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

       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)

       Not yet published...

       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.

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

-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.

massxpert(1)

minexpert [options][filename...]

       The program is documented fully in the mineXpertUserManual, 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).