Using “”

Using “”

Beware! These instructions refer to code which is under development.

Necessary files

This script is written in such a way that it can call MS-GF+ by itself. To do so, the configurations file must include some additional parameters:

  "search_engine": "MSGFPlus",
  "search_engine_options": {
    "dir": "/path/to/MSGFPlus_20181015",
    "frag": "HCD",
    "path_to_modsfile": "modification.txt",
    "min_length": 8,
    "min_charge": 2,
    "max_charge": 4
  • search_engine indicates which search engine to use, and in this case should read MSGFPlus
  • search_engine_options includes search settings and important paths:
    • dir should be the absolute path to the folder where the MSGFPlus.jar file is located;
    • frag is the fragmentation method, which can currently be either HCD or CID;
    • path_to_modsfile should be used if searching for modified peptides, and link an MS-GF+ modifications file;
    • min_length, min_charge and max_charge refers to the respective MS-GF+ search settings.

To run a search, a spectrum file in the .MGF format and a database in the .fasta format must be provided.

In this case, please open a text editor and in the file comment the following lines like so:

    #"Running MS-GF+")
    # MSGF_DIR = config["search_engine_options"]["dir"]
    # run_msgfplus(MSGF_DIR, args.spec_file, args.fasta_file, config["search_engine_options"])

However, to execute the script, you will have to “trick” the code! Pass the following arguments as input:

  • <mgf>: the name of your .mzid identifications file, but with .mgf as its suffix
  • <fasta>: anything really, this file is only used when a search is ran :)

Keep in mind that you will still need an .mgf file to execute the ReScore pipeline!


To generate a .PEPREC file that can be used to run the ReScore pipeline, execute the following command:

python <.mgf> <.fasta> <config.json>