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

Towards a human proteomics atlas

(2012) Giulia Gonnelli et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Standard Guidelines for the Chromosome-Centric Human Proteome Project

(2012) Young-Ki Paik et al.   JOURNAL OF PROTEOME RESEARCH

The PRoteomics IDEntification (PRIDE) Converter 2 Framework: An Improved Suite of Tools to Facilitate Data Submission to the PRIDE Database and the ProteomeXchange Consortium

(2012) Richard G. Côté et al.   MOLECULAR & CELLULAR PROTEOMICS

Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database

(2012) Christoph Schaab et al.   MOLECULAR & CELLULAR PROTEOMICS

The mzIdentML Data Standard for Mass Spectrometry-Based Proteomics Results

(2012) Andrew R. Jones et al.   MOLECULAR & CELLULAR PROTEOMICS

PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life

(2012) M. Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

PRIDE Inspector: a tool to visualize and validate MS proteomics data

(2012) Rui Wang et al.   NATURE BIOTECHNOLOGY

A home for raw proteomics data

(2012)   NATURE METHODS

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Improvements in the protein identifier cross-reference service

(2012) Samuel P. Wein et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Florian Reisinger et al.   PROTEOMICS

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

(2012) Johannes Griss et al.   PROTEOMICS

PASSEL: The PeptideAtlas SRMexperiment library

(2012) Terry Farrah et al.   PROTEOMICS

PRIDE: Quality control in a proteomics data repository

(2012) A. Csordas et al.   Database-The Journal of Biological Databases and Curation

Top-down mass spectrometry: Recent developments, applications and perspectives

(2011) Weidong Cui et al.   ANALYST

Published and Perished? The Influence of the Searched Protein Database on the Long-Term Storage of Proteomics Data

(2011) Johannes Griss et al.   MOLECULAR & CELLULAR PROTEOMICS

neXtProt: a knowledge platform for human proteins

(2011) L. Lane et al.   NUCLEIC ACIDS RESEARCH

MOPED: Model Organism Protein Expression Database

(2011) Eugene Kolker et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB “complete proteome” sets

(2011) Johannes Griss et al.   PROTEOMICS

A posteriori quality control for the curation and reuse of public proteomics data

(2011) Joseph M. Foster et al.   PROTEOMICS

BioMart: a data federation framework for large collaborative projects

(2011) J. Zhang et al.   Database-The Journal of Biological Databases and Curation

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations

(2011) Nelson Ndegwa et al.   Database-The Journal of Biological Databases and Curation

Asymmetric and non-uniform evolution of recently duplicated human genes

(2010) Alexander Y Panchin et al.   Biology Direct

Proteomics data repositories: Providing a safe haven for your data and acting as a springboard for further research

(2010) Juan Antonio Vizcaíno et al.   Journal of Proteomics

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteomics: a pragmatic perspective

(2010) Parag Mallick et al.   NATURE BIOTECHNOLOGY

The Ontology Lookup Service: bigger and better

(2010) R. Cote et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

jmzML, an open-source Java API for mzML, the PSI standard for MS data

(2010) Richard G. Côté et al.   PROTEOMICS

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

The Proteios Software Environment: An Extensible Multiuser Platform for Management and Analysis of Proteomics Data

(2009) Jari Häkkinen et al.   JOURNAL OF PROTEOME RESEARCH

NCBI Peptidome: a new public repository for mass spectrometry peptide identifications

(2009) Douglas J Slotta et al.   NATURE BIOTECHNOLOGY

PRIDE Converter: making proteomics data-sharing easy

(2009) Harald Barsnes et al.   NATURE BIOTECHNOLOGY

Database on Demand - An online tool for the custom generation of FASTA-formatted sequence databases

(2009) Florian Reisinger et al.   PROTEOMICS

A guide to the Proteomics Identifications Database proteomics data repository

(2009) Juan Antonio Vizcaíno et al.   PROTEOMICS

Recent developments in public proteomic MS repositories and pipelines

(2009) Jennifer A. Mead et al.   PROTEOMICS

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

(2008) Eric W Deutsch et al.   EMBO REPORTS

Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets

(2008) Michael Mueller et al.   PROTEOMICS

Analyzing Large-Scale Proteomics Projects with Latent Semantic Indexing

(2007) Sebastian Klie et al.   JOURNAL OF PROTEOME RESEARCH