Sciex wiff files fail to import on skyline

Sciex wiff files fail to import on skyline esthellehoedt  2023-03-28 18:02

Wiff files fail to import on Skyline. I've looked at the previous requests and installed Skyline daily to try to resolve the issue but the import still fails. I would greatly appreciate some timely help Thanks in advance.
Following is the error message:
At 5:56 PM:
Failed importing results file 'E:\Esthelle\Skyline\PiQuant_7500\ChargeState\Raw_Files\met1.wiff'.
Index was outside the bounds of the array.
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'E:\Esthelle\Skyline\PiQuant_7500\ChargeState\Raw_Files\met1.wiff'.
Index was outside the bounds of the array. ---> System.IndexOutOfRangeException: Index was outside the bounds of the array.
   at pwiz.Common.Collections.ImmutableList`1.Impl.get_Item(Int32 index) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Shared\Common\Collections\ImmutableList.cs:line 261
   at pwiz.Skyline.Model.Results.TimeIntensities.InterpolateTime(Single newTime) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\TimeIntensities.cs:line 346
   at pwiz.Skyline.Model.Results.ChromPeak.IntegrateWithoutBackground(TimeIntensities timeIntensities, Single startTime, Single endTime, FlagValues flags, MedianPeakShape medianPeakShape) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\ChromHeaderInfo.cs:line 1346
   at pwiz.Skyline.Model.Results.PeakIntegrator.IntegratePeakWithoutBackground(Single startTime, Single endTime, FlagValues flags) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\PeakIntegrator.cs:line 121
   at pwiz.Skyline.Model.Results.PeakIntegrator.IntegrateFoundPeak(IFoundPeak peakMax, FlagValues flags) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\PeakIntegrator.cs:line 107
   at pwiz.Skyline.Model.Results.ChromData.CalcChromPeak(PeakGroupIntegrator peakGroupIntegrator, IFoundPeak peakMax, FlagValues flags, IFoundPeak& peak) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\ChromData.cs:line 322
   at pwiz.Skyline.Model.Results.ChromDataSet.GeneratePeakData(TimeIntervals intersectedTimeIntervals) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\ChromDataSet.cs:line 774
   at pwiz.Skyline.Model.Results.PeptideChromDataSets.PickChromatogramPeaks(ExplicitPeakBoundsFunc explicitPeakBoundsFunc) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\PeptideChromData.cs:line 224
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.ScoreWriteChromDataSets(PeptideChromDataSets chromDataSets, Int32 threadIndex) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 106
   at pwiz.Common.SystemUtil.ProducerConsumerWorker`2.Consume(Object threadIndex) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Shared\Common\SystemUtil\ProducerConsumerWorker.cs:line 186
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.PostChromDataSet(PeptideChromDataSets chromDataSet) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 1316
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 441
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\Users\nicksh\git\sky_installer\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 264
Nick Shulman responded:  2023-03-28 18:44
This appears to be caused by a bug in Skyline. I will fix the bug.
It looks like this would only happen if Skyline was not doing background subtraction. There are two things that you could change to prevent Skyline from doing what it is doing:
1. When you go to:
Settings > Transition Settings > Instrument
if the checkbox next to "Triggered chromatogram acquisition" is checked, then uncheck it.
2. Go to:
Settings > Transition Settings > Full Scan
and for "MS/MS filtering Acquisition Method", choose something other than DDA.

If you do those two things then I believe this bug will stop happening to you.

I will fix this bug in a future version of Skyline-daily so that these workarounds would not be necessary.

I think this bug must be caused by some chromatogram that Skyline extracted having zero points in it.
If you feel like it, it would be helpful if you could send me your Skyline document and your .wiff and .wiff.scan files.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file and the .wiff and .wiff.scan files are less than 50MB you can attach them to this support request.
You can upload larger files here:

-- Nick
esthellehoedt responded:  2023-03-29 15:40
Many thanks Nick, it worked all fine!