ScoringParamGen

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

Installation

• ScoringParamGen is included in MSGFPlus.jar.

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)

Parameters:

• -i ResultPath - Required
  • Path to the folder containing MS-GF+ result files (*.mzid or *.tsv).
• -d SpecDir - Required
  • Path to the folder containing spectrum files used to generate MS-GF+ results.
• -m FragmentationMethodID - Required
  • Fragmentation method ID (0: CID, 1: ETD, 2: HCD)
• -inst InstrumentID - Required
  • ID specifying the instrument to measure product ions, i.e. MS/MS
  • 0: Low-res LCQ/LTQ, 1: High-res LTQ, 2: TOF, 3: Q-Exactive
• -e EnzymeID - Required
  • 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 - optional
  • Protocol ID
  • 0: NoProtocol (Default), 1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho, 4: TMT

Output

• A scoring parameter file containing scoring parameters (*.param).
• The name of the scoring parameter file represents the spectrum type (FragmentationMethod, InstrumentType, Enzyme, Protocol) used to generate the spectrum.
  • FragmentationMethod_InstrumentType_Enzyme.param
  • FragmentationMethod_InstrumentType_Enzyme_Protocol.param
  • E.g. ETD_LowRes_GluC.param, HCD_HighRes_Tryp_Phosphorylation.param

How to use a custom scoring parameter file?

• Place scoring parameter files in the "params" directory.
• MS-GF+ uses the (user-defined) scoring parameter files to analyze spectra of the specified type.

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

• Define new fragmentation methods in params/activationMethods.txt or new enzymes in params/enzymes.txt. The params directory must exist below the working directory.
• Run ScoringParamGen with no parameter: "-cp MSGFPlus.jar edu.ucsd.msjava.ui.ScoringParamGen". It will now print out the ID of the new enzyme or the new fragmentation method.
• Run ScoringParamGen with new FragmentationMethodID or new EnzymeID

What is "protocol" and how to define it?

• Protocol is a user-defined tag associated with a scoring parameter file.
• For example, one may want to create a scoring parameter file for phosphorylation-enriched sample because the fragmentation propensities of phosphopeptides are different from other peptides even if the exact same condition (CID_LowRes_Tryp) is used to generate them. In such a case, one can define a protocol "Phosphorylation" and create CID_LowRes_Tryp_Phosphorylation.param.
• Define new protocols in params/protocols.txt.
• New protocols will show up in the usage information.

Example

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