Failed importing results from mzML file

Failed importing results from mzML file michal zawadzki  2020-10-02

Dear Skyline Team,

I am trying to upload an mzML file converted from a Thermo .raw file with MSConvert into a Skyline document where I have already imported a chromatogram library generated by EncyclopeDIA. I do not think the file is corrupted as I am able to use it in EncyclopeDIA without any issues.

I use Skyline (64bit) (a0e7323e3) and MSConvert (Version: 3.0.20219-6a8ecb8e3 (developer build)).

Below is a full text of the error I am getting:

At 12:11:
Failed importing results file 'C:\Users\u525581\Desktop\Skyline EX4163G_DIA_maize_embryos_310720\20200731_EX4163C_001_01.mzML'.
[IO::HandlerBinaryDataArray] Unknown binary data type.

Inner exceptions:
Exception type: System.Exception
Error message: [IO::HandlerBinaryDataArray] Unknown binary data type.
[IO::HandlerBinaryDataArray] Unknown binary data type.
at pwiz.CLI.msdata.ChromatogramList.chromatogram(Int32 index, Boolean getBinaryData)
at pwiz.ProteowizardWrapper.MsDataFileImpl.GetChromatogram(Int32 chromIndex, String& id, Single[]& timeArray, Single[]& intensityArray) in C:\proj\skyline_20_1_x64\pwiz_tools\Shared\ProteowizardWrapper\MsDataFileImpl.cs:line 616
at pwiz.Skyline.Model.Results.GlobalChromatogramExtractor.GetChromatogram(Int32 index, Single[]& times, Single[]& intensities) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromDataProvider.cs:line 172
at pwiz.Skyline.Model.Results.SpectraChromDataProvider.GetChromatogram(Int32 id, Target modifiedSequence, Color peptideColor, ChromExtra& extra, TimeIntensities& timeIntensities) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 599
at pwiz.Skyline.Model.Results.ChromData.Load(ChromDataProvider provider, Target modifiedSequence, Color peptideColor) in C:\proj\skyline_20_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_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromDataSet.cs:line 236
at pwiz.Skyline.Model.Results.PeptideChromDataSets.Load(ChromDataProvider provider) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\PeptideChromData.cs:line 144
at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 439
at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_20_1_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 252

Would you be able to advice how to solve this problem, please?

Nick Shulman responded:  2020-10-02
It appears that current versions (newer than May, 2020) of msconvert produce .mzML files which are not compatible with older versions (20.1 or earlier) of Skyline.

I would recommend that you use Skyline-Daily for now instead of Skyline 20.1. We are going to release Skyline version 20.2 in a week or so. Skyline version 20.2 will be able to handle this data just fine.

We made a change to msconvert in May so that the TIC chromatogram includes extra information about the MS Level of each of the spectra. We did not realize that this would cause problems for older versions of Skyline. Thank you for letting us know about this problem.

I am going to ask around and find out if there is a way for us to fix this backwards-compatibility issue with msconvert.
-- Nick
michal zawadzki responded:  2020-10-02
The suggestion to use Skyline-Daily has worked great. It has solved the problem. I am looking forward to installing the new release in the near future.

Thank you for your prompt response and help.

Best wishes,