Using the PRIDE Database and ProteomeXchange for Submitting and Accessing Public Proteomics Datasets

Andrew F. Jarnuczak1, Juan Antonio Vizcaíno1

1 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL‐EBI), Cambridge
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 13.31
DOI:  10.1002/cpbi.30
Online Posting Date:  September, 2017
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The ProteomeXchange (PX) Consortium is the unifying framework for world‐leading mass spectrometry (MS)–based proteomics repositories. Current members include the PRIDE database (U.K.), PeptideAtlas/PASSEL, and MassIVE (U.S.A.), and jPOST (Japan). The Consortium standardizes submission and dissemination of public proteomics data worldwide. This is achieved through implementing common data submission guidelines and enforcing metadata requirements by each of the members. Furthermore, the members use a common identifier space. Each dataset receives a unique (PXD) accession number and is publicly accessible as soon as the associated scientific publications are released. The two basic protocols provide a step‐by‐step guide on how to submit data to the PRIDE database, and describe how to access the PX portal (called ProteomeCentral), which can be used to search datasets available in any of the PX members. © 2017 by John Wiley & Sons, Inc.

Keywords: PRIDE database; proteomics; data repository; mass spectrometry

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Table of Contents

  • Introduction
  • Basic Protocol 1: Performing a Complete Submission to ProteomeXchange via the PRIDE Database
  • Basic Protocol 2: Exploring Public Datasets in ProteomeXchange Resources Using ProteomeCentral
  • Commentary
  • Literature Cited
  • Figures
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Literature Cited

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  Desiere, F., Deutsch, E. W., King, N. L., Nesvizhskii, A. I., Mallick, P., Eng, J., … Aebersold, R. (2006). The PeptideAtlas project. Nucleic Acids Research, 34(90001), D655–D658. doi: 10.1093/nar/gkj040.
  Deutsch, E. W., Albar, J. P., Binz, P.‐A., Eisenacher, M., Jones, A. R., Mayer, G., … Hermjakob, H. (2015). Development of data representation standards by the human proteome organization proteomics standards initiative. Journal of the American Medical Informatics Association, 22(3), 495–506. doi: 10.1093/jamia/ocv001.
  Deutsch, E. W., Csordas, A., Sun, Z., Jarnuczak, A., Perez‐Riverol, Y., Ternent, T., … Vizcaíno, J. A. (2017). The ProteomeXchange consortium in 2017: Supporting the cultural change in proteomics public data deposition. Nucleic Acids Research, 45(D1), D1100–D1106. doi: 10.1093/nar/gkw936.
  Griss, J., Jones, A. R., Sachsenberg, T., Walzer, M., Gatto, L., Hartler, J., … Hermjakob, H. (2014). The mzTab data exchange format: Communicating mass‐spectrometry‐based proteomics and metabolomics experimental results to a wider audience. Molecular & Cellular Proteomics, 13(10), 2765–2775. doi: 10.1074/mcp.O113.036681.
  Griss, J., Perez‐Riverol, Y., Lewis, S., Tabb, D. L., Dianes, J. A., Del‐Toro, N., … Vizcaíno, J. A. (2016). Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets. Nature Methods, 13(8), 651–656. doi: 10.1038/nmeth.3902.
  Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O., Siepen, J., Hubbard, S. J., … Creasy, D. (2012). The mzIdentML data standard for mass spectrometry‐based proteomics results. Molecular & Cellular Proteomics, 11(7), M111.014381. doi: 10.1074/mcp.M111.014381.
  Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., … Apweiler, R. (2005). PRIDE: The proteomics identifications database. Proteomics, 5(13), 3537–3545. doi: 10.1002/pmic.200401303.
  Okuda, S., Watanabe, Y., Moriya, Y., Kawano, S., Yamamoto, T., Matsumoto, M., … Ishihama, Y. (2017). jPOSTrepo: An international standard data repository for proteomes. Nucleic Acids Research, 45. doi: 10.1093/nar/gkw1080.
  Perez‐Riverol, Y., Alpi, E., Wang, R., Hermjakob, H., & Vizcaíno, J. A. (2015). Making proteomics data accessible and reusable: Current state of proteomics databases and repositories. Proteomics, 15(5–6), 930–949. doi: 10.1002/pmic.201400302.
  Perez‐Riverol, Y., Xu, Q.‐W., Wang, R., Uszkoreit, J., Griss, J., Sanchez, A., … Vizcaíno, J. A. (2016). PRIDE Inspector toolsuite: Moving toward a universal visualization tool for proteomics data standard formats and quality assessment of proteomexchange datasets. Molecular & Cellular Proteomic, 15(1), 305–317. doi: 10.1074/mcp.O115.050229.
  Vizcaíno, J., Csordas, A., Del‐Toro, N., Dianes, J. A., Griss, J., Lavidas, I., … Hermjakob, H. (2016). 2016 update of the PRIDE database and its related tools. Nucleic Acids Research, 44(D1), D447–D456. doi: 10.1093/nar/gkv1145.
  Vizcaíno, J., Deutsch, E. E. W., Wang, R., Vizcaino, J. A., Deutsch, E. E. W., Wang, R., … Hermjakob, H. (2014). ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nature Biotechnology, 32(3), 223–226. doi: 10.1038/nbt.2839.
Internet Resources
  The ProteomeXchange Web page contains all the information about the current members of the Consortium, linking to the submission guidelines, and ways to access data.
  ProteomeXchange portal (ProteomeCentral). Web portal that enables access to public datasets in any of the PX resources.
  PRIDE database. Home page of the PRIDE database.
  Home pages of the remaining PX partner repositories: PeptideAtlas, MassIVE, and jPOST, respectively.
  A more detailed tutorial about how to submit datasets to PRIDE.
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