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 PSM file– The name of a PSM file in tab-delimited text, SQT, pepXML or mzIdentML format
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.
--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 =
Amino acid modifications
--mod-precision <integer>– Set the precision for modifications as written to .txt files. Default =
Input and output
--top-match <integer>– Specify the number of matches to report for each spectrum. Default =
--output-dir <string>– The name of the directory where output files will be created. Default =
--overwrite T|F– Replace existing files if true or fail when trying to overwrite a file if false. Default =
--parameter-file <string>– A file containing parameters. See the parameter documentation page for details. Default =
--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 =