title: Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas.
abstract: We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.
authors.affiliation: Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA. nking@systemsbiology.org
authors.forename: Nichole L
authors.initials: NL
authors.lastname: King
authors.forename: Eric W
authors.initials: EW
authors.lastname: Deutsch
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Ranish
authors.forename: Alexey I
authors.initials: AI
authors.lastname: Nesvizhskii
authors.forename: James S
authors.initials: JS
authors.lastname: Eddes
authors.forename: Parag
authors.initials: P
authors.lastname: Mallick
authors.forename: Jimmy
authors.initials: J
authors.lastname: Eng
authors.forename: Frank
authors.initials: F
authors.lastname: Desiere
authors.forename: Mark
authors.initials: M
authors.lastname: Flory
authors.forename: Daniel B
authors.initials: DB
authors.lastname: Martin
authors.forename: Bong
authors.initials: B
authors.lastname: Kim
authors.forename: Hookeun
authors.initials: H
authors.lastname: Lee
authors.forename: Brian
authors.initials: B
authors.lastname: Raught
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D003062:Codon; D030562:Databases, Protein; D005800:Genes, Fungal; D057927:Hydrophobic and Hydrophilic Interactions; D013058:Mass Spectrometry; D008970:Molecular Weight; D016366:Open Reading Frames / Q000235:genetics; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D020543:Proteome / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D003062:Codon; D010455:Peptides; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins