title: The PeptideAtlas project.
abstract: 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 (http://www.peptideatlas.org/) 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.
authors.affiliation: Institute for Systems Biology, Seattle, WA, USA. fdesiere@yahoo.com
authors.forename: Frank
authors.initials: F
authors.lastname: Desiere
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Nichole L
authors.initials: NL
authors.lastname: King
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
authors.forename: Parag
authors.initials: P
authors.lastname: Mallick
authors.forename: Jimmy
authors.initials: J
authors.lastname: Eng
authors.forename: Sharon
authors.initials: S
authors.lastname: Chen
authors.forename: James
authors.initials: J
authors.lastname: Eddes
authors.forename: Sandra N
authors.initials: SN
authors.lastname: Loevenich
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D030562:Databases, Protein / Q000706:statistics & numerical data; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics; D006801:Humans; D020407:Internet; D013058:Mass Spectrometry; D010446:Peptide Fragments / Q000032:analysis* / Q000737:chemistry; D020543:Proteome / Q000737:chemistry / Q000235:genetics*; D040901:Proteomics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
chemical_list: D029721:Drosophila Proteins; D010446:Peptide Fragments; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins