Domon, B. & Aebersold, R. Mass spectrometry and protein analysis. Science312, 212–217 (2006). ArticleCASPubMed Google Scholar
Carr, S. et al. The need for guidelines in publication of peptide and protein identification data. Mol. Cell. Proteomics3, 531–533 (2004). ArticleCASPubMed Google Scholar
Geer, L.Y. et al. Open mass spectrometry search algorithm. J. Proteome Res.3, 958–964 (2004). ArticleCASPubMed Google Scholar
Sadygov, R.G. & Yates, J.R. A hypergeometric probability model for protein identification and validation using tandem mass spectral data and protein sequence databases. Anal. Chem.75, 3792–3798 (2003). ArticleCASPubMed Google Scholar
Fenyo, D. & Beavis, R.C. A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem.75, 768–774 (2003). ArticlePubMedCAS Google Scholar
King, N.L. et al. Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biol. [online]7, R106 (2006). ArticleCAS Google Scholar
Brunner, E. et al. A high-quality catalog of the Drosophila melanogaster proteome. Nat. Biotechnol.25, 576–583 (2007). ArticleCASPubMed Google Scholar
Yates, J.R., Morgan, S.F., Gatlin, C.L., Griffin, P.R. & Eng, J.K. Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis. Anal. Chem.70, 3557–3565 (1998). ArticleCASPubMed Google Scholar
Craig, R., Cortens, J.C., Fenyo, D. & Beavis, R.C. Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res.5, 1843–1849 (2006). ArticleCASPubMed Google Scholar
Frewen, B.E., Merrihew, G.E., Wu, C.C., Noble, W.S. & MacCoss, M.J. Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem.78, 5678–5684 (2006). ArticleCASPubMed Google Scholar
Lam, H. et al. Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics7, 655–667 (2007). ArticleCASPubMed Google Scholar
Stein, S.E. & Scott, D.R. Optimization and testing of mass-spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom.5, 859–866 (1994). ArticleCASPubMed Google Scholar
Nesvizhskii, A.I. et al. 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. Proteomics5, 652–670 (2006). ArticleCASPubMed Google Scholar
Mann, M. & Wilm, M. Error tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem.66, 4390–4399 (1994). ArticleCASPubMed Google Scholar
Tabb, D.L., Saraf, A. & Yates, J.R. GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model. Anal. Chem.75, 6415–6421 (2003). ArticleCASPubMedPubMed Central Google Scholar
Tanner, S. et al. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal. Chem.77, 4626–4639 (2005). ArticleCASPubMed Google Scholar
Bern, M., Cai, Y.H. & Goldberg, D. Lookup peaks: a hybrid of de novo sequencing and database search for protein identification by tandem mass spectrometry. Anal. Chem.79, 1393–1400 (2007). ArticleCASPubMed Google Scholar
Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate—a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol.57, 289–300 (1995). Google Scholar
Elias, J.E. & Gygi, S.P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods4, 207–214 (2007). ArticleCASPubMed Google Scholar
Keller, A., Nesvizhskii, A.I., Kolker, E. & Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem.74, 5383–5392 (2002). ArticleCASPubMed Google Scholar
Kapp, E.A. et al. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: Sensitivity and specificity analysis. Proteomics5, 3475–3490 (2005). ArticleCASPubMed Google Scholar
Elias, J.E., Haas, W., Faherty, B.K. & Gygi, S.P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods2, 667–675 (2005). ArticleCASPubMed Google Scholar
Lopez-Ferrer, D. et al. Statistical model for large-scale peptide identification in databases from tandem mass spectra using SEQUEST. Anal. Chem.76, 6853–6860 (2004). ArticleCASPubMed Google Scholar
Anderson, D.C., Li, W.Q., Payan, D.G. & Noble, W.S. 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, 137–146 (2003). ArticleCASPubMed Google Scholar
Kislinger, T. et al. PRISM, a generic large scale proteomic investigation strategy for mammals. Mol. Cell. Proteomics2, 96–106 (2003). ArticleCASPubMed Google Scholar
Ulintz, P.J., Zhu, J., Qin, Z.H.S. & Andrews, P.C. Improved classification of mass spectrometry database search results using newer machine learning approaches. Mol. Cell. Proteomics5, 497–509 (2006). ArticleCASPubMed Google Scholar
Gentzel, M., Kocher, T., Ponnusamy, S. & Wilm, M. Preprocessing of tandem mass spectrometric data to support automatic protein identification. Proteomics3, 1597–1610 (2003). ArticleCASPubMed Google Scholar
