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ProHits: integrated software for mass spectrometry–based interaction proteomics

Nature Biotechnology volume 28, pages 1015–1017 (2010)Cite this article

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To the Editor:

Affinity purification coupled with mass spectrometric identification (AP-MS) is now a method of choice for charting novel protein-protein interactions and has been applied to a large number of both small-scale and high-throughput studies1. However, general and intuitive computational tools for sample tracking, AP-MS data analysis and annotation have not kept pace with rapid methodological and instrument improvements. To address this need, we have developed the ProHits laboratory information management system platform.

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Figure 1: Overview of ProHits.

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Acknowledgements

We thank G. Bader, H. Hermjakob, S. Orchard, J.A. Vizcaíno, C. Le Roy, R. Beavis and members of the Tyers and Gingras laboratories for helpful discussions. We are grateful to D. Figeys, S. Angers, D. Fermin, T. LeBihan, F. Ellisma, C. Poitras and B. Coulombe for testing beta versions of ProHits. We thank W. Dunham, E. Deutsch, D. Fermin, T. Glatter, M. Goudreault, L. D'Ambrosio and R. Ewing for critical reading of the manuscript and instruction manual and L. Ng, J. Wei and N. Mohammad for IT support. Supported by grants from the CIHR (MOP-84314 to A.-C.G., MOP-12246 to M.T., MOP-81268 to B.R., GSP-36651 to T.P., J.L.W. and M.T., FRN 82940 to M.T. and a resource grant to T.P., A.-C.G., J.L.W. and M.T.), the NIH (5R01RR024031 to M.T., 1R01GM094231-01 to A.I.N. and A.-C.G., and CA-126239 to A.I.N.), MRI-ORF (T.P., J.L.W. and A.-C.G.), the Canada Foundation for Innovation (T.P., J.L.W., A.-C.G. and M.T.), and Genome Canada through Ontario Genomics Institute (T.P. and J.L.W.). We wish to acknowledge support from the Mount Sinai Hospital Foundation; Canada Research Chairs in Functional Genomics and Bioinformatics to M.T., in Proteomics and Molecular Medicine to B.R., and in Functional Proteomics to A.-C.G.; the Lea Reichmann Chair in Cancer Proteomics to A.-C.G. and a Scottish Universities Life Sciences Alliance Research Professorship and a Royal Society Wolfson Research Merit Award to M.T.

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Authors and Affiliations

  1. Centre for Systems Biology, Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada

    Guomin Liu, Jianping Zhang, Brett Larsen, Chris Stark, Ashton Breitkreutz, Zhen-Yuan Lin, Bobby-Joe Breitkreutz, Yongmei Ding, Karen Colwill, Adrian Pasculescu, Tony Pawson, Jeffrey L Wrana, Mike Tyers & Anne-Claude Gingras

  2. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

    Tony Pawson, Jeffrey L Wrana, Mike Tyers & Anne-Claude Gingras

  3. Departments of Pathology and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA

    Alexey I Nesvizhskii

  4. Ontario Cancer Institute and McLaughlin Centre for Molecular Medicine, Toronto, Ontario, Canada

    Brian Raught

  5. Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK

    Mike Tyers

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  1. Guomin Liu
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Correspondence to Mike Tyers or Anne-Claude Gingras.

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Liu, G., Zhang, J., Larsen, B. et al. ProHits: integrated software for mass spectrometry–based interaction proteomics. Nat Biotechnol 28, 1015–1017 (2010). https://doi.org/10.1038/nbt1010-1015

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