I have received raw data from the Waters demo lab that was recorded on their Synapt G2-Si instrument. The experiment was bottom-up proteomics with data-dependent acquisition, but the twist is that MS/MS fragment ions were separated by ion mobility before detection. Thus, each MS/MS spectrum is actually composed of many TOF mass spectra (many ion mobility slices). The ProteoWizard tools do not seem to work, but there could be an important setting that I'm missing. The Waters guys have provided me with Mascot mgf peak list files, but what I would really like is either mzML or mzXML.
Hi, David. Yes, the newest builds of ProteoWizard (the last six months or so?) include support for ion mobility due to the efforts of Matt Chambers. Waters libraries don't include the functions for peak listing, charge state inference, and scan summing, but open-source functions for these purposes have recently been incorporated in ProteoWizard (see the recent paper by Will French in my group).
I took a closer look at the "msconvert" program. Would you recommend the "scanSumming" filter, which was alluded to in the paper?
Hello!
please, how did you convert .raw to mgf? Do you still have the guys contact?
Hello,
I am using mascot distiller to convert differents raw data from bruker, orbitrap and sciex. Mascot Distiller supports all the MS data file formats. Its really easy but its not free software. You can tray 30 days trial evaluation. Emerson
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