From proteomics to systems biology: MAPA, MASS WESTERN, PROMEX, and COVAIN as a user-oriented platform

Wolfram Weckwerth, Stefanie Wienkoop, Wolfgang Hoehenwarter, Volker Egelhofer, Xiaoliang Sun

    Publications: Contribution to journalArticlePeer Reviewed

    Abstract

    Genome sequencing and systems biology are revolutionizing life sciences. Proteomics emerged as a fundamental technique of this novel research area as it is the basis for gene function analysis and modeling of dynamic protein networks. Here a complete proteomics platform suited for functional genomics and systems biology is presented. The strategy includes MAPA (mass accuracy precursor alignment; http://www.univie.ac.at/mosys/software.html ) as a rapid exploratory analysis step; MASS WESTERN for targeted proteomics; COVAIN ( http://www.univie.ac.at/mosys/software.html ) for multivariate statistical analysis, data integration, and data mining; and PROMEX ( http://www.univie.ac.at/mosys/databases.html ) as a database module for proteogenomics and proteotypic peptides for targeted analysis. Moreover, the presented platform can also be utilized to integrate metabolomics and transcriptomics data for the analysis of metabolite-protein-transcript correlations and time course analysis using COVAIN. Examples for the integration of MAPA and MASS WESTERN data, proteogenomic and metabolic modeling approaches for functional genomics, phosphoproteomics by integration of MOAC (metal-oxide affinity chromatography) with MAPA, and the integration of metabolomics, transcriptomics, proteomics, and physiological data using this platform are presented. All software and step-by-step tutorials for data processing and data mining can be downloaded from http://www.univie.ac.at/mosys/software.html.
    Original languageEnglish
    Pages (from-to)15-27
    Number of pages13
    JournalMethods in Molecular Biology
    Volume1072
    DOIs
    Publication statusPublished - 2014

    Austrian Fields of Science 2012

    • 106037 Proteomics
    • 106044 Systems biology
    • 106005 Bioinformatics
    • 106014 Genomics

    Keywords

    • MAPA
    • MOAC
    • COVAIN
    • PROMEX
    • MASS WESTERN

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