PRIDE: new developments and new datasets

The PRIDE (http://www.ebi.ac.uk/pride) database of protein and peptide identifications was previously described in the NAR Database Special Edition in 2006. Since this publication, the volume of public data in the PRIDE relational database has increased by more than an order of magnitude. Several significant public datasets have been added, including identifications and processed mass spectra generated by the HUPO Brain Proteome Project and the HUPO Liver Proteome Project. The PRIDE software development team has made several significant changes and additions to the user interface and tool set associated with PRIDE. The focus of these changes has been to facilitate the submission process and to improve the mechanisms by which PRIDE can be queried. The PRIDE team has developed a Microsoft Excel workbook that allows the required data to be collated in a series of relatively simple spreadsheets, with automatic generation of PRIDE XML at the end of the process. The ability to query PRIDE has been augmented by the addition of a BioMart interface allowing complex queries to be constructed. Collaboration with groups outside the EBI has been fruitful in extending PRIDE, including an approach to encode iTRAQ quantitative data in PRIDE XML.

[1]  Y. Zhang,et al.  IntAct—open source resource for molecular interaction data , 2006, Nucleic Acids Res..

[2]  Imre Vastrik,et al.  Reactome: a knowledgebase of biological pathways , 2004, OTM Workshops.

[3]  Rolf Apweiler,et al.  The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries , 2006, BMC Bioinformatics.

[4]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[5]  Biaoyang Lin,et al.  A combined dataset of human cerebrospinal fluid proteins identified by multi‐dimensional chromatography and tandem mass spectrometry , 2007, Proteomics.

[6]  Rong Wang,et al.  The need for a public proteomics repository , 2004, Nature Biotechnology.

[7]  Jennifer A Mead,et al.  Public proteomic MS repositories and pipelines: available tools and biological applications , 2007, Proteomics.

[8]  R. Beavis,et al.  Using annotated peptide mass spectrum libraries for protein identification. , 2006, Journal of proteome research.

[9]  Lennart Martens,et al.  HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy , 2006 .

[10]  Vincent J. Denef,et al.  Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria , 2007, Nature.

[11]  Lennart Martens,et al.  PRIDE: a public repository of protein and peptide identifications for the proteomics community , 2005, Nucleic Acids Res..

[12]  Bart De Moor,et al.  BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis , 2005, Bioinform..

[13]  Lennart Martens,et al.  The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases , 2007, BMC Bioinformatics.

[14]  Fuchu He,et al.  The Human Liver Proteome Project (HLPP) Workshop during the 4th HUPO World Congress , 2006, Proteomics.

[15]  Hanno Steen,et al.  Development of human protein reference database as an initial platform for approaching systems biology in humans. , 2003, Genome research.

[16]  M. Ashburner,et al.  An ontology for cell types , 2005, Genome Biology.

[17]  Lincoln Stein,et al.  Reactome: a knowledgebase of biological pathways , 2004, Nucleic Acids Res..

[18]  Antje Chang,et al.  New Developments , 2003 .

[19]  R. Aebersold,et al.  A uniform proteomics MS/MS analysis platform utilizing open XML file formats , 2005, Molecular systems biology.

[20]  Lennart Martens,et al.  PRIDE: The proteomics identifications database , 2005, Proteomics.

[21]  Bernhard Kuster,et al.  Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors , 2007, Nature Biotechnology.

[22]  Lennart Martens,et al.  HUPO Brain Proteome Project: Summary of the pilot phase and introduction of a comprehensive data reprocessing strategy , 2006, Proteomics.

[23]  Rolf Apweiler,et al.  UniProt archive , 2004, Bioinform..

[24]  Democratizing proteomics data , 2007, Nature Biotechnology.

[25]  Fuchu He,et al.  Human Liver Proteome Project , 2005, Molecular & Cellular Proteomics.

[26]  Amos Bairoch,et al.  NEWT, a new taxonomy portal , 2003, Nucleic Acids Res..

[27]  김삼묘,et al.  “Bioinformatics” 특집을 내면서 , 2000 .

[28]  Rolf Apweiler,et al.  The Proteomics Identifications Database (PRIDE) and the ProteomExchange Consortium: making proteomics data accessible , 2006, Expert review of proteomics.

[29]  Andreas Prlic,et al.  Ensembl 2007 , 2006, Nucleic Acids Res..

[30]  Eric W. Deutsch,et al.  The PeptideAtlas project , 2005, Nucleic Acids Res..