Mujezinovic, N. et al. Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise. Proteomics6, 5117–5131 (2006). ArticleCASPubMed Google Scholar
Beer, I., Barnea, E., Ziv, T. & Admon, A. Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics4, 950–960 (2004). ArticleCASPubMed Google Scholar
Tabb, D.L., Thompson, M.R., Khalsa-Moyers, G., VerBerkmoes, N.C. & McDonald, W.H. MS2Grouper: Group assessment and synthetic replacement of duplicate proteomic tandem mass spectra. J. Am. Soc. Mass Spectrom.16, 1250–1261 (2005). ArticleCASPubMed Google Scholar
Zhang, N. et al. ProblDtree: an automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics5, 4096–4106 (2005). ArticleCASPubMed Google Scholar
Moore, R.E., Young, M.K. & Lee, T.D. Method for screening peptide fragment ion mass spectra prior to database searching. J. Am. Soc. Mass Spectrom.11, 422–426 (2000). ArticleCASPubMed Google Scholar
Wong, J.W.H., Sullivan, M.J., Cartwright, H.M. & Cagney, G. msmsEval: tandem mass spectral quality assignment for high-throughput proteomics. BMC Bioinformatics [online]8, 51 (2007). ArticleCAS Google Scholar
Flikka, K., Martens, L., Vandekerckhoe, J., Gevaert, K. & Eidhammer, I. Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering. Proteomics6, 2086–2094 (2006). ArticleCASPubMed Google Scholar
Xu, M. et al. Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry. J. Proteome Res.4, 300–305 (2005). ArticleCASPubMed Google Scholar
Colinge, J., Magnin, J., Dessingy, T., Giron, M. & Masselot, A. Improved peptide charge state assignment. Proteomics3, 1434–1440 (2003). ArticleCASPubMed Google Scholar
Tabb, D.L. et al. Determination of peptide and protein ion charge states by Fourier transformation of isotope-resolved mass spectra. J. Am. Soc. Mass Spectrom.17, 903–915 (2006). ArticleCASPubMed Google Scholar
Resing, K.A. et al. Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal. Chem.76, 3556–3568 (2004). ArticleCASPubMed Google Scholar
Price, T.S. et al. EBP, a program for protein identification using multiple tandem mass spectrometry data sets. Mol. Cell. Proteomics6, 527–536 (2007). ArticleCASPubMed Google Scholar
Higgs, R.E. et al. Estimating the statistical significance of peptide identifications from shotgun proteomics experiments. J. Proteome Res.6, 1758–1767 (2007). ArticleCASPubMed Google Scholar
Keller, A., Eng, J., Zhang, N., Li, X.-J. & Aebersold, R. A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. [online]1, E1–E8 (2005). ArticleCAS Google Scholar
Olsen, J.V. & Mann, M. Improved peptide identification in proteomics by two consecutive stages of mass spectrometric fragmentation. Proc. Natl. Acad. Sci. USA101, 13417–13422 (2004). ArticleCASPubMedPubMed Central Google Scholar
Strittmatter, E.F. et al. Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J. Proteome Res.3, 760–769 (2004). ArticleCASPubMed Google Scholar
Qian, W.J. et al. Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome. J. Proteome Res.4, 53–62 (2005). ArticleCASPubMed Google Scholar
Malmstrom, J. et al. Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. J. Proteome Res.5, 2241–2249 (2006). ArticlePubMedCAS Google Scholar
Xie, H. & Griffin, T.J. Trade-off between high sensitivity and increased potential for false positive peptide sequence matches using a two-dimensional linear ion trap for tandem mass spectrometry-based proteomics. J. Proteome Res.5, 1003–1009 (2006). ArticleCASPubMed Google Scholar
Cargile, B.J., Bundy, J.L., Freeman, T.W. & Stephenson, J.L. Gel based isoelectric focusing of peptides and the utility of isoelectric point in protein identification. J. Proteome Res.3, 112–119 (2004). ArticleCASPubMed Google Scholar
Zhang, H. et al. High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol. Cell. Proteomics4, 144–155 (2005). ArticleCASPubMed Google Scholar
Heller, M. et al. Added value for tandem mass spectrometry shotgun proteomics data validation through isoelectric focusing of peptides. J. Proteome Res.4, 2273–2282 (2005). ArticleCASPubMed Google Scholar
Olsen, J.V. et al. Parts per million mass accuracy on an orbitrap mass spectrometer via lock mass injection into a C-trap. Mol. Cell. Proteomics4, 2010–2021 (2005). ArticleCASPubMed Google Scholar
Rudnick, P.A., Wang, Y.J., Evans, E., Lee, C.S. & Balgley, B.M. Large scale analysis of MASCOT results using a mass accuracy-based THreshold (MATH) effectively improves data interpretation. J. Proteome Res.4, 1353–1360 (2005). ArticleCASPubMed Google Scholar
