Fail to import SWATH results: Sequence contains no elements

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Fail to import SWATH results: Sequence contains no elements laura declerck  2017-12-18 08:12
 
Dear Skyline team,

Yet, another issue appeared.

I fail to insert my SWATH results (.wiff files):


At 5:00 PM:
Failed importing results file 'C:\Skyline\Histones_Micro\data\171205_LDC_Hist_SWATH_60W_4000_B.wiff'.
Sequence contains no elements


Inner exceptions:
Exception type: System.Reflection.TargetInvocationException
Error message: Sequence contains no elements
Sequence contains no elements
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Util\Util.cs:line 1832
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Collectors.ReleaseChromatogram(Int32 chromatogramIndex, ChromGroups chromGroups, TimeIntensities& timeIntensities) in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 1143
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.GetChromatogram(Int32 id, Target modifiedSequence, Color peptideColor, ChromExtra& extra, TimeIntensities& timeIntensities) in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 555
   at pwiz.Skyline.Model.Results.ChromData.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\ChromData.cs:line 76
   at pwiz.Skyline.Model.Results.ChromDataSet.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\ChromDataSet.cs:line 213
   at pwiz.Skyline.Model.Results.PeptideChromDataSets.Load(ChromDataProvider provider) in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\PeptideChromData.cs:line 142
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 455
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 272
---------------------------------------------------------------
Exception type: System.InvalidOperationException
Error message: Sequence contains no elements
Sequence contains no elements
   at System.Linq.Enumerable.Average(IEnumerable`1 source)
   at pwiz.Skyline.Model.Results.OverlapDeconvSolverHandler.BuildDeconvBlock() in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\OverlapDemultiplexer.cs:line 142
   at pwiz.Skyline.Model.Results.AbstractDeconvSolverHandler.Solve(ILsSolver solver) in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\AbstractDemultiplexer.cs:line 524
   at pwiz.Skyline.Model.Results.AbstractDemultiplexer.GetDeconvolvedSpectra(Int32 index, MsDataSpectrum originalSpectrum) in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\AbstractDemultiplexer.cs:line 388
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatogramsLocked() in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 318
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatograms() in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 215
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.<SetRequestOrder>b__8() in c:\Users\nicksh\svn\skyline_4_1\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 540



First I thought it had something to do with the fact that my library is built out of multiple .dat files searches with different parameters to be able to extract iRT.
But, when I do not use iRT calculation, this problem still appears.

Would you be able to help me?
I put the .Sky file and the .wiff file in a dropbox link (https://www.dropbox.com/sh/t1l7uuygdy8n31x/AACJc5l1CO8JRVhf7ixPZvkCa?dl=0).


Kind rergards,
Laura
 
 
Nick Shulman responded:  2017-12-18 09:12
It looks like you might be trying to do deconvolution.
That is, you have chosen something other than "None" for "Deconvolution" on the Isolation Scheme editor at:
Setting > Transition Settings > Full Scan > MS/MS filtering > Isolation Scheme

Did you intend to do that? When you do that, Skyline does a bunch of matrix math to handle MS2 scans whose isolation windows overlap with each other (and that is where the error is happening in Skyline).

You probably meant to choose "None" for "Deconvolution".

If you were trying to do Deconvolution, we no longer recommend doing it in Skyline. Instead, you would use ProteoWizard MSConvert to create a deconvoluted .mzML file.