localize-modification

Usage:

crux localize-modification [options] <input PSM file>

Description:

This command finds, for each peptide-spectrum match (PSM) in a given set, the most likely location along the peptide for a post-translational modification (PTM). The mass of the PTM is inferred from the difference between the spectrum neutral mass and the peptide mass.

Input:

• input PSM file – The name of a PSM file in tab-delimited text, SQT, pepXML or mzIdentML format

Output:

The program writes files to the folder crux-output by default. The name of the output folder can be set by the user using the --output-dir option. The following files will be created:

• localize-modification[.target|.decoy].txt – a tab-delimited text file containing the target PSMs. See txt file format for a list of the fields. The filename depends on whether the input file contained targets, decoys, or both.
• localize-modification.params.txt – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other Crux programs.
• localize-modification.log.txt – a log file containing a copy of all messages that were printed to the screen during execution.

Options:

• localize-modification options

  • --min-mod-mass <float> – Ignore implied modifications where the absolute value of its mass is below this value and only score the unmodified peptide. Default = 0.

• Amino acid modifications

  • --mod-precision <integer> – Set the precision for modifications as written to .txt files. Default = 4.

• Input and output

  • --top-match <integer> – Specify the number of matches to report for each spectrum. Default = 5.
  • --output-dir <string> – The name of the directory where output files will be created. Default = crux-output.
  • --overwrite T|F – Replace existing files if true or fail when trying to overwrite a file if false. Default = false.
  • --parameter-file <string> – A file containing parameters. See the parameter documentation page for details. Default = <empty>.
  • --verbosity <integer> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = 30.