i2MassChroQ User Manual
- Preface
- 1 Generalities
- 2 Fundamentals in Bottom-up Proteomics
- 3 The main program window
- 4 Exploring identification data
- 5 Exploring post-translational modification data
- 6 Advanced Proteomics Configurations
- 7 i2MassChroQ and Quantitative Proteomics
- 8 Specific procedures for the timsTOF line of instruments
- A GNU General Public License version 3
Preface
1 Software feature offerings and intended audience #
This manual is about the i2MassChroQ protein identification software project.
i2MassChroQ has the following features:
Load mass spectometry data files in the mzXML or mzML format, thanks to the excellent libpwiz library of ProteoWizard[1] fame.
Configure the way the peptide/mass spectrum matches (PSM) are to be performed;
Configure the database files to be used (target organism databases and contaminant databases);
Use the MS/MS data in the file to feed the X!Tandem program that produces peptide identification results by matching the measured ion masses with peptide fragments calculated in silico on the basis of the databases contents;
Perform the protein inference step that leads to reliable protein identifications on the basis of the peptide identifications performed by X!Tandem
Display the data obtained at any step in powerful ways in a unified graphical user interface to allow the user to inspect the peptide identifications and also control the way these identifications are used to infer the protein identifications.
Export the data after the results exploration above in a variety of formats.
Perform quantitative proteomics on the basis of the results obtained at the previous steps.
Perform bio-statistical analyses on the quantitative proteomics data obtained at the previous step.
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 i2MassChroQ software suite are available at http://pappso.inrae.fr/en/bioinfo/xtandempipeline/. 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/xtandempipeline/download/)
but are also built in the
Debian[2] 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.