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MSGFPlus / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.
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Preferred way of analyzing mzid files #65

Closed tivdnbos closed 5 years ago

tivdnbos commented 5 years ago

Hi,

I was wondering what the preferred way is to analyze .mzid files on a linux machine, meaning, given a certain FDR, get a list of spectra and the identified peptide sequences back. I tried MzidToTsvConvertor, but the output generates a 0 for all q-values. Any idea what can cause this?

Best wishes.

FarmGeek4Life commented 5 years ago

Well, the MzidToTsvConverter just outputs whatever values are in the mzid file. If all of the q-values are zero, then they were all reported as '0' in the mzid file.

alchemistmatt commented 5 years ago

MzidToTsvConverter is the correct tool to use. Try a less strict filter threshold and you should start to see non-zero Q-values. Note, though, for Q-values to be computed properly, you need to let MS-GF+ create the decoy FASTA file, and decoy proteins will need to be preceded by XXX_

tivdnbos commented 5 years ago

Thanks! I searched a concatenated target-decoy database (with the XXX_ prefix), but with -tda 0. With the target db only and -tda 1 it worked.