ScoringParamGen

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

Installation

  • ScoringParamGen is included in .
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, 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.
  • 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
  • Purpose: creating a scoring parameter file for HCD, HighRes, CNBr
  • Add "CNBr,M,C,CNBr" in the params/enzyme.txt file.
  • Run MS-GF+ with no parameter and check the id of CNBr (assume the id is 10).
  • Run MS-GF+ by specifying -m 3 (HCD), -inst 2 (HighRes), -e 10 (CNBr). Suppose that the spectrum file name is test.mzML and the MS-GF+ result file is "test.mzid".
  • Create a folder "results" and move test.mzid into it.
  • Run ScoringParamGen:
java -Xmx3500M -cp MSGFPlus.jar edu.ucsd.msjava.ui.ScoringParamGen -i results -d . -m 2 -inst 1 -e 10
  • Check if "HCD_HighRes_CNBr.param" is created. Create a directory named "params" and move "HCD_HighRes_CNBr.param" into "params".
  • From now on, running MS-GF+ with "-m 3 -inst 2 -e 10" will use HCD_HighRes_CNBr.param.
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