PRIDE: The proteomics identifications database

By Lennart Martens, H. Hermjakob, Philip Jones, M. Adamski, Chris F. Taylor, D. States, Kris Gevaert, J. Vandekerckhove, Rolf Apweiler. Proteomics, 2005

603 citations recorded by the source corpus.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/8cbae8809ee33c512ea5180f5c4721137d848e6f

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Citations in the corpus

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, background): “[287] Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, et al.”
Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database (2012, background): “PRoteomics IDEntifications data-base (PRIDE) is a large effort at the European Bioinformatics Institute, which has collected peptide and protein identification data from more than 10,000 experiments (14, 15).”
A Guided Tour of the Trans-Proteomic Pipeline (2010, methodology): “From within the TPP interface, users will be able to easily upload their results to one of the repositories such as PeptideAtlas [21], PRIDE [49], Tranche [50], or Peptidome (http://www.ncbi.nlm.nih.gov/projects/ peptidome/).”
Human protein reference database—2006 update (2005, neutral): “Experimentally derived peptide sequences obtained by mass spectrometry that have been deposited in PeptideAtlas (http://www.peptideatlas.org) (16) and PRIDE (17) repositories are also mapped onto the genomic sequence in GenProt Viewer.”
Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry* (2009, background): “Data repositories have been created to store the vast amount of mass spectrometric data (Craig, Cortens et al. 2004; Desiere, Deutsch et al. 2005; Martens, Hermjakob et al. 2005; King, Deutsch et al. 2006).”
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics (2009, neutral): “for subsequent submission to the Proteomics Identifications Database (PRIDE”
The PRIDE database and related tools and resources in 2019: improving support for quantification data (2018, background): “…(PRIDE) database (https: //www.ebi.ac.uk/pride/) was set up in 2004 at the European Bioinformatics Institute (EMBL-EBI, Hinxton, Cam-bridge, UK) to enable public data deposition of MS proteomics data, providing access to the experimental data described in scientific publications (1).”
mzML—a Community Standard for Mass Spectrometry Data (2010, neutral): “One format, mzData, was developed by HUPO-PSI as a data exchange and archive standard (14, 15), and was implemented as such in PRIDE (16).”
The Human Proteome Project: Current State and Future Direction (2011, background): “We will have a greatly expanded ProteomeXchange comprising EBI/ PRIDE, ISB/PeptideAtlas, Tranche, GPMDB, and any additional major data repositories.”
Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial (2018, neutral): “…types of MS data that could conceivably also be used as prior knowledge in the analysis of SWATH-MS data continues to increase (Craig et al , 2004; Martens et al , 2005; Deutsch et al , 2008; Picotti et al , 2008; Sharma et al , 2014; Whiteaker et al , 2014; Wilhelm et al , 2014; Zolg et al ,…”