DIA to mzML question

[jane n]

Hi all,

I have acquired a bunch of files on my Eclipse to build a DIA library using an 8mz window in overlap mode (ie essentially 4mz windows) and I'm not clear if the Convert to MzML is demultiplexing to 4mz windows?  I've tried doing it manually in MSconvert but the conversion fails.  On the other hand, do I need to demulitplex?

Cheers!

-Jane

[David Shteynberg]

Dear Jane,

I cannot help you with the demultiplexing, because I have not used that feature before in MSConvert.  But if you do manage to get a regular DIA mzML file out of the conversion you can use the DISCo tool available in the TPP under Tools->DIA->Extract MS2 Fragments that will generate a new mzML file that you can search and analyze with DDA tools.  As DISCo has recently seen major improvements I can provide you with a release candidate version if you are interested.

Cheers,

-David

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[Science Gurl]

Hey David!

Yes, I'd like to know more about DISCo.  I was poking around that tool too and kinda got lost :)  That's what 3 years away from proteomics will do for you!  The MSconvert within TPP creates mzML files fine, I guess I don't know how to check to see if they have been demultiplexed.  Can I use them in DISCo or should I use the MS2 fragment extractor?

-JN

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[Mark Athanason]

Jane,

See this from the Skyline team:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=DemultiplexingOverlappingDIAWindows

Best

Mark

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[Science Gurl]

Hi Mark,

Thanks for the suggestion... This is what I've been doing but I get an error.  I'll switch this query to the SkyLine team for some more troubleshooting!

-jane

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[Mark Athanason]

If you follow the link further

https://skyline.ms/wiki/home/software/Skyline/page.view?name=OverlappingWindowScheme&_docid=wiki%3A41195689-d578-1036-894e-e465a393d561

they explain how to actually make the isolation scheme in skyline that is compatible with several MS manufacturers; I believe the file is quite large. You may need to re-acquire your data under these circumstances.

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[Science Gurl]

Thanks!

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