The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation

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• 作者：Sandra N Loevenich (1) (2) (3)
  Erich Brunner (2)
  Nichole L King (4) (5)
  Eric W Deutsch (4)
  Stephen E Stein (6)
  Ruedi Aebersold (1) (4) (7) (8)
  Ernst Hafen (1)
  
• 刊名：BMC Bioinformatics
• 出版年：2009
• 出版时间：December 2009
• 年：2009
• 卷：10
• 期：1
• 全文大小：1582KB
• 参考文献：1. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, / et al.: Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. / Science 1995, 269:496鈥?12. CrossRef
  2. Lee NH, Saeed AI: Microarrays: an overview. / Methods Mol Biol 2007, 353:265鈥?00.
  3. Anderson L, Hunter CL: Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. / Mol Cell Proteomics 2006, 5:573鈥?88.
  4. Kuster B, Schirle M, Mallick P, Aebersold R: Scoring proteomes with proteotypic peptide probes. / Nat Rev Mol Cell Biol 2005, 6:577鈥?83. CrossRef
  5. Stahl-Zeng J, Lange V, Ossola R, Eckhardt K, Krek W, Aebersold R, Domon B: High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. / Mol Cell Proteomics 2007, 6:1809鈥?817. CrossRef
  6. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, / et al.: The genome sequence of Drosophila melanogaster. / Science 2000, 287:2185鈥?195. CrossRef
  7. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, / et al.: A whole-genome assembly of Drosophila. / Science 2000, 287:2196鈥?204. CrossRef
  8. FlyBaseConsortium: FlyBase 鈥?the Drosophila database. The FlyBase Consortium. / Nucleic Acids Res 1994, 22:3456鈥?458. CrossRef
  9. FlyBaseConsortium: FlyBase: the Drosophila database. The Flybase Consortium. / Nucleic Acids Res 1996, 24:53鈥?6. CrossRef
  10. FlyBaseConsortium: FlyBase: a Drosophila database. Flybase Consortium. / Nucleic Acids Res 1998, 26:85鈥?8. CrossRef
  11. FlyBaseConsortium: The FlyBase database of the Drosophila Genome Projects and community literature. The FlyBase Consortium. / Nucleic Acids Res 1999, 27:85鈥?8. CrossRef
  12. FlyBaseConsortium: The FlyBase database of the Drosophila genome projects and community literature. / Nucleic Acids Res 2002, 30:106鈥?08. CrossRef
  13. FlyBaseConsortium: The FlyBase database of the Drosophila genome projects and community literature. / Nucleic Acids Res 2003, 31:172鈥?75. CrossRef
  14. Gelbart WM, Crosby M, Matthews B, Rindone WP, Chillemi J, Russo Twombly S, Emmert D, Ashburner M, Drysdale RA, Whitfield E, / et al.: FlyBase: a Drosophila database. The FlyBase consortium. / Nucleic Acids Res 1997, 25:63鈥?6. CrossRef
  15. Celniker SE, Wheeler DA, Kronmiller B, Carlson JW, Halpern A, Patel S, Adams M, Champe M, Dugan SP, Frise E, / et al.: Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. / Genome Biol 2002, 3:RESEARCH0079. CrossRef
  16. Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, / et al.: Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. / Genome Biol 2002, 3:RESEARCH0085. CrossRef
  17. Lin MF, Carlson JW, Crosby MA, Matthews BB, Yu C, Park S, Wan KH, Schroeder AJ, Gramates LS, St Pierre SE, / et al.: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. / Genome Res 2007, 17:1823鈥?836. CrossRef
  18. Stapleton M, Carlson J, Brokstein P, Yu C, Champe M, George R, Guarin H, Kronmiller B, Pacleb J, Park S, / et al.: A Drosophila full-length cDNA resource. / Genome Biol 2002, 3:RESEARCH0080. CrossRef
  19. Stapleton M, Liao G, Brokstein P, Hong L, Carninci P, Shiraki T, Hayashizaki Y, Champe M, Pacleb J, Wan K, / et al.: The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. / Genome Res 2002, 12:1294鈥?300. CrossRef
  20. Choudhary JS, Blackstock WP, Creasy DM, Cottrell JS: Matching peptide mass spectra to EST and genomic DNA databases. / Trends Biotechnol 2001, 19:S17鈥?2. CrossRef
  21. Choudhary JS, Blackstock WP, Creasy DM, Cottrell JS: Interrogating the human genome using uninterpreted mass spectrometry data. / Proteomics 2001, 1:651鈥?67. CrossRef
  22. Colinge J, Cusin I, Reffas S, Mahe E, Niknejad A, Rey PA, Mattou H, Moniatte M, Bougueleret L: Experiments in searching small proteins in unannotated large eukaryotic genomes. / J Proteome Res 2005, 4:167鈥?74. CrossRef
  23. Fermin D, Allen BB, Blackwell TW, Menon R, Adamski M, Xu Y, Ulintz P, Omenn GS, States DJ: Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. / Genome Biol 2006, 7:R35. CrossRef
  24. Tanner S, Shen Z, Ng J, Florea L, Guigo R, Briggs SP, Bafna V: Improving gene annotation using peptide mass spectrometry. / Genome Res 2007,17(2):231鈥?39. CrossRef
  25. Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, / et al.: Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. / Genome Biol 2004, 6:R9. CrossRef
  26. Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R: The PeptideAtlas project. / Nucleic Acids Res 2006, 34:D655鈥?58. CrossRef
  27. King NL, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB, / et al.: Analysis of the S. cerevisiae proteome with PeptideAtlas. / Genome Biol 2006, 7:R106. CrossRef
  28. Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, / et al.: A high-quality catalog of the Drosophila melanogaster proteome. / Nat Biotechnol 2007.
  29. Sashimi 鈥?Open Source Proteomics Software[http://sourceforge.net/projects/sashimi]
  30. Lundgren DH, Han DK, Eng JK: Protein identification using TurboSEQUEST. / Curr Protoc Bioinformatics 2005., Chapter 13:
  31. Keller A, Nesvizhskii AI, Kolker E, Aebersold R: Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. / Anal Chem 2002, 74:5383鈥?392. CrossRef
  32. Nesvizhskii AI, Keller A, Kolker E, Aebersold R: A statistical model for identifying proteins by tandem mass spectrometry. / Anal Chem 2003, 75:4646鈥?658. CrossRef
  33. Kyte J, Doolittle RF: A simple method for displaying the hydropathic character of a protein. / J Mol Biol 1982, 157:105鈥?32. CrossRef
  34. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. / Nucleic Acids Research 1997, 25:3389鈥?402. CrossRef
  35. The Systems Biology Experiment Management System Database[http://www.sbeams.org]
  36. The Systems Biology Experiment Management System Database[http://www.sbeams.org]
  37. PeptideAtlas.org[http://www.peptideatlas.org]
  38. Ahrens C, Brunner E, Hafen E, Aebersold R, Basler K: A Proteome Catalog of Drosophila melanogaster: An Essential Resource for Targeted Quantitative Proteomics. / Fly 2007, 1:182鈥?86.
  39. Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP: Discovery and revision of Arabidopsis genes by proteogenomics. / Proc Natl Acad Sci USA 2008, 105:21034鈥?1038. CrossRef
  40. de Godoy LM, Olsen JV, de Souza GA, Li G, Mortensen P, Mann M: Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. / Genome Biol 2006, 7:R50. CrossRef
  41. Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R: Building consensus spectral libraries for peptide identification in proteomics. / Nat Methods 2008, 5:873鈥?75. CrossRef
  42. Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R: Development and validation of a spectral library searching method for peptide identification from MS/MS. / Proteomics 2007, 7:655鈥?67. CrossRef
  43. Craig R, Beavis RC: TANDEM: matching proteins with tandem mass spectra. / Bioinformatics 2004, 20:1466鈥?467. CrossRef
  44. Eng JK, McCormack AL, Yates JR 3rd: An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. / J Am Soc Mass Spectrom 1994, 5:976鈥?89. CrossRef
  45. Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH: Open mass spectrometry search algorithm. / J Proteome Res 2004, 3:958鈥?64. CrossRef
  46. Lynn AJ, Baker PR, Chalkley RJ, Burlingame AL: Comparison of database search engine expectation values. / 55th ASMS Conference of Mass Spectrometry and Allied Topics; Indianapolis, Indiana 2007.
  47. Stein SE, Scott DR: Optimization and testing of mass spectral library search algorithms for compound identification. / Journal of the American Society for Mass Spectrometry 1994, 5:859鈥?66. CrossRef
  48. Domon B, Aebersold R: Mass spectrometry and protein analysis. / Science 2006, 312:212鈥?17. CrossRef
  49. Deutsch EW, Lam H, Aebersold R: PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. / EMBO Rep 2008, 9:429鈥?34. CrossRef
  50. Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, / et al.: Evolution of genes and genomes on the Drosophila phylogeny. / Nature 2007, 450:203鈥?18. CrossRef
  51. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, / et al.: Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. / Nature 2007, 450:219鈥?32. CrossRef
  52. Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R: Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. / Mol Cell Proteomics 2006, 5:652鈥?70.
  
