File Formats

Raw Data

We generally accept two formats mzML and mzXML. These are preferred with some caveats on conversion.

MGF is accepted but its frowned upon as a raw data format as its not really standardized.

MS/MS spectral libraries

We generally support libraries from GNPS, but we also note that you might want to use your own libraries. To that end you could make your own MGF file as a private library. You do miss out on other niceties within the GNPS2 ecosystem but it can be done. The format example is as follows:

BEGIN IONS
TITLE=SOMEUNIQUEID
PEPMASS=981.54
CHARGE=0
MSLEVEL=2
SOURCE_INSTRUMENT=LC-ESI-qTof
SEQ=*..*
IONMODE=Positive
NAME=3-Des-Microcystein_LR M+H
PI=Gerwick
DATACOLLECTOR=Jenia
SMILES=CC(C)CC1NC(=O)C(C)NC(=O)C(=C)N(C)C(=O)CCC(NC(=O)C(C)C(NC(=O)C(CCCNC(N)=N)NC(=O)C(C)C(NC1=O)C(O)=O)\C=C\C(\C)=C\C(C)C(O)Cc1ccccc1)C(O)=O
INCHI=N/A
PUBMED=N/A
SUBMITUSER=mwang87
SPECTRUMID=SOMEUNIQUEID
SCANS=1
289.286377  8068.0
295.545288  22507.0
298.489624  3925.0
317.324951  18742.0
319.655945  8604.0
324.482422  8041.0
325.316284  9738.0
339.789429  16145.0
343.947021  18094.0
347.020508  13981.0
347.913391  6765.0
END IONS