Does Skyline perform RT alignment of EI-GC-MS chromatograms spiked-in with deuterated internal standards

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Does Skyline perform RT alignment of EI-GC-MS chromatograms spiked-in with deuterated internal standards capocherokee24500  2021-05-11
 

Hi All,

I am interested in doing untargeted and targeted metabolomics using Ei-GC-MS Orbitraps and I would be keen to know if :

  1. Skyline does RT alignment of EI-GC-MS chromatograms spiked-in with deuterated internal standards and

  2. If skyline can be used to do the following:

    • Import in Skyline EI-GC-MS thermo files as .raw then
    • RT align the files then
    • Perform targeted feature extraction in Skyline then
    • Export the EI-GC-MS thermo files KEEPING THE ALIGNMENT ALREADY performed by skyline then
    • Import the RT aligned thermo files as .raw in compound discoverer (Thermo Scientific) and lastly
    • Perform untargeted feature extraction in Compound discoverer

I am using Compound Discoverer (Thermo) for untargeted analysis but the software does not provide a RT alignment tool that works well with EI-GC-MS data.

Thanks

Best

Carlo

 
 
Brian Pratt responded:  2021-05-12

Hi Carlo,

The mass spec vendors provide DLLs for reading their raw formats, but not for writing them. I don't think you're going to find a tool that can alter raw files the way you're hoping.

Best regards,

Brian Pratt

 
capocherokee24500 responded:  2021-05-13

Thanks Brian,
really appreciate the quick answer.

I have noticed that Skyline supports from 2019 untargeted metabolomics in GC-MS (here is the link of Pawel Sadowski: https://skyline.ms/_webdav/home/software/Skyline/events/2019 User Group Meeting at ASMS/%40files/Presentations/04-Sadowski.pdf)

In the last slide Pawel says that "The pipeline has not yet been optimized for analysis of large datasets over the period of multiple days
where significant RT shift or intensity differences may occur because it does not include RT alignment and correction based on PBQC"

Are you aware if a RT alignment tool is now available to perform GC-MS untargeted metabolomics in Skyline ?

Thanks

Carlo

 
Brendan MacLean responded:  2021-05-13

Hi Carlo,
I know that multiple labs are doing RT alignment now for small molecules, specifically Kaylie Kirkwood for lipids in Erin Baker's lab, and Chris Ashwood for glycans in Rebekah Gundry's lab. They are both LCMS applications, but we did implement non-linear alignment for them.

I will point Pawel Sadowski to this thread and he can perhaps respond about GCMS applications and whether he thinks it is feasible and just hasn't done it himself or he thinks there is still work to be done on our side.

Just to be clear, Skyline is inherently a targeted tool. You always need to specify the molecules you want to target. That can be over 1 million transitions as we see in DIA for proteomics, but you must have some prioir knowledge of what you are looking for.

Thanks for your interest in using Skyline in your research.

--Brendan