2022 march 12
&progName; 1 &progName; converts any TimsTOF pro data, mzML, MGF... to standard mzXML easily readable by X!Tandem
&progName; converts data from Bruker's timsTOF line of instruments to mzXML
`&progname;` `options`

## DESCRIPTION

This manual page documents briefly the `&progName;` software. This program can be used to convert data from Bruker's timsTOF line of instruments to mzXML directly to the standard output or in an output file

## OPTIONS

`-h | --help`

  Displays detailed usage information and exits.

`-v | --version`

  Print the version of the software program.

`-o, --output output`

  Optionally set mzXML output path. If not given, mzXML is written on the standard output.

`-i mz data file`
  path to the Bruker's data directory or to the mz data file (mgf, mzML...)
`-d, --dalton dalton`
  Optionally set TimsTOF MS2 measurement precision in dalton (+-0.02 by default) to build suitable MS2 filters. Only relevant when converting TimsTOF data.
`-c, --cpus number`
  Number of CPUs to use.

## Bibliographic reference to be cited

Langella O, Valot B, Balliau T, Blein-Nicolas M, Bonhomme L, Zivy M. (2017) X!TandemPipeline: A Tool to Manage Sequence Redundancy for Protein Inference and Phosphosite Identification. J. Proteome Res., 2 (16) 494-503