Tried uploading mzML and mzXML files does not work

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Tried uploading mzML and mzXML files does not work rodriguezj5  2020-02-27
 

I have proteowizard and tried uploading mzML and mzXML files. I also tried converting my raw files using the peak picking option on proteowizard. Peak picking option says "Vendor (does not work for...."
Please let me know how to upload mzML files to skyline.

 
 
Nick Shulman responded:  2020-02-28
Can you tell us a little more about your data so that we can point you at the most appropriate tutorials?

If you have done a peptide search and would like to use Skyline to extract chromatograms from MS1 scans, then you should take a look at the MS1 Full Scan Filtering tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering

The "Peak Picking" option in MSConvert actually refers to converting scans from profile to centroided data, and is not what you want.
-- Nick
 
rodriguezj5 responded:  2020-02-28
Thermo Raw file and specifically analyzing glycosaminoglycans. It is not proteomics data
 
Nick Shulman responded:  2020-02-28
If you have a triple quadrupole, you should have a look at the Small Molecule Targets tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_small_molecule

Otherwise, you might find the high resolution metabolomics tutorial more helpful:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_hi_res_metabolomics

-- Nick