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Failed importing Thermo QE-HF PRM Raw File

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Failed importing Thermo QE-HF PRM Raw File lbeer  2017-06-22 12:26
 
Hello,

I received the following error while importing Thermo PRM Raw files...Please advise.

Specified argument was out of the range of valid values.
Parameter name: The value 66277 must be between 0 and 65535.
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.PostChromDataSet(PeptideChromDataSets chromDataSet) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1273
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 454
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 270

Inner exceptions:
Exception type: System.ArgumentOutOfRangeException
Error message: Specified argument was out of the range of valid values.
Parameter name: The value 66277 must be between 0 and 65535.
Specified argument was out of the range of valid values.
Parameter name: The value 66277 must be between 0 and 65535.
   at pwiz.Skyline.Model.Results.ChromGroupHeaderInfo.CheckValue(Int32 value, Int32 min, Int32 max, Boolean allowNegativeOne) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromHeaderInfo.cs:line 314
   at pwiz.Skyline.Model.Results.ChromGroupHeaderInfo..ctor(SignedMz precursor, Int32 textIdIndex, Int32 textIdLen, Int32 fileIndex, Int32 numTransitions, Int32 startTransitionIndex, Int32 numPeaks, Int32 startPeakIndex, Int32 startScoreIndex, Int32 maxPeakIndex, Int32 numPoints, Int32 compressedSize, Int32 uncompressedSize, Int64 location, FlagValues flags, Int32 statusId, Int32 statusRank, Nullable`1 startTime, Nullable`1 endTime, Nullable`1 collisionalCrossSection) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromHeaderInfo.cs:line 250
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.WriteChromDataSet(ChromDataSet chromDataSet, Dictionary`2 dictScoresToIndex, Boolean saveRawTimes, Boolean isProcessedScans) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1373
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.WriteChromDataSets(PeptideChromDataSets chromDataSets) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1287
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.ScoreWriteChromDataSets(PeptideChromDataSets chromDataSets, Int32 threadIndex) in c:\proj\skyline_3_7_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 101
   at pwiz.Common.SystemUtil.QueueWorker`1.Consume(Object threadIndex) in c:\proj\skyline_3_7_x64\pwiz_tools\Shared\Common\SystemUtil\QueueWorker.cs:line 165


Thanks,
Lynn Beer
 
 
Nick Shulman responded:  2017-06-22 13:34
It looks like Skyline cannot handle more than 65535 points in a chromatogram. You are the first person to run into this limitation.

It would be very helpful to look at your data.
In Skyline, you can use the menu item:
File > Share > (Complete)
to create a .zip file containing your Skyline document and supporting files.

It would be helpful if you could upload that .zip file and the .raw file here:
https://skyline.ms/files.url

Is it true that your .raw file has that many MS1 scans in it? (Alternatively, does it have that many MS2 PRM scans targeting the same precursor?)

You might be able to work around this limitation by changing the "Retention Time Filtering" settings on:
Settings > Transition Settings > Full Scan

If your .raw file really does have that many MS1 scans in it, then we should increase the limit in Skyline.
 
Nick Shulman responded:  2017-06-23 09:44
Actually, this is my mistake. Skyline is incorrectly preventing you from having a chromatogram where the number of MS1 and MS2 matching a particular precursor is more than 65535.
I will try to fix this in the next update of Skyline 3.7.

Thanks for reporting this.
 
lbeer responded:  2017-09-07 08:37
Hi I was wondering if there is any update to this error or an expected fix? We are testing 3H method (Full-MS followed by PRM) on a Q-Exactive HF. I do have over 65,000 MS1 scans in these RAW files, and hence cannot import the data into Skyline. Do you have any suggestions for cutting down on the number of MS1 scans, either in the mass-spec method or by filtering in Skyline? The Retention Time filtering that you had suggested didn't work.

Thanks.
 
Nick Shulman responded:  2017-09-07 09:55
I believe this has been fixed in Skyline-Daily.

We have not any updates of Skyline 3.7 since June, so the bug still exists in the current Skyline 3.7.