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There are two options for converting an MS-GF+ output file (.mzid) into a tab-separated file (.tsv)

  1. The MzIDToTsv utility built into MSGFPlus.jar
  2. The Mzid-To-Tsv-Converter standalone application, available on GitHub

    MzidToTsvConverter.exe -mzid:SearchResults.mzid -unroll -showDecoy

MzIDToTsv Utility

Converts MS-GF+ output (.mzid) into the tsv format (.tsv)

Usage: java -Xmx3500M -cp MSGFPlus.jar edu.ucsd.msjava.ui.MzIDToTsv
	-i MzIDFile (MS-GF+ output file (*.mzid))
	[-o TSVFile] (TSV output file (*.tsv) (Default: MzIDFileName.tsv))
	[-showQValue 0/1] (0: do not show Q-values, 1: show Q-values (Default))
	[-showDecoy 0/1] (0: do not show decoy PSMs (Default), 1: show decoy PSMs)
	[-unroll 0/1] (0: merge shared peptides (Default), 1: unroll shared peptides)