2022 march 12
&progName; 1 &progName; wraps execution of X!Tandem software to run it on TimsTOF pro data or modern mzML files
&progName; run X!Tandem given its parameter file and path to X!Tandem software
`&progname;` `options` `filename ...`

## DESCRIPTION

This manual page documents briefly the `&progName;` software. This program can be used to run X!Tandem on data from Bruker's timsTOF line of instruments. It can also run X!Tandem on modern mzML files (any kind of compression type)

## OPTIONS

`-h | --help`

  Displays detailed usage information and exits.

`-v | --version`

  Print the version of the software program.

`--tandem`

  Full path to the X!Tandem executable file (tandem or tandem.exe).

`-t | --tmp`

  Optionally set the temporary directory to store temporary data.

filename

  X!Tandem parameter file (see the X!Tandem documentation on https://www.thegpm.org/TANDEM/.

## 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