Using ProtMAX to create high-mass-accuracy precursor alignments from label-free quantitative mass spectrometry data generated in shotgun proteomics experiments

Volker Egelhofer, Wolfgang Hoehenwarter, David Lyon, Wolfram Weckwerth, Stefanie Wienkoop

    Publications: Contribution to journalArticlePeer Reviewed

    Abstract

    Recently, new software tools have been developed for improved protein quantification using mass spectrometry (MS) data. However, there are still limitations especially in high-sample-throughput quantification methods, and most of these relate to extensive computational calculations. The mass accuracy precursor alignment (MAPA) strategy has been shown to be a robust method for relative protein quantification. Its major advantages are high resolution, sensitivity and sample throughput. Its accuracy is data dependent and thus best suited for precursor mass-to-charge precision of ∼1 p.p.m. This protocol describes how to use a software tool (ProtMAX) that allows for the automated alignment of precursors from up to several hundred MS runs within minutes without computational restrictions. It comprises features for 'ion intensity count' and 'target search' of a distinct set of peptides. This procedure also includes the recommended MS settings for complex quantitative MAPA analysis using ProtMAX (http://www.univie.ac.at/mosys/software.html).
    Original languageEnglish
    Pages (from-to)595-601
    Number of pages7
    JournalNature Protocols
    Volume8
    Issue number3
    DOIs
    Publication statusPublished - 28 Feb 2013

    Austrian Fields of Science 2012

    • 106013 Genetics
    • 106037 Proteomics
    • 106026 Ecosystem research

    Keywords

    • Chromatography, High Pressure Liquid
    • Mass Spectrometry
    • Proteins
    • Proteomics
    • Software
    • ProtMAX

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