mineXpert — Open mass spectrometric data files
of a wide variety of formats and mine data graphically
minexpert [options]
[filename ...]
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.
- -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.
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).
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.