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PRIDE Cluster: building a consensus of proteomics data

Nature Methods volume 10, pages 95–96 (2013)Cite this article

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To the Editor:

The amount of mass spectrometry (MS) proteomics data in public repositories is growing rapidly1, but (re)use of these data to increase the reliability of newly performed experiments is still limited. Two of the major obstacles are the high heterogeneity of the data present in repositories and the inflation of false positive identifications when data sets are combined. Here we present the Proteomics Identifications database (PRIDE) Cluster, comprising a tool to identify reliable peptide identifications in heterogeneous MS-based proteomics data in the PRIDE database2 (http://www.ebi.ac.uk/pride/) and a resource of regularly updated, reliable spectral libraries based on these identifications.

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Figure 1: Peptide identification 'ratio' is sufficient to identify reliable identifications from the clustering results of the PRIDE repository.

References

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Acknowledgements

We want to acknowledge all other members of the PRIDE team, who contributed to some aspects of this work in terms of technical implementation and discussion of the results. Additional thanks go to Matrix Science for providing a Mascot license. Special thanks go to all data submitters to the PRIDE database, whose data are the foundation of the work presented here. J.G. is supported by the Wellcome Trust (grant no. WT085949MA). J.A.V. is supported by the European Union FP7 grants LipidomicNet (202272) and ProteomeXchange (260558). J.M.F. is supported by a Biotechnology and Biological Sciences Research Council CASE studentship, also funded by Philips.

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Authors and Affiliations

  1. European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK

    Johannes Griss, Joseph M Foster, Henning Hermjakob & Juan Antonio Vizcaíno

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  1. Johannes Griss
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  2. Joseph M Foster
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  3. Henning Hermjakob
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  4. Juan Antonio Vizcaíno
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Correspondence to Johannes Griss.

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The authors declare no competing financial interests.

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Supplementary Figures 1–9, Supplementary Table 1, Supplementary Protocol and Supplementary Notes 1–7 (PDF 2524 kb)

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Griss, J., Foster, J., Hermjakob, H. et al. PRIDE Cluster: building a consensus of proteomics data. Nat Methods 10, 95–96 (2013). https://doi.org/10.1038/nmeth.2343

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