Problem with Importing a Particular Document roman sakson  2020-01-23
 
Dear Skyline-Team,

I am trying to import one Skyline document (To_Import.sky) into another (Target.sky). When I do that (I choose to add new replicates and to merge matching peptides), I get the following error message:

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Skyline-daily
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Data cache files with different score types cannot be joined.
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OK More Info
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System.IO.InvalidDataException: Data cache files with different score types cannot be joined.
   at pwiz.Skyline.Model.Results.ChromCacheJoiner.JoinNextPart() in C:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Results\ChromCacheJoiner.cs:line 135
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In the resulting file, it seems that the import worked for one of the two peptides but not for other. Also, things like "order according to acquired time" do not work anymore but when I manually import the corresponding wiff-files, everything seems fine. I cannot share the resulting file, when I try I get another error message:

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Skyline-daily
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The document must be fully loaded before it can be shared.
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OK More Info
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System.IO.IOException: Settings.MeasuredResults Not all chromatogram sets are loaded - No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\19.07.19_Arsenite\Wiff\19.07.19_RS_Arsenite_R1_Ctrl.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\190516_43_degree\19.07.19_RS_Arsenite_R1_0h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\190516_43_degree\19.07.19_RS_Arsenite_R1_1h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\19.07.19_Arsenite\Wiff\19.07.19_RS_Arsenite_R1_6h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\19.07.19_Arsenite\Wiff\19.07.19_RS_Arsenite_R1_12h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\190516_43_degree\19.07.19_RS_Arsenite_R1_24h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\190516_43_degree\19.07.19_RS_Arsenite_R3_Ctrl.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\190516_43_degree\19.07.19_RS_Arsenite_R3_0h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\190516_43_degree\19.07.19_RS_Arsenite_R3_1h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\190516_43_degree\19.07.19_RS_Arsenite_R3_6h_II.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\190516_43_degree\19.07.19_RS_Arsenite_R3_12h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\190516_43_degree\19.07.19_RS_Arsenite_R3_24h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\19.07.19_Arsenite\Wiff\19.07.19_RS_Arsenite_R2_Ctrl.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\19.07.19_Arsenite\Wiff\19.07.19_RS_Arsenite_R2_0h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\19.07.19_Arsenite\Wiff\19.07.19_RS_Arsenite_R2_1h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\19.07.19_Arsenite\Wiff\19.07.19_RS_Arsenite_R2_6h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\19.07.19_Arsenite\Wiff\19.07.19_RS_Arsenite_R2_12h.wiff;No ChromFileInfo.FileWriteTime for C:\Users\Roman Sakson\Desktop\Sophie_London\SK_Uebergabe\19.07.19_Arsenite\Wiff\19.07.19_RS_Arsenite_R2_24h.wiff
   at pwiz.Skyline.SkylineWindow.ShareDocument() in C:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1183
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I used to move those Skyline-files quite a bit after I have imported the results for the first time and if I get it right, at some point the link between the skyd file and the wiff files got lost somehow? I would just like to know whether I am allowed to relocate my Skyline documents to be able to import them somewhere else later on.

Thank you!

Roman
 
 
Nick Shulman responded:  2020-01-23
Roman,

You need to do a "rescore" on that "To_Import.sky".

That is, you should go to:
Edit > Manage Results > Rescore

After you do that, I expect that you will be able to import this rescored document into Target.sky.

When you extract chromatograms, Skyline calculates all of the scores that require looking at the chromatogram peak shapes. Some of those scores involve comparing the peak shape of the heavy and light peptides. These are called "reference peak shape scores". As an optimization, Skyline does not calculate these reference peak shape scores if Skyline does not believe that you have any heavy peptides in your document. The way that Skyline decides whether you have any heavy peptides is by seeing whether you have any Isotope Modifications checked at "Settings > Peptide Settings > Modifications".

I believe that when you extracted chromatograms in the file "To_Import.sky" you did not have any isotope modifications checked in your Peptide Settings. I think your settings have been changed in this file since the time when chromatograms were extracted. This is why doing a "rescore" works to make it so that the set of scores in "Target.sky" are the same as those in "To_Import.sky".

I will try to fix this in the next version of Skyline so that these documents can be merged without doing this rescore. For now, if you want to merge documents you need to make sure that both documents either have or do not have any isotope modifications checked in the peptide settings, and you potentially have to do a rescore after bring the set of modifications into alignment.

Thank you for reporting this problem and I hope my instructions are understandable and fix your problem.
-- Nick
 
roman sakson responded:  2020-01-24
Hi Nick,

thank you for the fast response! Indeed, rescoring seems to have solved my problem! Do I understand it correctly that peak integration boundaries might change in larger documents after rescoring? If so, would it be possible to rescore and save as new and then import the peak boundaries from the old version of "To_Import.sky" into the new rescored one?

Thanks a lot,

Roman
 
Nick Shulman responded:  2020-01-24
Roman,

Skyline remembers whether a particular peak was chosen by Skyline, or whether the user manually adjusted the peak boundaries. In the document grid, the column "User Set" (on the Transition Result) tells you whether a peak was manually adjusted.

When you do a "reimport" or "rescore" from the Manage Results dialog, Skyline will always preserve the peak boundaries of the manually adjusted peaks.

By the way, I noticed a bug in Skyline where you will get an error if you try to do "File > Import > Document" after having done a "rescore". We will fix that error in an upcoming release of Skyline-Daily, but, for now, if you want to import a document into a document that has just been rescored you should reopen the document in Skyline. The easiest way to reopen a document in Skyline is to choose its filename from the list at the bottom of the file menu.

-- Nick
 
roman sakson responded:  2020-01-28
Nick,

great, I was not aware of "User Set", this is very helpful as I used to be quite paranoid about such things! Thank you very much for your quick help!

Hope to see you at the Skyline User Meeting in Houston!

Roman