MSFragger pipeline

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KaiLiCn edited this page Oct 21, 2019 · 6 revisions

Inputs

MS/MS data in mzML;
PSM table in TSV format.

PDV only requires the following columns being present in PSM table file:

(1). "Spectrum": spectrum title

(2). "Peptide": peptide sequence

(3). "Charge": PSM charge

(4). "Calculated M/Z": calculated M/Z based on peptide

(5). "Observed M/Z": observed M/Z based on MS

(6). "Assigned Modifications": modifications in standard format

example:

Spectrum	Peptide	Charge	Calculated M/Z	Observed M/Z	Assigned Modifications
b1930_293T_proteinID_10A_QE3_122212 .02109.02109.3	LTNSMMMHGR	3	409.1756	409.1741	5M(15.9949), 6M(15.9949), 7M(15.9949), N-term(42.0106)