Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

Nichole L. King, Eric W. Deutsch, Jeffrey A. Ranish, Alexey I. Nesvizhskii, James S. Eddes, Parag Mallick, Jimmy Eng, Frank Desiere, Mark Flory, Daniel B. Martin, Bong Kim, Hookeun Lee, Brian Raught, Ruedi Aebersold

Research output: Contribution to journalArticle

47 Citations (Scopus)

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.

Original languageEnglish (US)
Article numberR106
JournalGenome biology
Volume7
Issue number11
DOIs
StatePublished - Nov 13 2006
Externally publishedYes

Fingerprint

Proteome
proteome
Open Reading Frames
Saccharomyces cerevisiae
open reading frames
genome
Saccharomyces
proteomics
gene
data mining
peptide
Software Validation
Genome
Databases
Molecular Sequence Annotation
Gene Ontology
protein
Data Mining
resource
Proteomics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

King, N. L., Deutsch, E. W., Ranish, J. A., Nesvizhskii, A. I., Eddes, J. S., Mallick, P., ... Aebersold, R. (2006). Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome biology, 7(11), [R106]. https://doi.org/10.1186/gb-2006-7-11-r106

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. / King, Nichole L.; Deutsch, Eric W.; Ranish, Jeffrey A.; Nesvizhskii, Alexey I.; Eddes, James S.; Mallick, Parag; Eng, Jimmy; Desiere, Frank; Flory, Mark; Martin, Daniel B.; Kim, Bong; Lee, Hookeun; Raught, Brian; Aebersold, Ruedi.

In: Genome biology, Vol. 7, No. 11, R106, 13.11.2006.

Research output: Contribution to journalArticle

King, NL, Deutsch, EW, Ranish, JA, Nesvizhskii, AI, Eddes, JS, Mallick, P, Eng, J, Desiere, F, Flory, M, Martin, DB, Kim, B, Lee, H, Raught, B & Aebersold, R 2006, 'Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas', Genome biology, vol. 7, no. 11, R106. https://doi.org/10.1186/gb-2006-7-11-r106
King NL, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P et al. Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome biology. 2006 Nov 13;7(11). R106. https://doi.org/10.1186/gb-2006-7-11-r106
King, Nichole L. ; Deutsch, Eric W. ; Ranish, Jeffrey A. ; Nesvizhskii, Alexey I. ; Eddes, James S. ; Mallick, Parag ; Eng, Jimmy ; Desiere, Frank ; Flory, Mark ; Martin, Daniel B. ; Kim, Bong ; Lee, Hookeun ; Raught, Brian ; Aebersold, Ruedi. / Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. In: Genome biology. 2006 ; Vol. 7, No. 11.
@article{30aa5fd372134c189681bff4bc7a59c6,
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.",
author = "King, {Nichole L.} and Deutsch, {Eric W.} and Ranish, {Jeffrey A.} and Nesvizhskii, {Alexey I.} and Eddes, {James S.} and Parag Mallick and Jimmy Eng and Frank Desiere and Mark Flory and Martin, {Daniel B.} and Bong Kim and Hookeun Lee and Brian Raught and Ruedi Aebersold",
year = "2006",
month = "11",
day = "13",
doi = "10.1186/gb-2006-7-11-r106",
language = "English (US)",
volume = "7",
journal = "Genome Biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "11",

}

TY - JOUR

T1 - Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

AU - King, Nichole L.

AU - Deutsch, Eric W.

AU - Ranish, Jeffrey A.

AU - Nesvizhskii, Alexey I.

AU - Eddes, James S.

AU - Mallick, Parag

AU - Eng, Jimmy

AU - Desiere, Frank

AU - Flory, Mark

AU - Martin, Daniel B.

AU - Kim, Bong

AU - Lee, Hookeun

AU - Raught, Brian

AU - Aebersold, Ruedi

PY - 2006/11/13

Y1 - 2006/11/13

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=33847699732&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33847699732&partnerID=8YFLogxK

U2 - 10.1186/gb-2006-7-11-r106

DO - 10.1186/gb-2006-7-11-r106

M3 - Article

VL - 7

JO - Genome Biology

JF - Genome Biology

SN - 1474-7596

IS - 11

M1 - R106

ER -