• 作者单位：Sandra N Loevenich (1) (2) (3)
  Erich Brunner (2)
  Nichole L King (4) (5)
  Eric W Deutsch (4)
  Stephen E Stein (6)
  Ruedi Aebersold (1) (4) (7) (8)
  Ernst Hafen (1)
  
  1. Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
  2. Center for Model Organism Proteomes, University of Zurich, 8057, Zurich, Switzerland
  3. Ph.D. Program in Molecular Life Sciences, University of Zurich, 8093, Zurich, Switzerland
  4. Institute for Systems Biology, Seattle, WA, 98103-8904, USA
  5. Incorporated Research Institutions for Seismology, Data Management Center, Seattle, WA, 98105, USA
  6. National Institute of Standards & Technology, Gaithersburg, MD, 20899-8380, USA
  7. Faculty of Science, University of Zurich, 8057, Zurich, Switzerland
  8. Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093, Zurich, Switzerland
  
• ISSN：1471-2105

文摘

Background Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn based on correct gene models increase the correctness, sensitivity, and quantitative accuracy of systems biology genome-scale experiments. Results In this manuscript, we present the Drosophila melanogaster PeptideAtlas, a fly proteomics and genomics resource of unsurpassed depth. Based on peptide mass spectrometry data collected in our laboratory the portal http://www.drosophila-peptideatlas.org allows querying fly protein data observed with respect to gene model confirmation and splice site verification as well as for the identification of proteotypic peptides suited for targeted proteomics studies. Additionally, the database provides consensus mass spectra for observed peptides along with qualitative and quantitative information about the number of observations of a particular peptide and the sample(s) in which it was observed. Conclusion PeptideAtlas is an open access database for the Drosophila community that has several features and applications that support (1) reduction of the complexity inherently associated with performing targeted proteomic studies, (2) designing and accelerating shotgun proteomics experiments, (3) confirming or questioning gene models, and (4) adjusting gene models such that they are in line with observed Drosophila peptides. While the database consists of proteomic data it is not required that the user is a proteomics expert.