Sciex analyst .wiff files fails to import showing: Object reference not set to an instance of an object. kamal  2019-09-02

Dear Skyline Team,

In my experiment, each replication’s retention time is 6 hour. However the *.wiff and *.wiff.scan files comes in 3 part for each run. For example, P100_Cold_30min (Cold stress for 30 min) comes in P100_Cold_30min-1_1, P100_Cold_30min-1_2, P100_Cold_30min-1_3

On the other hand, the *.group and *.group.xmlcomes in single file P100_Cold_30min-1 as the following screenshot.
The MGF files also come in a single part which I used to generate mascot DAT file as an alternative to the group.xml files for creating the spectral library.

I am using these *.group and *.group.xml or just mascot DAT files to create the spectral library for MS1 based DDA analysis. However, it seems like that when importing the final results the following problem is occurring-

At 5:42 PM:
Failed importing results file 'C:\Kamal RIKEN DATA\190614\P100_Cold_30min-1_3.wiff'.
Object reference not set to an instance of an object.

Inner exceptions:
Exception type: System.NullReferenceException
Error message: Object reference not set to an instance of an object.
Object reference not set to an instance of an object.
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.Spectra.get_PercentComplete() in C:\proj\skyline_19_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 805
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.UpdatePercentComplete() in C:\proj\skyline_19_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 598
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.GetChromatogram(Int32 id, Target modifiedSequence, Color peptideColor, ChromExtra& extra, TimeIntensities& timeIntensities) in C:\proj\skyline_19_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 586
at pwiz.Skyline.Model.Results.ChromData.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in C:\proj\skyline_19_1_x64\pwiz_tools\Skyline\Model\Results\ChromData.cs:line 77
at pwiz.Skyline.Model.Results.ChromDataSet.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in C:\proj\skyline_19_1_x64\pwiz_tools\Skyline\Model\Results\ChromDataSet.cs:line 236
at pwiz.Skyline.Model.Results.PeptideChromDataSets.Load(ChromDataProvider provider) in C:\proj\skyline_19_1_x64\pwiz_tools\Skyline\Model\Results\PeptideChromData.cs:line 144
at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_19_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 460
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_19_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 263

I am in desperate need of help because of my graduation deadline is approaching soon.

Best regards,

Nick Shulman responded:  2019-09-03

I think I have seen this error before and you can work around this bug by going to:
Settings > Transition Settings > Full Scan
and under "Retention Time Filtering" at the bottom choose anything other than the one about MS/MS IDs.

This error can happen if the retention times in your spectral library are bogus so that it is not possible for Skyline to do a linear regression between the retention times in the runs in the library.

It would be helpful if you could send us your Skyline document and your .wiff and .wiff.scan files, and I will be sure to fix this bug.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including spectral library.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:

It would also be helpful if you could send me P100_Cold_30min-1_3.wiff and P100_Cold_30min-1_3.wiff.scan

-- Nick
kamal responded:  2019-09-16
Hi Nick,

Sorry for the late feedback. Thanks for your detailed suggestions. I was able to import all the results using your instructions.