Nesvizhskii, A.I. & Aebersold, R. Analysis, statistical validation and dissemination of large-scale proteomics data sets generated by tandem MS. Drug Discov. Today9, 173–181 (2004). ArticleCASPubMed Google Scholar
Nesvizhskii, A.I. & Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics4, 1419–1440 (2005). ArticleCASPubMed Google Scholar
Nesvizhskii, A.I., Keller, A., Kolker, E. & Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem.75, 4646–4658 (2003). ArticleCASPubMed Google Scholar
Omenn, G.S. 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 data set of 3020 proteins and a publicly-available database. Proteomics5, 3226–3245 (2005). ArticleCASPubMed Google Scholar
Rappsilber, J. & Mann, M. What does it mean to identify a protein in proteomics? Trends Biochem. Sci.27, 74–78 (2002). ArticleCASPubMed Google Scholar
Yang, X. et al. DBParser: web-based software for shotgun proteomic data analyses. J. Proteome Res.3, 1002–1008 (2004). ArticleCASPubMed Google Scholar
Weatherly, D.B. et al. A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results. Mol. Cell. Proteomics4, 762–772 (2005). ArticleCASPubMed Google Scholar
Bandeira, N., Tsur, D., Frank, A. & Pevzner, P.A. Protein identification by spectral networks analysis. Proc. Natl. Acad. Sci. USA104, 6140–6145 (2007). ArticleCASPubMedPubMed Central Google Scholar
States, D.J. et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat. Biotechnol.24, 333–338 (2006). ArticleCASPubMed Google Scholar
Sadygov, R.G., Liu, H.B. & Yates, J.R. Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal. Chem.76, 1664–1671 (2004). ArticleCASPubMed Google Scholar
Mallick, P. et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol.25, 125–131 (2007). ArticleCASPubMed Google Scholar
Goshe, M.B. & Smith, R.D. Stable isotope-coded proteomic mass spectrometry. Curr. Opin. Biotechnol.14, 101–109 (2003). ArticleCASPubMed Google Scholar
Old, W.M. et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics4, 1487–1502 (2005). ArticleCASPubMed Google Scholar
Ishihama, Y. et al. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics4, 1265–1272 (2005). ArticleCASPubMed Google Scholar
Zybailov, B., Coleman, M.K., Florens, L. & Washburn, M.P. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal. Chem.77, 6218–6224 (2005). ArticleCASPubMed Google Scholar
Liu, H., Sadygov, R.G. & Yates, J.R. III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem.76, 4193–4201 (2004). ArticleCASPubMed Google Scholar
Silva, J.C., Gorenstein, M.V., Li, G.Z., Vissers, J.P.C. & Geromanos, S.J. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell. Proteomics5, 144–156 (2006). ArticleCASPubMed Google Scholar
Lu, P., Vogel, C., Wang, R., Yao, X. & Marcotte, E.M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol.25, 117–124 (2007). ArticleCASPubMed Google Scholar
Blondeau, F. et al. Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling. Proc. Natl. Acad. Sci. USA101, 3833–3838 (2004). ArticleCASPubMedPubMed Central Google Scholar
Radulovic, D. et al. Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics3, 984–997 (2004). ArticleCASPubMed Google Scholar
Jaffe, J.D. et al. PEPPeR, a platform for experimental proteomic pattern recognition. Mol. Cell. Proteomics5, 1927–1941 (2006). ArticleCASPubMed Google Scholar
Li, X.-J., Yi, E.C., Kemp, C.J., Zhang, H. & Aebersold, R. A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol. Cell. Proteomics4, 1328–1340 (2005). ArticleCASPubMed Google Scholar
Listgarten, J. & Emili, A. Statistical and computational methods for comparative proteomic profiling using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics4, 419–434 (2005). ArticleCASPubMed Google Scholar
Qian, W.-J., Jacobs, J.M., Liu, T., Camp, D.G. II & Smith, R.D. Advances and challenges in liquid chromatography-mass spectrometry-based proteomics profiling for clinical applications. Mol. Cell. Proteomics5, 1727–1744 (2006). ArticleCASPubMed Google Scholar
Anderson, L. & Hunter, C.L. Quantitative mass spectrometric MRM assays for major plasma proteins. Mol. Cell. Proteomics5, 573–588 (2006). ArticleCASPubMed Google Scholar
Gentleman, R.C. et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. [online]5, R80 (2004). Article Google Scholar
Meng, F., Forbes, A.J., Miller, L.M. & Kelleher, N.L. Detection and localization of protein modifications by high resolution tandem mass spectrometry. Mass Spectrom. Rev.24, 126–134 (2005). ArticleCASPubMed Google Scholar
