03 july 2017
&progName; 1 &progName; module of the msXpertSuite for mass spectrometry
&progName; Open mass spectrometric data files of a wide variety of formats and mine data graphically
`&progname;` `options` `filename ...`

## DESCRIPTION

This manual page documents briefly the `&progName;` software shipped within the `msXpertSuite` software suite. This program can be used to load mass spectrometry data files and show the spectral data in a plot widget for further analysis according to a variety of available integrations. While this program can operate integrally in a graphical mode, it is also widely scriptable using JavaScript as a scripting language. A typical data mining session would involve the following steps/actions:

- Open a mass spectrometry file and immediately compute a TIC chromatogram, show that chromatogram in a dedicated window. If the data are from an ion mobility mass spectrometry experiment, compute a mz = f(dt) color map. The TIC chromatogram and the color map are then the starting points for the mining of the data.

- Perform a wide variety of integrations to a mass spectrum or a drift spectrum. Each new spectrum is displayed in its dedicated window (the TIC chromatogram window, the Color map window, the Mass spectrum window and the Drift spectrum window). Each new plot (be it a TIC chromatogram, a mass spectrum or a drift spectrum) is potentially the start of another integration such that the analysis can drill at each step further in the depth of the data.

- Perform isotopic cluster calculations and shape the obtained mass peak centroids into fully shaped mass peaks (Gaussian or Lorentizan mathematical models).

- Each plot has specific functions associated to it: export as a (x,y) file, automatic recording of the relevant data of signalled peaks into a file using a specific easy-to-understand grammar, slicing of the data file into smaller data files.

- One feature of importance is the fact that a large part of the functionalities of the program are scriptable (JavaScript) and a powerful scripting console is available to elaborate scripts before storing them in script files to be automatically executed.

## 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`.