Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

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.

[1]  Sean R. Collins,et al.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.

[2]  R. Aebersold,et al.  A uniform proteomics MS/MS analysis platform utilizing open XML file formats , 2005, Molecular systems biology.

[3]  R. Aebersold,et al.  Gene Expression Analyzed by High-resolution State Array Analysis and Quantitative Proteomics , 2004, Molecular & Cellular Proteomics.

[4]  Roger E Bumgarner,et al.  The Transcriptome and Its Translation during Recovery from Cell Cycle Arrest in Saccharomyces cerevisiae* , 2003, Molecular & Cellular Proteomics.

[5]  Alexey I Nesvizhskii,et al.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.

[6]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[7]  Ruedi Aebersold,et al.  Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. , 2007, Methods in molecular biology.

[8]  Gary D Bader,et al.  Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.

[9]  Ruedi Aebersold,et al.  Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane , 2004, The Journal of cell biology.

[10]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[11]  Nichole L. King,et al.  Human Plasma PeptideAtlas , 2005, Proteomics.

[12]  J. Ranish,et al.  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 , 2004, Molecular and Cellular Biology.

[13]  Rong Wang,et al.  The need for a public proteomics repository , 2004, Nature Biotechnology.

[14]  Ruedi Aebersold,et al.  The Application of New Software Tools to Quantitative Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem Mass Spectrometry , 2003, Molecular & Cellular Proteomics.

[15]  Joshua E. Elias,et al.  Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. , 2003, Journal of proteome research.

[16]  R. Aebersold,et al.  The Application of New Software Tools to Quantitative Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem Mass Spectrometry , 2003, Molecular & Cellular Proteomics.

[17]  R. Beavis,et al.  An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC , 2004, Molecular & Cellular Proteomics.

[18]  Xiaoyu Yang,et al.  Characterizing complex peptide mixtures using a multi-dimensional liquid chromatography-mass spectrometry system: Saccharomyces cerevisiae as a model system. , 2004, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[19]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[20]  Mathias Dreger,et al.  Subcellular proteomics , 2021, Nature Reviews Methods Primers.

[21]  O. Jensen.  Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry. , 2004, Current opinion in chemical biology.

[22]  R. Aebersold,et al.  A statistical model for identifying proteins by tandem mass spectrometry. , 2003, Analytical chemistry.

[23]  C. Mant,et al.  Prediction of peptide retention times in reversed-phase high-performance liquid chromatography I. Determination of retention coefficients of amino acid residues of model synthetic peptides , 1986 .

[24]  R. Young,et al.  RNA Polymerase II Holoenzymes and Subcomplexes* , 1998, The Journal of Biological Chemistry.

[25]  C. Chabanet,et al.  Prediction of peptide retention time in reversed-phase high-performance liquid chromatography. , 1992, Journal of chromatography.

[26]  Eric W. Deutsch,et al.  The PeptideAtlas project , 2005, Nucleic Acids Res..

[27]  M. Mann,et al.  Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway*S , 2005, Molecular & Cellular Proteomics.

[28]  Chris F. Taylor,et al.  A common open representation of mass spectrometry data and its application to proteomics research , 2004, Nature Biotechnology.

[29]  J. Yates,et al.  Large-scale analysis of the yeast proteome by multidimensional protein identification technology , 2001, Nature Biotechnology.

[30]  L. Breci,et al.  Comprehensive proteomics in yeast using chromatographic fractionation, gas phase fractionation, protein gel electrophoresis, and isoelectric focusing , 2005, Proteomics.

[31]  Roger E Bumgarner,et al.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. , 2001, Science.

[32]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[33]  C. Pickart,et al.  Mechanisms underlying ubiquitination. , 2001, Annual review of biochemistry.

[34]  S. Gygi,et al.  Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R. Aebersold,et al.  Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics , 2004, Nature Structural &Molecular Biology.

[36]  P. Bork,et al.  Proteome survey reveals modularity of the yeast cell machinery , 2006, Nature.

[37]  N. Sonenberg,et al.  Translational control of gene expression , 2000 .

[38]  Nichole L. King,et al.  Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry , 2004, Genome Biology.

[39]  Ruedi Aebersold,et al.  The study of macromolecular complexes by quantitative proteomics , 2003, Nature Genetics.

[40]  Brian Raught,et al.  Advances in protein complex analysis using mass spectrometry , 2005, The Journal of physiology.

[41]  Blagoy Blagoev,et al.  A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling , 2003, Nature Biotechnology.

[42]  S. Gygi,et al.  Quantitative analysis of complex protein mixtures using isotope-coded affinity tags , 1999, Nature Biotechnology.

[43]  Ruedi Aebersold,et al.  Gene expression in yeast responding to mating pheromone: Analysis by high-resolution translation state analysis and quantitative proteomics , 2004 .