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) Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction. PROTEOMICS, 9 (13) 1457-1466
    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.