The PeptideAtlas project

By Frank Desiere, Eric W. Deutsch, Nichole L. King, Alexey I. Nesvizhskii, Parag Mallick, Jimmy K. Eng, Sharon Chen, J. Eddes, S. Loevenich, R. Aebersold. Nucleic Acids Res., 2005

812 citations recorded by the source corpus.

The completion of the sequencing of the human genome and the concurrent, rapid development of high-throughput proteomic methods have resulted in an increasing need for automated approaches to archive proteomic data in a repository that enables the exchange of data among researchers and also accurate integration with genomic data. PeptideAtlas () addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. A meaningful comparison of data across different experiments generated by different groups using different types of instruments is enabled by the implementation of a uniform analytic process. This uniform statistical validation ensures a consistent and high-quality set of peptide and protein identifications. The raw data from many diverse proteomic experiments are made available in the associated PeptideAtlas repository in several formats. Here we present a summary of our process and details about the Human, Drosophila and Yeast PeptideAtlas builds.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/76a3548d1c50130ac235db73151662c7050c810d

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Citations in the corpus

Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database (2012, background): “The Global Proteome Machine (9) and PeptideAtlas (10, 11) are two of the earliest such collections, with the primary goal of providing a collection of peptide identifications.”
The Human Proteome Project: Current State and Future Direction (2011, background): “A specialized SRMAtlas database is currently being generated from fragment ion spectra for multiple proteotypic peptides of nearly every protein in the human proteome (5, 6), providing the information for the definitive identification and accurate quantification of each protein in biological samples”
Selected reaction monitoring for quantitative proteomics: a tutorial (2008, background): “PeptideAtlas http://www.peptideatlas.org/ Desiere et al (2006) Human proteinpedia http://www.humanproteinpedia.org/ Mathivanan et al (2008) GPM Proteomics database http://gpmdb.thegpm.org/ Craig et al (2004) PRIDE http://www.ebi.ac.uk/pride/ Jones et al (2008) ISPIDER central http://ispider.smith.”
UniProt: the universal protein knowledgebase in 2021 (2020, background): “…and visualizes unique and non-unique peptides identified by mass spectrometry proteomic data deposited through the ProteomeXchange Consortium (31) (e.g. PeptideAtlas (32), MassIVE (33) and jPOST (34)) and other large-scale initiatives (CPTAC (35), ProteomicsDB (36), MaxQB (37), ETD and CTDP (38)).”
PaxDb, a Database of Protein Abundance Averages Across All Three Domains of Life (2012, methodology): “The data sets were either curated directly from published literature (29–52) (whereby the actual data files were often retrieved via PRIDE), or were downloaded from PeptideAtlas (15, 53), taking advantage of PeptideAtlas “Builds.””
A fast Peptide Match service for UniProt Knowledgebase (2013, background): “So far, to our knowledge, no other peptide match services provide all of the key characteristics in our new service, including search speed, support for any query peptide of 3 amino acids long, coverage of all UniProtKB sequences including isoforms (UniProt Consortium, 2013) and frequent update.”
The UniProtKB guide to the human proteome (2016, background): “This includes peptides from PeptideAtlas (32) and MaxQB (33) for the human proteome as well as for a number of other species.”
GENCODE: The reference human genome annotation for The ENCODE Project (2012, methodology): “Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas.”
Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* (2012, neutral): “Additionally, through community effort, several publicly available databases of tandem MS spectra (33-39) and validated SRM assays (40,41) are available to provide empirical guides to transition selection and assay development.”
PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows (2008, background): “…spectra are of inadequate quality to ever be identified, a considerable fraction can be identified with more effort and newer techniques (nesvizhskii et al, 2006). peptideatlas aims to be an active repository in which only raw data are accepted and these raw data are periodically…”
GENCODE: reference annotation for the human and mouse genomes in 2023 (2022, methodology): “The GENCODE Riboseq ORF set has now been taken forward by PeptideAtlas (16) on behalf of HUPO (https://hupo.”
The UCSC Genome Browser database: 2015 update (2014, background): “Proteomics resources such as PeptideAtlas (48,49), GPM (50) and ProteomeXchange (51) provide centralized data and metadata collection, uniform spectrum mapping and quality filtering for experimental results from diverse studies.”