Documentation

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Antonio Vizcaíno J, Hermjakob H, Stephan C, Meyer HE, Eisenacher M,

Database (Oxford) 2013 (2013) bat009

Quality meets quantity - quality control, data standards and repositories.

Eisenacher M, Schnabel A, Stephan C

Proteomics 11 (2011) 1031-1036

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

Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H

Nucleic Acids Res. 41 (2013) D1063-9

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.

Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA

Mol. Cell Proteomics 11 (2012) 1682-1689

A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS.

Qi D, Brownridge P, Xia D, Mackay K, Gonzalez-Galarza FF, Kenyani J, Harman V, Beynon RJ, Jones AR

OMICS 16 (2012) 489-495

Towards a human proteomics atlas.

Gonnelli G, Hulstaert N, Degroeve S, Martens L

Anal Bioanal Chem 404 (2012) 1069-1077

Sigpep: calculating unique peptide signature transition sets in a complete proteome background.

Helsens K, Mueller M, Hulstaert N, Martens L

Proteomics 12 (2012) 1142-6

Improvements in the protein identifier cross-reference service.

Wein SP, Cote RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaino JA

Nucleic Acids Res. 40 (2012) W276-80

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.

Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolome S, Vizcaino JA, Hermjakob H

Proteomics 12 (2012) 351-5

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Griss J, Reisinger F, Hermjakob H, Vizcaino JA

Proteomics 12 (2012) 795-8

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.

Reisinger F, Krishna R, Ghali F, Rios D, Hermjakob H, Vizcaino JA, Jones AR

Proteomics 12 (2012) 790-4

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results.

Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaino JA, Chambers M, Pizarro A, Creasy D

Mol. Cell Proteomics 11 (2012) M111.014381

PRIDE: Quality control in a proteomics data repository.

Csordas A, Ovelleiro D, Wang R, Foster JM, Rios D, Vizcaino JA, Hermjakob H

Database (Oxford) 2012 (2012) bas004

Isoelectric point optimization using peptide descriptors and support vector machines.

Perez-Riverol Y, Audain E, Millan A, Ramos Y, Sanchez A, Vizcaino JA, Wang R, Muller M, Machado YJ, Betancourt LH, Gonzalez LJ, Padron G, Besada V

J Proteomics 75 (2012) 2269-74

TraML: a standard format for exchange of selected reaction monitoring transition lists.

Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY

Mol. Cell Proteomics 11(4) (2012) R111.015040

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