Interface between Bruker raw files and Skyline.
Once a dataset is acquired:
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Run MALDISkylink (converts a Bruker file into mzxml file via msconvert, then adds the required blank scans and duplicated data scans {C# GUI}).
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Run Skyline Batch or Skyline on all the files in the folder:
a. Import each mzml
b. Refine for idotp >0.9 (therefore include the M-1 for every glycan composition in the Skyline document)
c. New Skyline document should then be made with all the matching compositions quantified
d. Run an R script, making an excel spreadsheet with relative intensities for the monoisotopic peak quant AND full isotopic envelope quant
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Upload your Skyline document to
Requires Proteowizard and Skyline to be installed. MSConvert should also be added to the path on Windows 10 (https://www.architectryan.com/2018/03/17/add-to-the-path-on-windows-10/).