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Mass-spectrometry-based draft of the human proteome

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  • Mathias Wilhelm

    (Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
    SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany)

  • Judith Schlegl

    (SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany)

  • Hannes Hahne

    (Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany)

  • Amin Moghaddas Gholami

    (Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany)

  • Marcus Lieberenz

    (SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany)

  • Mikhail M. Savitski

    (Cellzome GmbH, Meyerhofstraße 1, 69117 Heidelberg, Germany)

  • Emanuel Ziegler

    (SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany)

  • Lars Butzmann

    (SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany)

  • Siegfried Gessulat

    (SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany)

  • Harald Marx

    (Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany)

  • Toby Mathieson

    (Cellzome GmbH, Meyerhofstraße 1, 69117 Heidelberg, Germany)

  • Simone Lemeer

    (Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany)

  • Karsten Schnatbaum

    (JPT Peptide Technologies GmbH, Volmerstraße 5, 12489 Berlin, Germany)

  • Ulf Reimer

    (JPT Peptide Technologies GmbH, Volmerstraße 5, 12489 Berlin, Germany)

  • Holger Wenschuh

    (JPT Peptide Technologies GmbH, Volmerstraße 5, 12489 Berlin, Germany)

  • Martin Mollenhauer

    (Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675 München, Germany)

  • Julia Slotta-Huspenina

    (Institute of Pathology, Technische Universität München, Trogerstraße 18, 81675 München, Germany)

  • Joos-Hendrik Boese

    (SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany)

  • Marcus Bantscheff

    (Cellzome GmbH, Meyerhofstraße 1, 69117 Heidelberg, Germany)

  • Anja Gerstmair

    (SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany)

  • Franz Faerber

    (SAP AG, Dietmar-Hopp-Allee 16, 69190 Walldorf, Germany)

  • Bernhard Kuster

    (Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, Germany
    Center for Integrated Protein Science Munich)

Abstract

Proteomes are characterized by large protein-abundance differences, cell-type- and time-dependent expression patterns and post-translational modifications, all of which carry biological information that is not accessible by genomics or transcriptomics. Here we present a mass-spectrometry-based draft of the human proteome and a public, high-performance, in-memory database for real-time analysis of terabytes of big data, called ProteomicsDB. The information assembled from human tissues, cell lines and body fluids enabled estimation of the size of the protein-coding genome, and identified organ-specific proteins and a large number of translated lincRNAs (long intergenic non-coding RNAs). Analysis of messenger RNA and protein-expression profiles of human tissues revealed conserved control of protein abundance, and integration of drug-sensitivity data enabled the identification of proteins predicting resistance or sensitivity. The proteome profiles also hold considerable promise for analysing the composition and stoichiometry of protein complexes. ProteomicsDB thus enables navigation of proteomes, provides biological insight and fosters the development of proteomic technology.

Suggested Citation

  • Mathias Wilhelm & Judith Schlegl & Hannes Hahne & Amin Moghaddas Gholami & Marcus Lieberenz & Mikhail M. Savitski & Emanuel Ziegler & Lars Butzmann & Siegfried Gessulat & Harald Marx & Toby Mathieson , 2014. "Mass-spectrometry-based draft of the human proteome," Nature, Nature, vol. 509(7502), pages 582-587, May.
    • Handle: RePEc:nat:nature:v:509:y:2014:i:7502:d:10.1038_nature13319
    DOI: 10.1038/nature13319
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    Cited by:

    1. Angela Re & Levi Waldron & Alessandro Quattrone, 2016. "Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites," PLOS Computational Biology, Public Library of Science, vol. 12(12), pages 1-25, December.
    2. Nora Linscheid & Alberto Santos & Pi Camilla Poulsen & Robert W Mills & Kirstine Calloe & Ulrike Leurs & Johan Z Ye & Christian Stolte & Morten B Thomsen & Bo H Bentzen & Pia R Lundegaard & Morten S O, 2021. "Quantitative proteome comparison of human hearts with those of model organisms," PLOS Biology, Public Library of Science, vol. 19(4), pages 1-22, April.
    3. Xiaojuan Fan & Yun Yang & Chuyun Chen & Zefeng Wang, 2022. "Pervasive translation of circular RNAs driven by short IRES-like elements," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

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