Computational prediction of proteotypic peptides for quantitative proteomics View Full Text


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Article Info

DATE

2006-12-31

AUTHORS

Parag Mallick, Markus Schirle, Sharon S Chen, Mark R Flory, Hookeun Lee, Daniel Martin, Jeffrey Ranish, Brian Raught, Robert Schmitt, Thilo Werner, Bernhard Kuster, Ruedi Aebersold

ABSTRACT

Mass spectrometry–based quantitative proteomics has become an important component of biological and clinical research. Although such analyses typically assume that a protein's peptide fragments are observed with equal likelihood, only a few so-called 'proteotypic' peptides are repeatedly and consistently identified for any given protein present in a mixture. Using >600,000 peptide identifications generated by four proteomic platforms, we empirically identified >16,000 proteotypic peptides for 4,030 distinct yeast proteins. Characteristic physicochemical properties of these peptides were used to develop a computational tool that can predict proteotypic peptides for any protein from any organism, for a given platform, with >85% cumulative accuracy. Possible applications of proteotypic peptides include validation of protein identifications, absolute quantification of proteins, annotation of coding sequences in genomes, and characterization of the physical principles governing key elements of mass spectrometric workflows (e.g., digestion, chromatography, ionization and fragmentation). More... »

PAGES

125-131

References to SciGraph publications

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  • 2003-12-23. Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells in GENOME BIOLOGY
  • 2005-06-15. Scoring proteomes with proteotypic peptide probes in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • 2006-01-22. Proteome survey reveals modularity of the yeast cell machinery in NATURE
  • 2004-07-18. Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture in NATURE BIOTECHNOLOGY
  • Journal

    TITLE

    Nature Biotechnology

    ISSUE

    1

    VOLUME

    25

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nbt1275

    DOI

    http://dx.doi.org/10.1038/nbt1275

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/17195840


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