MassChroQ User Manual
Preface
1 Software feature offerings and intended audience #
This manual is about the MassChroQ proteomics quantification software project.
MassChroQ has the following features:
Load an XML file mainly describing the precursor peptidic ions that were fragmented to produce tandem mass spectra that allowed to identify proteins.
Compute extracted ion current (XIC) chromatograms for the precursor ions by looking into the mass spectrometry data files;
Perform under-the-curve calculations to provide intensity values for the precursor ions.
2 Feedback from the users #
We are always grateful to any constructive feedback from the users.
The PAPPSO software team might be contacted via the following contact page:
http://pappso.inrae.fr/en/travailler_avec_nous/contact/ (search for team members having the “Bioinformatics” specialty mentioned, like Olivier Langella or Filippo Rusconi).
3 Program and Documentation Availability and License #
The programs and all the documentation that are shipped along with the MassChroQ software suite are available at http://pappso.inrae.fr/en/bioinfo/masschroq/. Most of the time, a new version is published as source, and as binary install packages for MS-Windows (64-bit systems only).
For GNU/Linux, binary packages are created
locally (see http://pappso.inrae.fr/en/bioinfo/masschroq/download/)
but are also built in the
Debian[1] autobuilders and are
uploaded to the distribution servers. These packages are available using the
system's software management infrastructure (like using the
Debian's apt command, for
example, or the graphical application).
The software and all the documentation are all provided under the Free Software license GNU General Public License, Version 3, or later, at your option. For an in-depth study of the Free Software philosphy, the reader is kindly urged to visit http://www.gnu.org/philosophy.