GC-MS SIM data import

support
GC-MS SIM data import fiammetta dimarco  2022-07-27
 
Hello,
I have a problem in importing GC-MS data acquired in SIM mode. I followed the guideline "GCMS Data Analysis" and I was able to import GC-MS of Shimadzu coverted in mzXML acquired in scan mode but when I try to import the SIM GC-MS data it doesn´t work and it gives the following error:

At 22:07:
Failed importing results file 'C:\Users\b1064562\Desktop\GC-MS steroids\raw file\270725_FDM_mix std overnight_5ugmL_50MO_SIM_1.mzXML'.
Unable to determine isolation width for the scan targeted at 268
pwiz.Skyline.Model.Results.ChromCacheBuildException: Failed importing results file 'C:\Users\b1064562\Desktop\GC-MS steroids\raw file\270725_FDM_mix std overnight_5ugmL_50MO_SIM_1.mzXML'.
Unable to determine isolation width for the scan targeted at 268 ---> System.IO.InvalidDataException: Unable to determine isolation width for the scan targeted at 268
   at pwiz.Skyline.Model.Results.SpectrumFilter.CalcDiaIsolationValues(SignedMz& isolationTargetMz, Nullable`1& isolationWidth) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\SpectrumFilter.cs:line 1211
   at pwiz.Skyline.Model.Results.SpectrumFilter.FindFilterPairs(IsolationWindowFilter isoWin, FullScanAcquisitionMethod acquisitionMethod, Boolean ignoreIsolationScheme) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\SpectrumFilter.cs:line 1093
   at pwiz.Skyline.Model.Results.SpectrumFilter.<Extract>d__105.MoveNext() in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\SpectrumFilter.cs:line 820
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ProcessSpectrumList(MsDataSpectrum[] spectra, ChromDataCollectorSet chromMap, Single rt, SpectrumFilter filter, String scanId) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 511
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatogramsLocked() in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 353
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.ExtractChromatograms() in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 239
   at pwiz.Skyline.Model.Results.SpectraChromDataProvider.SetRequestOrder(IList`1 chromatogramRequestOrder) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\SpectraChromDataProvider.cs:line 594
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.Read(ChromDataProvider provider) in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 384
   at pwiz.Skyline.Model.Results.ChromCacheBuilder.BuildCache() in C:\proj\skyline_20_2_x64\pwiz_tools\Skyline\Model\Results\ChromCacheBuilder.cs:line 252
   --- End of inner exception stack trace ---

Do you have an idea of what is wrong? Shall I change the transition settings (they are set as described in the guideline "GCMS Data Analysis")?

Thank you for the help!
 
 
Nick Shulman responded:  2022-07-27
I think that error means that the isolation scheme specified at "Settings > Transition Settings > Full Scan" says "Use results data isolation targets" and also, says "Results" for the Isolation Width, and the Results File (i.e. the .mzXML file) does not say how wide the isolation window was.

One way to deal with this would be to change the isolation scheme so that you are explicitly telling Skyline how wide the windows are.

If possible, I would also recommend that you use the mzML format instead of the mzXML format. The mzXML format is very old, and is missing a lot of information that Skyline relies on to figure out what the DIA isolation scheme was.
-- Nick
 
fiammetta dimarco responded:  2022-07-27
Dear Nick,
Thank you for the answer. At "Settings > Transition Settings > Full Scan" I set "All ions". How should I explicity tell skyline the wide of the isolation windows?
Thank you,
Fiammetta
 
fiammetta dimarco responded:  2022-07-27
Dear Nick,
Also regarding the mzXML format, I have a Shimadzu instrument and I can only convert the file in mzXML format, I didn't find a way to convert it in mzML.
Thank you,
Fiammetta
 
Nick Shulman responded:  2022-07-27
It's not supposed to be possible to get the "Unable to determine isolation width..." error if your isolation scheme is "All Ions".
Can you send us your Skyline document and mzXML file? I will figure out what is going on.

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 .mzXML file are less than 50MB you can attach them to this support request. You can upload larger files here:
https://skyline.ms/files.url

What type of file was the mzXML file converted from? Skyline knows how to read Shimadzu ".lcd" files, so if that is what you were starting with, then you would not need to convert it to mzXML. If you had some other sort of file, then, yes, whatever conversion you had available might be all there is.
-- Nick
 
fiammetta dimarco responded:  2022-07-27
Dear Nick,
Thank you for your help. The file format is .qgd because it's a GC-MS file from Shimadzu, this is why I converted it as described in the guideline "GCMS data analysis".
I attached the skyline file containg the GC-MS data in scan mode already imported and the mzXML file of the GC-MS file in SIM mode that I have problem to import.
Thank you,
Fiammetta
 
Nick Shulman responded:  2022-07-27
Thank you for sending that file.
I see that you are using Skyline version 20.2.
The latest released version of Skyline is 21.2.
If you use a current version of Skyline, you will not get that error when you try to import chromatograms from that .mzXML file in All Ions mode.

It appears that this scenario was fixed last October in response to the following support request:
https://skyline.ms/announcements/home/support/thread.view?rowId=52898
That other support request does not sound like it has much similarity to your scenario, but it does mention "All Ions" somewhere in the middle of it.

Please try this with the current version of Skyline and let us know if something else might need fixing.
-- Nick
 
fiammetta dimarco responded:  2022-07-28
Dear Nick,
THank you, I solved the problem of importing changing the skyline version to 21.2 but anyway I am not able to recognize all the ion peaks in the transition list even if I am sure from the Shimadzu software that these ions are present. Can this be an issue of the mzXML format used with skyline?
Thank you,
Fiammetta
 
Nick Shulman responded:  2022-07-28
If I right-click on your chromatograms, and choose "Transform > None", I see that your chromatograms are very jagged, and jump between zero and some other number. This usually indicates that there were two different types of spectra which are contributing to the extracted chromatogram.

There was another user who also had chromatograms from Shimadzu mzXML files that looked like that:
https://skyline.ms/announcements/home/support/thread.view?rowId=53031
-- Nick