Home LiteratureArticle Details
PMID: 17101051 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas.

Genome biology ·Vol. 7 ·No. 11 ·2006-00-00 ·Pages R106

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

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.

MeSH Terms
Codon Databases, Protein Genes, Fungal Hydrophobic and Hydrophilic Interactions Mass Spectrometry Molecular Weight Open Reading Frames/genetics Peptides/chemistry,metabolism Proteome/chemistry,genetics,metabolism Saccharomyces cerevisiae/chemistry,genetics,metabolism Saccharomyces cerevisiae Proteins/chemistry,genetics,metabolism User-Computer Interface
Chemicals
Codon Peptides Proteome Saccharomyces cerevisiae Proteins
Authors & Affiliations
14 authors, click to expand affiliations / ORCID
King Nichole L
Institute for Systems Biology, N 34th Street, Seattle, WA 98103, USA. nking@systemsbiology.org
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
References (40)
40 references, click to expand
  1. Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics.
    Nat Struct Mol Biol. 2004 Jan;11(1):73-80 PMID: 14718926
  2. Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone.
    Mol Cell Proteomics. 2004 May;3(5):478-89 PMID: 14766929
  3. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway.
    Mol Cell Proteomics. 2005 Mar;4(3):310-27 PMID: 15665377
  4. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
    Anal Chem. 2002 Oct 15;74(20):5383-92 PMID: 12403597
  5. The ubiquitin system.
    Annu Rev Biochem. 1998;67:425-79 PMID: 9759494
  6. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
    Nature. 2006 Mar 30;440(7084):637-43 PMID: 16554755
  7. Advances in protein complex analysis using mass spectrometry.
    J Physiol. 2005 Feb 15;563(Pt 1):11-21 PMID: 15611014
  8. Global analysis of protein localization in budding yeast.
    Nature. 2003 Oct 16;425(6959):686-91 PMID: 14562095
  9. Global analysis of protein expression in yeast.
    Nature. 2003 Oct 16;425(6959):737-41 PMID: 14562106
  10. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.
    Genome Biol. 2005;6(1):R9 PMID: 15642101
  11. The need for a public proteomics repository.
    Nat Biotechnol. 2004 Apr;22(4):471-2 PMID: 15085804
  12. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome.
    J Proteome Res. 2003 Jan-Feb;2(1):43-50 PMID: 12643542
  13. RNA polymerase II holoenzymes and subcomplexes.
    J Biol Chem. 1998 Oct 23;273(43):27757-60 PMID: 9774381
  14. Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry.
    Curr Opin Chem Biol. 2004 Feb;8(1):33-41 PMID: 15036154
  15. An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS.
    Mol Cell Proteomics. 2004 Sep;3(9):908-19 PMID: 15238601
  16. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling.
    Nat Biotechnol. 2003 Mar;21(3):315-8 PMID: 12577067
  17. The PeptideAtlas project.
    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D655-8 PMID: 16381952
  18. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
    Nature. 2002 Jan 10;415(6868):180-3 PMID: 11805837
  19. The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts.
    Mol Cell Proteomics. 2003 Jul;2(7):426-7 PMID: 12832456
  20. Proteome survey reveals modularity of the yeast cell machinery.
    Nature. 2006 Mar 30;440(7084):631-6 PMID: 16429126
  21. A common open representation of mass spectrometry data and its application to proteomics research.
    Nat Biotechnol. 2004 Nov;22(11):1459-66 PMID: 15529173
  22. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  23. Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags.
    Anal Chem. 2004 Jul 15;76(14):4104-11 PMID: 15253649
  24. Large-scale analysis of the yeast proteome by multidimensional protein identification technology.
    Nat Biotechnol. 2001 Mar;19(3):242-7 PMID: 11231557
  25. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.
    Nat Biotechnol. 1999 Oct;17(10):994-9 PMID: 10504701
  26. Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane.
    J Cell Biol. 2004 Dec 20;167(6):1099-112 PMID: 15596542
  27. Characterizing complex peptide mixtures using a multi-dimensional liquid chromatography-mass spectrometry system: Saccharomyces cerevisiae as a model system.
    J Chromatogr B Analyt Technol Biomed Life Sci. 2004 Oct 15;810(1):69-76 PMID: 15358309
  28. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.
    Science. 2001 May 4;292(5518):929-34 PMID: 11340206
  29. Mechanisms underlying ubiquitination.
    Annu Rev Biochem. 2001;70:503-33 PMID: 11395416
  30. RNA polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: the major stable Pol II complexes and their activity in transcription initiation and reinitiation.
    Mol Cell Biol. 2004 Feb;24(4):1709-20 PMID: 14749386
  31. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS.
    Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):6940-5 PMID: 12771378
  32. A uniform proteomics MS/MS analysis platform utilizing open XML file formats.
    Mol Syst Biol. 2005;1:2005.0017 PMID: 16729052
  33. A statistical model for identifying proteins by tandem mass spectrometry.
    Anal Chem. 2003 Sep 1;75(17):4646-58 PMID: 14632076
  34. Interpretation of shotgun proteomic data: the protein inference problem.
    Mol Cell Proteomics. 2005 Oct;4(10):1419-40 PMID: 16009968
  35. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database.
    J Am Soc Mass Spectrom. 1994 Nov;5(11):976-89 PMID: 24226387
  36. The transcriptome and its translation during recovery from cell cycle arrest in Saccharomyces cerevisiae.
    Mol Cell Proteomics. 2003 Mar;2(3):191-204 PMID: 12684541
  37. The study of macromolecular complexes by quantitative proteomics.
    Nat Genet. 2003 Mar;33(3):349-55 PMID: 12590263
  38. Subcellular proteomics.
    Mass Spectrom Rev. 2003 Jan-Feb;22(1):27-56 PMID: 12768603
  39. Human Plasma PeptideAtlas.
    Proteomics. 2005 Aug;5(13):3497-500 PMID: 16052627
  40. Comprehensive proteomics in yeast using chromatographic fractionation, gas phase fractionation, protein gel electrophoresis, and isoelectric focusing.
    Proteomics. 2005 May;5(8):2018-28 PMID: 15852344
Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2006-7-11-r106
Email
nking@systemsbiology.org
Published
2006-00-00
Pages
R106
Language
English
Region
England
NLM ID
100960660
PMCID
PMC1794584
Subset
IM
Grants
NHLBI NIH HHS · N01HV28179 · United States
NHLBI NIH HHS · N01-HV-28179 · United States
External Links
PubMed source DOI: 10.1186/gb-2006-7-11-r106 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2