Documentation

DOCUMENTATION OF THE DATABASES

Publications

PRIDE Inspector: a tool to visualize and validate MS proteomics data.
Wang R, Fabregat A, Rios D, Ovelleiro D, Foster JM, Cote RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaino JA
Nat. Biotechnol. 30 (2012) 135-7
Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany.
Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaino JA, Hermjakob H
Proteomics 11 (2011) 4284-90
jTraML: An Open Source Java API for TraML, the PSI Standard for Sharing SRM Transitions.
Helsens K, Brusniak MY, Deutsch E, Moritz RL, Martens L
J. Proteome Res. 10 (2011) 5260-3
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.
Ndegwa N, Cote RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaino JA, Croft D
Database (Oxford) 2011 (2011) bar047
Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB 'complete proteome' sets.
Griss J, Martin M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaino JA
Proteomics (2011)
The ProteoRed MIAPE web toolkit: A user-friendly framework to connect and share proteomics standards.
Medina-Aunon JA, Martinez-Bartolome S, Lopez-Garcia MA, Salazar E, Navajas R, Jones AR, Paradela A, Albar JP
Mol. Cell Proteomics (2011)
Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.
Griss J, Cote RG, Gerner C, Hermjakob H, Vizcaino JA
Mol. Cell Proteomics 10 (2011) M111.008490
Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.
Colaert N, Barsnes H, Vaudel M, Helsens K, Timmerman E, Sickmann A, Gevaert K, Martens L
J. Proteome Res. 10 (2011) 3840-3

Deliverables
D1.1 ProteomeXchange consortium website
D2.1 Maintenance report of the PSI existing standards: mzML, mzIdentML, TraML
D4.1 ProteomeXchange repository data flow definition
D4.2 ProteomeXchange metadata format definition
D4.3 Implementation of MIAPE/journal validation system
D4.4 Tranche implementation of ProteomeXchange data flow
D4.5 PRIDE implementation of ProteomeXchange data flow
D4.6 ProteomeXchange repository data flow definition - quantitation extension
D4.7 MIAPE validation - quantitation extension
D1.2 ProteomeXchange consortium documentation (Year 1)
D1.3 ProteomeXchange consortium documentation (Year 2)
D1.4 ProteomeXchange consortium documentation (Year 3)
D2.2 Release of mzQuantML core standard documents, according to the PSI document process
D6.5 Web-based tutorial 2 about "Proteomics Data Deposition and Dissemination through ProteomeXchange"
D2.3 Development of module for quantitation techniques (level 1)
D2.4 Development of module for quantitation techniques (level 2)
D2.5 Development of module for quantitation techniques (level 3)
D5.1 Create central ProteomeXchange dataset identifier lookup service - ProteomeCentral
D5.2 Implement reprocessed-data broadcast mechanism
D5.3 ProteomeXchange data import - UniProt implementation
D3.1 Implementation of ProteomeXchange data export functionality for OmicsHub
D3.2 Implementation of ProteomeXchange data export functionality for ProteinScape 1.3 and 2.x (ProCon)
D3.3 Implementation of ProteomeXchange data export functionality for Phenyx
D3.4 Update PRIDE Converter to ProteomeXchange submissions
D3.5 ms_limsX requirements functional specification
D3.6 ms_limsX alpha release
D3.7 ms_limsX beta release
D3.8 Implementation of ProteomeXchange export functionality in ms_limsX
D3.9 Official release of ms_limsX, including full documentation and installation guide
D5.4 ProteomeXchange data import - PeptideAtlas implementation
D6.1 Stakeholder meeting (Year 1)
D6.2 Stakeholder meeting (Year 2)
D6.3 Stakeholder meeting (Year 3)
D6.4 Web-based tutorial 1 about "Proteomics Data Deposition and Dissemination through ProteomeXchange"
D6.6 ProteomeXchange training workshops (Year 2)
D6.7 ProteomeXchange training workshops (Year 3)