Mass-spectrometry-based draft of the human proteome

Mathias Wilhelm, Judith Schlegl, Hannes Hahne, Amin Moghaddas Gholami, Marcus Lieberenz, Mikhail M. Savitski, Emanuel Ziegler, Lars Butzmann, Siegfried Gessulat, Harald Marx, Toby Mathieson, Simone Lemeer, Karsten Schnatbaum, Ulf Reimer, Holger Wenschuh, Martin Mollenhauer, Julia Slotta-Huspenina, Joos-Hendrik Boese, Marcus Bantscheff, Anja Gerstmair, Franz Faerber and Bernhard Kuster ()
Additional contact information
Mathias Wilhelm: Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer Forum 5, 85354 Freising, 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

Nature, 2014, vol. 509, issue 7502, 582-587

Abstract: 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.

Date: 2014
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DOI: 10.1038/nature13319

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