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Review

Genome annotating proteomics pipelines: available tools

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Pages 621-629 | Published online: 09 Jan 2014

References

  • Shadforth I, Crowther D, Bessant C. Protein and peptide identification algorithms using mass spectrometry for use in high-throughput, automated pipelines. Proteomics5(16) 4082–4095 (2005).
  • Kapp EA, Schutz F, Connolly LM et al. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics5(13), 3475–3490 (2005).
  • Xu C , Ma B. Software for computational peptide identification from MS-MS data. Drug Discov. Today11(13–14), 595–600 (2006).
  • Frewen BE, Merrihew GE, Wu CC, Noble WS, MacCoss MJ. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem.78(16), 5678–5684 (2006).
  • 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.74(20), 5383–5392 (2002).
  • Shadforth I, Dunkley T, Lilley KS, Crowther D, Bessant C. Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds. Rapid Commun. Mass Spectrom.19(22), 3363–3368 (2005).
  • Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem.75(17), 4646–4658 (2003).
  • Moore RE, Young MK, Lee TD. Qscore: an algorithm for evaluating SEQUEST database search results. J. Am. Soc. Mass Spectrom.13(4), 378–386 (2002).
  • MacCoss MJ, Wu CC, Yates JR. Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal. Chem.74(21), 5593–5599 (2002).
  • Anderson DC, Li WQ, Payan DG, Noble WS. A new algorithm for the evaluation of shotgun peptide sequencing in proteomics: support vector machine classification of peptide MS/MS spectra and SEQUEST scores. J. Proteome Res.2(2), 137–146 (2003).
  • Martens L, Hermjakob H, Jones P et al. PRIDE: the proteomics identifications database. Proteomics5(13), 3537–3545 (2005).
  • Bluggel M, Kortnig G, Glandorf J et al. ProteinScape: an integrated bioinformatics platform for proteome analysis. Brucker Daltonics Technical Note003, 1–4 (2002).
  • Altschul SF, Gish W, Miller W, Meyers EW, Lipman DJ. Basic local alignment search tool. J. Mol. Biol.215(3), 403–410 (1990).
  • Choudhary JS, Blackstock WP, Creasey DM, Cottrell JS. Interrogating the human genome using uninterpreted mass spectrometry data. Proteomics1(5), 651–667 (2001).
  • Kuster B, Mortensen P, Andersen JS, Mann M. Mass spectrometry allows direct identification of proteins in large genomes. Proteomics1(5), 641–650 (2001).
  • Jaffe JD, Berg HC, Church GM. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics4(1), 59–77 (2004).
  • Craig R, Beavis RC. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun. Mass Spectrom.17(20), 2310–2316 (2003).
  • Shadforth I, Xu W, Crowther D, Bessant C. GAPP: a fully automated software for the confident identification of human peptides from tandem mass spectra. J. Proteome Res.5(10), 2849–2852 (2006).
  • Omenn GS, States DJ, Adamski M et al. Overview of the HUPO plasma proteome project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics5(13), 3226–3245 (2005).
  • Desiere F, Deutsch E, Nesvizhskii A et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol.6(1), R9 (2005).
  • 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.5(11), 976–989 (1994).
  • Hubbard T, Andrews D, Caccamo M et al. Ensembl 2005. Nucleic Acids Res.33(Suppl. 1), D447–D453 (2005).
  • Creasy DM, Cottrell JS. Error tolerant searching of uninterpreted tandem mass spectrometry data. Proteomics2(10), 1426–1434 (2002).
  • Hermjakob H, Taylor C, Zhu W, Apweiler R. The HUPO proteomics standards initiative: towards a common lab book. BSPR/EBI Meeting, Cambridge, UK (2004).
  • Old WM, Meyer-Arendt K, Aveline-Wolf L et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell Proteomics4(10), 1487–1502 (2005).
  • Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol.17(10), 994–999 (1999).
  • Krijgsveld J, Ketting RF, Mahmoudi T et al. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat. Biotechnol.21(8), 927–931 (2003).
  • Ong SE, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics1(5), 376–386 (2002).
  • Ross PL, Huang YLN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics3(12), 1154–1169 (2004).
  • Craig R, Cortens JP, Beavis RC. The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass Spectrom.19(13), 1844–1850 (2005).
  • Craig R, Cortens JC, Fenyo D, Beavis RC. Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res.5(8), 1843–1849 (2006).
  • Craig R, Cortens JP, Beavis RC. Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res.3(6), 1234–1242 (2004).
  • Keller A, Purvine S, Nesvizhskii AI, Stolyar S, Goodlett DR, Kolker E. Experimental protein mixture for validating tandem mass spectral analysis. OMICS6(2), 207–212 (2002).

Websites

  • Laboratorytalk. Proteomics mass spectrometry market survey. Frost and Sullivan, CA, USA. (2003) www.laboratorytalk.com/news/fro/fro159. html
  • Proxeon www.proxeon.com
  • ProteomeCommons www.proteomecommons.org/dev/dfs/
  • Scaffold www.proteomesoftware.com
  • The Arabidopsis Information Resource (TAIR) www.arabidopsis.org/
  • PeptideAtlas www.peptideatlas.org
  • GAPP information www.gapp.info
  • Mascot Integra: data management for proteomics www.matrixscience.com/integra.html
  • Proteome Center http://tools.proteomecenter.org

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