# 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`.