Ubuntu Manpage: mineXpert — Open mass spectrometric data files of a wide variety of

Provided by: msxpertsuite-minexpert_5.8.6-2build1_amd64

NAME

       mineXpert            —             Open mass spectrometric data files of a wide variety of
       formats and mine data graphically

SYNOPSIS

       minexpert [options]  [filename ...]

DESCRIPTION

This manual page documents briefly the mineXpert 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...

Useful reading

       The program is documented fully  in  the  mineXpert  User  Manual,  that  is  packaged  in
       msxpertsuite-doc.   That  manual  is  available  in  the  form  of  a  PDF-formatted  file
       (/usr/share/doc/msxpertsuite/minexpert-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.

                                                                          mineXpert           (1)