am running a DDA MSamanda search now and look forward to comparing the results with other search engines.
Thanks!
Dietmar