The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

By Juan Antonio Vizcaíno, R. Côté, A. Csordas, José A. Dianes, A. Fabregat, Joseph M. Foster, J. Griss, E. Alpi, Melih Birim, Javier Contell and 8 more. Nucleic Acids Res., 2012

1,941 citations recorded by the source corpus.

The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/3b3ad5eaddd5a970519b8c9b4097816fe374e8ec

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In Molecular Biology

1. Damian Szklarczyk
2. C. von Mering
3. Milan Simonovic
4. B. Aslam
5. M. Khurshid
6. M. Basit
7. M. Rasool
8. M. A. Nisar

In Spectroscopy

1. Damian Szklarczyk
2. B. Aslam
3. Milan Simonovic
4. C. von Mering
5. M. Khurshid
6. M. Basit
7. M. Rasool
8. M. A. Nisar

Citations in the corpus

• Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell‐lines (2015, methodology): “Of these, the largest repositories of primary, raw data are those that are organized in the ProteomeXchange consortium [8]: PRIDE [9], PeptideAtlas [10], MassIVE [11], and PASSEL [10].”
• Proteomics: Technologies and Their Applications. (2017, methodology): “The largest proteome repositories including PRIDE proteomics identification database, Proteome Commons and PeptideAtlas project provide direct access to most of stored data and are valuable tools for data mining (141, 142).”