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Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories

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Mass Spectrometry Data Analysis in Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1007))

Abstract

Both the existence of data standards and public databases or repositories have been key factors behind the development of the existing “omics” approaches. In this book chapter we first review the main existing mass spectrometry (MS)-based proteomics resources: PRIDE, PeptideAtlas, GPMDB, and Tranche. Second, we report on the current status of the different proteomics data standards developed by the Proteomics Standards Initiative (PSI): the formats mzML, mzIdentML, mzQuantML, TraML, and PSI-MI XML are then reviewed.

Finally, we present an easy way to query and access MS proteomics data in the PRIDE database, as a representative of the existing repositories, using the workflow management system (WMS) tool Taverna. Two different publicly available workflows are explained and described.

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Abbreviations

CV:

Controlled vocabulary

DAS:

Distributed annotation system

(HUPO) PSI:

(Human Proteome Organisation) proteomics standards initiative

GO:

Gene ontology

GPMDB:

Global Proteome Machine DataBase

IMEX:

International Molecular EXchange (collaboration)

MGF:

Mascot Generic Format

MI:

Molecular interaction

MIAPE:

Minimum information about a proteomics experiment

MOPED:

Model Organism Protein Expression Database

MRM:

Multiple reaction monitoring

PASSEL:

PeptideAtlas SRM Experiment Library

PRIDE:

PRoteomics IDEntifications (database)

PSICQUIC:

Proteomics Standard Initiative Common QUery InterfaCe

SRM:

Selected reaction monitoring

TPP:

Trans proteomic pipeline

WMS:

Workflow management system

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Acknowledgments

R.C.J. is supported by the NHLBI Proteomics Center Award HHSN268201000035C. J.A.V. is supported by the EU FP7 grants LipidomicNet [grant number 202272] and ProteomeXchange [grant number 260558].

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Authors and Affiliations

  1. EMBL-EBI, Hinxton, Cambridge, UK

    Rafael C. Jiménez & Juan Antonio Vizcaíno

Authors
  1. Rafael C. Jiménez
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  2. Juan Antonio Vizcaíno
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Editors and Affiliations

  1. Inst. Molecular Pathology & Immunology, Universidade do Porto Inst. Molecular Pathology & Immunology, Porto, Portugal

    Rune Matthiesen

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Jiménez, R.C., Vizcaíno, J.A. (2013). Proteomics Data Exchange and Storage: The Need for Common Standards and Public Repositories. In: Matthiesen, R. (eds) Mass Spectrometry Data Analysis in Proteomics. Methods in Molecular Biology, vol 1007. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-392-3_14

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  • DOI: https://doi.org/10.1007/978-1-62703-392-3_14

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-391-6

  • Online ISBN: 978-1-62703-392-3

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