Han, X., Jin, M., Breuker, K. & McLafferty, F.W. Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons. Science314, 109–112 (2006). ArticleCASPubMed Google Scholar
Kuster, B., Schirle, M., Mallick, P. & Aebersold, R. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol.6, 577–583 (2005). ArticleCASPubMed Google Scholar
Eng, J.K., McCormack, A.L. & Yates, J.R. An approach to correlate tandem mass-spectral data of peptides with amino-acid-sequences in a protein database. J. Am. Soc. Mass Spectrom.5, 976–989 (1994). ArticleCASPubMed Google Scholar
Perkins, D.N., Pappin, D.J.C., Creasy, D.M. & Cottrell, J.S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis20, 3551–3567 (1999). ArticleCASPubMed Google Scholar
Clauser, K.R., Baker, P. & Burlingame, A.L. Role of accurate mass measurement (+/− 10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem.71, 2871–2882 (1999). ArticleCASPubMed Google Scholar
Zhang, N., Aebersold, R. & Schwilkowski, B. ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics2, 1406–1412 (2002). ArticleCASPubMed Google Scholar
Craig, R. & Beavis, R.C. TANDEM: matching proteins with tandem mass spectra. Bioinformatics20, 1466–1467 (2004). ArticleCASPubMed Google Scholar
Colinge, J., Masselot, A., Giron, M., Dessingy, T. & Magnin, J. OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics3, 1454–1463 (2003). ArticleCASPubMed Google Scholar
Matthiesen, R., Trelle, M.B., Hojrup, P., Bunkenborg, J. & Jensen, O.N. VEMS 3.0: algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. J. Proteome Res.4, 2338–2347 (2005). ArticleCASPubMed Google Scholar
Tabb, D.L., Fernando, C.G. & Chambers, M.C. MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res.6, 654–661 (2007). ArticleCASPubMedPubMed Central Google Scholar
Craig, R., Cortens, J.P. & Beavis, R.C. The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass Spectrom.19, 1844–1850 (2005). ArticleCASPubMed Google Scholar
Johnson, R.S. & Taylor, J.A. Searching sequence databases via de novo peptide sequencing by tandem mass spectrometry. Mol. Biotechnol.22, 301–315 (2002). ArticleCASPubMed Google Scholar
Frank, A. & Pevzner, P. PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal. Chem.77, 964–973 (2005). ArticleCASPubMed Google Scholar
Ma, B. et al. PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun. Mass Spectrom.17, 2337–2342 (2003). ArticleCASPubMed Google Scholar
Hernandez, P., Gras, R., Frey, J. & Appel, R.D. Popitam: towards new heuristic strategies to improve protein identification from tandem mass spectrometry data. Proteomics3, 870–878 (2003). ArticleCASPubMed Google Scholar
Desiere, F. et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. [online]6, R9 (2005). Article Google Scholar
Rauch, A. et al. Computational proteomics analysis system (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments. J. Proteome Res.5, 112–121 (2006). ArticleCASPubMed Google Scholar
Martens, L. et al. PRIDE: the proteomics identifications database. Proteomics5, 3537–3545 (2005). ArticleCASPubMed Google Scholar
Li, X.J., Zhang, H., Ranish, J.A. & Aebersold, R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Anal. Chem.75, 6648–6657 (2003). ArticleCASPubMed Google Scholar
MacCoss, M.J., Wu, C.C., Liu, H.B., Sadygov, R. & Yates, J.R. A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem.75, 6912–6921 (2003). ArticleCASPubMed Google Scholar
Dudoit, S., Yang, Y.H., Callow, M.J. & Speed, T.P. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat. Sinica12, 111–139 (2002). Google Scholar
Tusher, V.G., Tibshirani, R. & Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA98, 5116–5121 (2001). ArticleCASPubMedPubMed Central Google Scholar
Efron, B., Tibshirani, R., Storey, J.D. & Tusher, V. Empirical Bayes analysis of a microarray experiment. J. Am. Stat. Assoc.96, 1151–1160 (2001). Article Google Scholar
Fermin, D. et al. Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics. Genome Biol. [online]7, R35 (2006). ArticleCAS Google Scholar
Edwards, N.J. Novel peptide identification from tandem mass spectra using ESTs and sequence database compression. Mol. Syst. Biol. [online]3, 102 (2007). Google Scholar
Pedrioli, P.G.A. et al. A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol.22, 1459–1466 (2004). ArticleCASPubMed Google Scholar
Martens, L. et al. Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. Proteomics5, 3501–3505 (2005). ArticleCASPubMed Google Scholar