Hi Tobi,
Standard as it may be, you are the first actual Skyline user to ever request this. Also, I have offered multiple times to help anyone producing TraML to implement a TraML reader in Skyline, or also a TraML converter would not be a bad idea.

It is clear from the data supplement to this paper that the authors used Skyline. Maybe you could ask them to post their Skyline documents to Panorama Public for public access? We just presented a tutorial webinar on how to do this:

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/events/2015%20Webinars/Webinar%2011/begin.view

And there is also a 24 page tutorial that covers the step-by-step.

Otherwise, I am surprised that they have not provided the standard tab separated format also in use at the Aebersold lab, which is in fact more widely supported by DIA/SWATH tools other than OpenSWATH.

It may finally be time that the Skyline team devote our own resources to implementing TraML support, and this is certainly a very nice test case for us. Until just now, it has not seemed in use enough to require such an effort. I have added it to our very long list of todos:

https://skyline.gs.washington.edu/labkey/issues/home/issues/details.view?issueId=436

No promises on how quickly we can get to it. I think your best workaround at the moment is to contact the authors about a Skyline document or TSV formatted "assay library", use of which is covered in the "Importing Assay Libraries" tutorial on the following wiki page:

https://skyline.gs.washington.edu/labkey/wiki/home/software/Skyline/page.view?name=other_tools

Note also that assay library import has been greatly improved since Skyline v3.1, so if you go that route, it is highly recommended that you use Skyline-daily until after the next public release.

Thanks for bringing this issue with the supplementary data in this manuscript to our attention.

--Brendan

Hi Tobi,
Also from one of the authors:

"A good solution may be to convert the TraML to csv format which should be readable by Skyline. This can be done for example using the ConvertTraMLToTSV tool available in the OpenMS software collection."

So, apparently, there is a TraML2csv (or at least TraMLToTSV) as you had suggested. Another option.

Thanks for getting this onto the support board. I am sure others may find the discussion useful.

--Brendan

Hi Brendan,

thx for your great help! It is interesting that so many of these "official" XML-based data formats (mz(X)ML, traML, identML) are so little appreciated by the proteomics community. But I guess this is for a reason. ;-)

I will try to convert the traML file using the openMS tool box. I report how it worked out for me.

Greetings,
Tobi

btw: Are you aware of any project/initiative that wants to implement more user friendly/performant/none-greedy open-source data formats for MS-based proteomics?

Hi Tobi and Brendan,

Tobi, would you be able to let me know how you converted traML to TSV in the end? Did you use openMS, if so, could you please let me know how you did the conversion?

I've successfully converted a traml to tsv using TOPPAS. When I try to import this transition list csv file into skyline via import - transition lists I receive an error message.

Failed reading the file ...test.tsv. Unrecognized Unimod id 35 in modified peptide sequence

Below is more info.
Would appreciate any help on this.
regards,
Moe


System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence. ---> System.IO.InvalidDataException: Unrecognized Unimod id 35 in modified peptide sequence.
   at pwiz.Skyline.Model.ModificationMatcher.SimplifyUnimodSequence(String seq) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 277
   at pwiz.Skyline.Model.ModificationMatcher.IsMatch(String seq, PeptideDocNode nodePep, TransitionGroupDocNode& nodeGroup) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 350
   at pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String seq, PeptideDocNode nodePep, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 493
   at pwiz.Skyline.Model.AbstractModificationMatcher.CreateDocNodeFromSettings(String seq, Peptide peptide, SrmSettingsDiff diff, TransitionGroupDocNode& nodeGroupMatched) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 466
   at pwiz.Skyline.Model.ModificationMatcher.MoveNextSequence() in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 60
   at pwiz.Skyline.Model.AbstractModificationMatcher.InitMatcherSettings(SrmSettings settings, MappedList`2 defSetStatic, MappedList`2 defSetHeavy) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\AbstractModificationMatcher.cs:line 79
   at pwiz.Skyline.Model.ModificationMatcher.CreateMatches(SrmSettings settings, IEnumerable`1 sequences, MappedList`2 defSetStatic, MappedList`2 defSetHeavy) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\ModificationMatcher.cs:line 44
   at pwiz.Skyline.Model.MassListImporter.MassListRowReader..ctor(IFormatProvider provider, Char separator, ColumnIndices indices, SrmSettings settings, IEnumerable`1 sequences) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 615
   at pwiz.Skyline.Model.MassListImporter.GeneralRowReader.Create(IList`1 lines, IList`1 headers, Int32 iDecoy, IFormatProvider provider, Char separator, SrmSettings settings, Int32 iirt, Int32 iLibrary) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 1164
   at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, ColumnIndices indices, IDictionary`2 dictNameSeq, List`1& irtPeptides, List`1& librarySpectra, List`1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 413
   at pwiz.Skyline.Model.MassListImporter.Import(IProgressMonitor progressMonitor, List`1& irtPeptides, List`1& librarySpectra, List`1& errorList) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Import.cs:line 334
   at pwiz.Skyline.Model.SrmDocument.ImportMassList(MassListInputs inputs, IProgressMonitor progressMonitor, IdentityPath to, IdentityPath& firstAdded, List`1& irtPeptides, List`1& librarySpectra, List`1& errorList, List`1& peptideGroups) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1075
   at pwiz.Skyline.SkylineWindow.<>c__DisplayClass15b.<ImportMassList>b__14f(IProgressMonitor longWaitBroker) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1602
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 213
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1587
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 161
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 115
   at pwiz.Skyline.SkylineWindow.ImportMassList(MassListInputs inputs, String description) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1600
   at pwiz.Skyline.SkylineWindow.ImportMassList(String fileName) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 1576