Abstract

We describe ProteomeTools, a project building molecular and digital tools from the human proteome to facilitate biomedical research. Here we report the generation and multimodal liquid chromatography–tandem mass spectrometry analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products, and we exemplify the utility of these data in several applications. The resource (available at http://www.proteometools.org) will be extended to >1 million peptides, and all data will be shared with the community via ProteomicsDB and ProteomeXchange.

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Acknowledgements

The authors wish to thank numerous colleagues including S. Eluik, G. Tan, X. Sun, X. Liu (Thermo Fisher Scientific), A. Hubauer, J. Mergner, J. Zecha, P. Samaras and the entire Kuster team as well as H. Hahne (OmicScouts), R. Weise, D. Riehn, K. Schrödter, F. Schumacher, N. Kolls and R.A. Castro-Alvaro (JPT) for fruitful discussions and technical assistance. We thank D. Campbell and Z. Sun for their efforts and the entire Moritz group at ISB and the Aebersold group at ETH Zurich for their efforts in peptide selection and synthesis. This work was in part funded by the German Federal Ministry of Education and Research (BMBF; grant no. 031L0008A). A postdoctoral fellowship from the Alexander von Humboldt Foundation (to P.Y.) is also gratefully acknowledged. This work was also performed in part with federal funds from the American Recovery and Reinvestment Act (ARRA) funds through the NIH, from the National Human Genome Research Institute grant no. RC2HG005805 (to R.L.M.); the National Institute of General Medical Sciences grant nos. R01GM087221, S10RR027584 and 2P50 GM076547/Center for Systems Biology (to R.L.M.); the European Research Council grant nos. ERC-2008-AdG 233226 and ERC-2014-AdG 670821; and the Swiss National Science Foundation (grant no. 31003A-130530 to R.A.), and DAAD (fellowship to U.K.).

Author information

Author notes

    • Daniel P Zolg
    •  & Mathias Wilhelm

    These authors contributed equally to this work.

Affiliations

  1. Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.

    • Daniel P Zolg
    • , Mathias Wilhelm
    • , Siegfried Gessulat
    • , Maximilian Weininger
    • , Peng Yu
    • , Karl Kramer
    • , Tobias Schmidt
    •  & Bernhard Kuster
  2. JPT Peptide Technologies GmbH, Berlin, Germany.

    • Karsten Schnatbaum
    • , Johannes Zerweck
    • , Tobias Knaute
    • , Holger Wenschuh
    •  & Ulf Reimer
  3. Thermo Fisher Scientific, Bremen, Germany.

    • Bernard Delanghe
    •  & Thomas Moehring
  4. Thermo Fisher Scientific, San Jose, California, USA.

    • Derek J Bailey
    •  & Andreas Huhmer
  5. SAP SE, Potsdam, Germany.

    • Siegfried Gessulat
    • , Hans-Christian Ehrlich
    •  & Stephan Aiche
  6. SAP SE, Walldorf, Germany.

    • Judith Schlegl
  7. Institute for Systems Biology, Seattle, Washington, USA.

    • Ulrike Kusebauch
    • , Eric W Deutsch
    •  & Robert L Moritz
  8. Department of Biology, Institute of Molecular Systems Biology, ETH, Zürich, Switzerland.

    • Ruedi Aebersold
  9. Faculty of Science, University of Zürich, Zürich, Switzerland.

    • Ruedi Aebersold
  10. Center for Integrated Protein Science Munich, Freising, Germany.

    • Bernhard Kuster
  11. Bavarian Center for Biomolecular Mass Spectrometry, Freising, Germany.

    • Bernhard Kuster

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Contributions

R.A., H.W., T.M., A.H., U.R. and B.K. conceived the study. D.P.Z., M. Wilhelm, K.S., J.Z., T.K., B.D., K.K., U.K., R.L.M. and B.K. designed experiments. D.P.Z., M. Wilhelm, K.S., J.Z., T.K., B.D., D.J.B., P.Y., K.K., E.W.D. and T.S. performed the experiments and analyzed data. M. Wilhelm, S.G., H.-C.E., M. Weininger, J.S., T.S. and S.A. extended the web resource. D.P.Z., M. Wilhelm and B.K. wrote the manuscript.

Competing interests

M. Wilhelm and B.K. are founders and shareholders of OmicScouts, which operates in the field of proteomics. They have no operational role in the company. R.A. is a cofounder and shareholder of Biognosys, which operates in the field of proteomics. He has no operational involvement in the company. K.S., J.Z., T.K., H.W. and U.R. are employees of JPT. B.D., D.J.B, T.M. and A.H. are employees of Thermo Fisher Scientific. S.G., H.-C.E., J.S. and S.A. are employees of SAP SE. Retention time peptides will be commercialized by JPT.

Corresponding author

Correspondence to Bernhard Kuster.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–14 and Supplementary Notes 1–4

Excel files

  1. 1.

    Supplementary Table 1

    Peptide pool mapping

  2. 2.

    Supplementary Table 2

    Peptide identifications

  3. 3.

    Supplementary Table 3

    Overlap with mouse

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DOI

https://doi.org/10.1038/nmeth.4153