Hi,
I hope you can give me some advice. My Skyline document contains 12 SWATH files from a 5600+ instrument (the skyd file is 35GB). The library contains 3500 proteins. When trying to run MSstats group comparison, I get the error message below (Skyline daily ran out of memory). I am wondering how to solve this. Would you have any suggestions? I am using the latest Skyline daily version. Do I have to use Skyline runner?
Many thanks,
Silvia
pwiz.Skyline.Model.Tools.ToolExecutionException: The tool MSstats\Group Comparison had an error, it returned the message:
Array dimensions exceeded supported range. ---> System.OutOfMemoryException: Array dimensions exceeded supported range.
at System.Windows.Forms.Control.MarshaledInvoke(Control caller, Delegate method, Object[] args, Boolean synchronous)
at System.Windows.Forms.Control.Invoke(Delegate method, Object[] args)
at pwiz.Skyline.Model.Tools.ToolDescription.CallArgsCollector(Control parent, String args, String reportCsv, String pathReportCsv, ProcessStartInfo startInfo) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 530
--- End of inner exception stack trace ---
at pwiz.Skyline.Model.Tools.ToolDescription.CallArgsCollector(Control parent, String args, String reportCsv, String pathReportCsv, ProcessStartInfo startInfo) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 548
at pwiz.Skyline.Model.Tools.ToolDescription.RunExecutableBackground(SrmDocument document, IToolMacroProvider toolMacroProvider, TextWriter textWriter, IProgressMonitor progressMonitor, Control parent) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 393
at pwiz.Skyline.Model.Tools.ToolDescription.<>c__DisplayClassa.<RunExecutable>b__9() in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Tools\ToolDescription.cs:line 335 |
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| Nick Shulman responded: |
2018-04-18 11:24 |
There is a limit on the size of a report that the MSstats external tool can handle. I don't remember exactly what that limit is, but it's approximately 2GB.
I believe it would be straightforward to remove this limitation.
Could you send me your Skyline document?
In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
You can upload that .zip file here:
https://skyline.ms/files.url |
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| sas28 responded: |
2018-04-19 03:00 |
ok uploading at the moment. After using your instructions the skyline file didn't compress a lot, it is still 34GB, I hope it won't be too large. I can see largest files are only 2-7GB on the file sharing folder. |
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| Nick Shulman responded: |
2018-04-19 15:24 |
I have attached a new version of the MSstats external tool which can handle larger documents.
This tool would still choke if you had twice as much data in your Skyline document as you currently have. I am going to keep working on fixing Skyline to remove all of the size limitations in this area, and then I will update the official version of the MSstats external tool in the Skyline Tool Store.
To use this special external tool in Skyline, first download the attached .zip file.
Then, in Skyline, use the menu item:
Tools > External Tools
Then press the "Add" button and choose "From File" and browse to where you downloaded the attached .zip file.
Note that in the Skyline document that you sent me, you have some duplicated peptides which are going to cause MSstats to choke. You should use the Skyline menu item:
Edit > Refine > Remove repeated peptides
to get rid of the extra copies of the peptides that you have. |
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| sas28 responded: |
2018-04-20 03:12 |
Thanks a lot for sending the zip file. I have installed the new version of MS stats (v 3.8.5), removed any duplicated peptides (though i didn't see any and refine > remove repeated peptides has not decreased the number of peptides in the document). Unfortunately MS stats > group comparison is still running out of memory (same error as above).
I don't think i have duplicated peptides but how can i manually check for this? |
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| Nick Shulman responded: |
2018-04-20 09:42 |
It turns out that after you install the new version of the MSstats external tool that I sent you, you have to exit and restart Skyline in order to actually be running with the new code.
The .sky file that you sent me only had about 3 repeated peptides in it. If you do have repeated peptides in your Skyline document, MSstats will give you an error about duplicate rows that will show up in the Immediate Window. |
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| sas28 responded: |
2018-04-25 04:50 |
Great. It is working now. Thank you so much for your help. You are incredibly efficient. |
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MSstats.zip