The PeptideAtlas project.
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.
Desiere
Frank
F
Institute for Systems Biology, Seattle, WA, USA. fdesiere@yahoo.com
Deutsch
Eric W
EW
King
Nichole L
NL
Nesvizhskii
Alexey I
AI
Mallick
Parag
P
Eng
Jimmy
J
Chen
Sharon
S
Eddes
James
J
Loevenich
Sandra N
SN
Aebersold
Ruedi
R
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
D029721:Drosophila Proteins; D010446:Peptide Fragments; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins