Logiciel

  • i2MassChroQ

    i2MassChroQ

    i2MassChroQ is a free software (GPL v3) that helps the user

    • filter and group peptide/protein identifications from MS/MS mass spectra;
    • perform area-under-the-peak XIC-based quantification of proteins.

    i2MassChroQ is fully described in:

  • MassChroQ

    MassChroQ

    MassChroQ (Mass Chromatogram Quantification) is a fast and versatile software that performs alignment, XIC extraction, peak detection and quantification on data obtained from Liquid Chromatography-Mass Spectrometry (LC-MS) techniques.

  • PROTICdb

    PROTICdb

    PROTICdb is a web-based application designed to store and analyze proteome data obtained by mass spectrometry.

    Langella O, Valot B, Jacob D, Balliau T, Flores R, Hoogland C, Joets J, Zivy M. (2013-03-06) Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction. Proteomics, ()
    Langella O, Zivy M, Joets J. (2007) The PROTICdb database for 2-DE proteomics. Methods Mol. Biol., (355) 279-303
    Ferry-Dumazet H, Houel G, Montalent P, Moreau L, Langella O, Negroni L, Vincent D, Lalanne C, Daruvar A, Plomion C, Zivy M, Joets J. (2005) PROTICdb: a web-based application to store, track, query, and compare plant proteome data. Proteomics, 8 (5) 2069-2081

    The PAPPSO PROTICdb public site is available here

  • ALL-P

    ALL-P is a statistical framework based on a hierarchical modeling that takes into account shared peptide information for estimating protein abundances. ALL-P performs a simultaneous analysis of all the quantified peptides, handling the biological and technical errors as well as the peptide effect. Compared to a method based on the analysis of one protein at a time that does not include shared peptides (ONE-P method), ALL-P proved to be far more reliable for estimating protein abundances and testing abundance changes.