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Creates a scoring parameter file (UserParam) to be used for MS-GF+.


Usage: java -Xmx3500M -cp MSGFPlus.jar edu.ucsd.msjava.ui.ScoringParamGen
        -i ResultPath (MSGFDBResultFile (*.mzid) or MSGFDBResultDir)
        -d SpecDir (Path to directory containing spectrum files)
        -m FragmentMethodID (0: CID, 1: ETD, 2: HCD)
        -inst InstrumentID (0: Low-res LCQ/LTQ, 1: High-res LTQ, Orbitrap, Lumos, 2: TOF, 3: Q-Exactive)
        -e EnzymeID (0: Trypsin, 1: Chymotrypsin, 2: Lys-C, 3: Lys-N, 4: glutamyl endopeptidase, 5: Arg-C, 6: Asp-N, 7: alphaLP, 8: no cleavage)
        [-protocol ProtocolID] (0: NoProtocol (Default), 1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho, 4: TMT)



How to use a custom scoring parameter file?

How to make a parameter file for a new fragmentation method or a new enzyme?

What is "protocol" and how to define it?


java -Xmx3500M -cp MSGFPlus.jar edu.ucsd.msjava.ui.ScoringParamGen -i results -d . -m 2 -inst 1 -e 10