1st june 25
&ProgName; 1 &ProgName; module of the MsXpertSuite for mass spectrometry
&ProgName; Open mass spectrometric data files of a wide variety of formats, visualize and mine data graphically
`&progname;` `options` `filename ...`

## DESCRIPTION

This manual page documents briefly the `&progName;` command used to run the &ProgName; application software shipped as a module of the `MsXpertSuite` software suite. This program can be used to load mass spectrometry data files and show the spectral data in a variety of graphical representations like plots, color maps. Any plot or color map can serve as a starting point for a mass data integration, like integrating a region of a TIC chromatogram to a mass spectrum or to a drift spectrum. Integrations can be performed in any direction, like from a RT|MZ color map to a TIC chromatogram, for example, or from a drift spectrum to a TIC chromatogram. The `&progName;` program allows the user to perform the following tasks:

- Open mass spectrometry data files (mzML, mzXML, asc, xy, ...);

- Display in a table view the full data set, for easy filtering;

- Calculate and display the TIC chromatogram;

- Calculate and display a mz=f(rt) color map;

- For mobility data, calculate and display a mz=f(dt) color map;

- Integrate the mass spectrometric data from any kind of data representation (mass | drift spectra, TIC | XIC chromatogram, 2D color maps) to any other kind of data representation;

- For any mass data feature (mass peak, TIC | XIC peak, color map) integrate to a XIC single intensity value);

- Powerful isotopic cluster calculation starting from a chemical formula, optionally with user-defined isotopic abundance ratios;

- Gaussian fit over any isotopic cluster to estimate the average mass of a given ion;

- Mouse-driven deconvolution of m/z data (charge envelope-based or isotopic cluster-based);

- Export the data to text files;

- Export the graphical representation of mass spectrometric data to graphics files of a number of formats (jpg, png, pdf).

## OPTIONS

`-h | --help`

  Displays detailed usage information and exits.

`-c | --config`

  Display program configuration at build time and the Qt version used to build it.

`-V | --Version`

  Print the version of the software program along the with version of the Qt libraries used to build it.

`-l | --license`

  Print the license of this software.

`-s | --streamed`

  When opening one or more files in the gui, do that in streamed mode, otherwise in full.

`-j | --scriptFile <filename>`

  Start the program and immediately run the JavaScript script.

filename ...

  One or more names of files to be opened.

## Bibliographic reference to be cited

Not yet published...

## See also

massxpert (1)

## Useful reading

The program is documented fully in the &progName; User Manual, that is packaged in msxpertsuite-doc. That manual is available in the form of a PDF-formatted file (`/usr/share/doc/msxpertsuite/&progname;-doc.pdf`).

## AUTHOR

Filippo Rusconi <lopippo@debian.org>

This manual page was written by Filippo Rusconi <lopippo@debian.org> (initial writing 03 july 2017). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 3, published by the Free Software Foundation.

On a Debian system the complete text of the GNU General Public License version 3 can be found in the file `/usr/share/common-licenses/GPL\-3`.