{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T04:55:55Z","timestamp":1761540955933},"publisher-location":"Totowa, NJ","reference-count":64,"publisher":"Humana Press","isbn-type":[{"type":"print","value":"9781607614432"},{"type":"electronic","value":"9781607614449"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010]]},"DOI":"10.1007\/978-1-60761-444-9_3","type":"book-chapter","created":{"date-parts":[[2009,12,15]],"date-time":"2009-12-15T12:26:23Z","timestamp":1260879983000},"page":"23-42","source":"Crossref","is-referenced-by-count":5,"title":["Computational Approaches to Peptide Identification via Tandem MS"],"prefix":"10.1007","author":[{"given":"Simon J.","family":"Hubbard","sequence":"first","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2009,12,5]]},"reference":[{"key":"3_CR1_3","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1371\/journal.pcbi.0030114","volume":"3","author":"J Colinge","year":"2007","unstructured":"Colinge, J., and Bennett, K. L. (2007) Introduction to computational proteomics. Plos Computational Biology\n                3, 1151-60.","journal-title":"Plos Computational Biology"},{"key":"3_CR2_3","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1002\/mas.20068","volume":"25","author":"P Hernandez","year":"2006","unstructured":"Hernandez, P., Muller, M., and Appel, R. D. (2006) Automated protein identification by tandem mass spectrometry: Issues and strategies. Mass Spectrometry Reviews\n                25, 235-54.","journal-title":"Mass Spectrometry Reviews"},{"key":"3_CR3_3","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1038\/nrm1468","volume":"5","author":"H Steen","year":"2004","unstructured":"Steen, H., and Mann, M. (2004) The ABC\u2019s (and XYZ\u2019s) of peptide sequencing. Nature Reviews Molecular Cell Biology\n                5, 699-711.","journal-title":"Nature Reviews Molecular Cell Biology"},{"key":"3_CR4_3","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1093\/bib\/bbn007","volume":"9","author":"P Veltri","year":"2008","unstructured":"Veltri, P. (2008) Algorithms and tools for analysis and management of mass spectrometry data. Briefings in Bioinformatics\n                9, 144-55.","journal-title":"Briefings in Bioinformatics"},{"key":"3_CR5_3","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1093\/bib\/bbm023","volume":"8","author":"BJM Webb-Robertson","year":"2007","unstructured":"Webb-Robertson, B. J. M., and Cannon, W. R. (2007) Current trends in computational inference from mass spectrometry-based proteomics. Briefings in Bioinformatics\n                8, 304-17.","journal-title":"Briefings in Bioinformatics"},{"key":"3_CR6_3","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/85686","volume":"19","author":"MP Washburn","year":"2001","unstructured":"Washburn, M. P., Wolters, D., and Yates, J. R., 3rd (2001) Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol\n                19, 242-7.","journal-title":"Nat Biotechnol"},{"key":"3_CR7_3","doi-asserted-by":"publisher","first-page":"4598","DOI":"10.1021\/pr800420s","volume":"7","author":"JK Eng","year":"2008","unstructured":"Eng, J. K., Fischer, B., Grossmann, J., and MacCoss, M. J. (2008) A fast SEQUEST cross correlation algorithm. Journal of Proteome Research\n                7, 4598-602.","journal-title":"Journal of Proteome Research"},{"key":"3_CR8_3","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1016\/1044-0305(94)80016-2","volume":"5","author":"JK Eng","year":"1994","unstructured":"Eng, J. K., McCormack, A. L., and Yates, J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry\n                5, 976-89.","journal-title":"Journal of the American Society for Mass Spectrometry"},{"key":"3_CR9_3","doi-asserted-by":"publisher","first-page":"3551","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2","volume":"20","author":"DN Perkins","year":"1999","unstructured":"Perkins, D. N., Pappin, D. J. C., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis\n                20, 3551-67.","journal-title":"Electrophoresis"},{"key":"3_CR10_3","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1021\/pr0499491","volume":"3","author":"LY Geer","year":"2004","unstructured":"Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X. Y., Shi, W. Y., and Bryant, S. H. (2004) Open mass spectrometry search algorithm. Journal of Proteome Research\n                3, 958-64.","journal-title":"Journal of Proteome Research"},{"key":"3_CR11_3","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1093\/bioinformatics\/bth092","volume":"20","author":"R Craig","year":"2004","unstructured":"Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics\n                20, 1466-67.","journal-title":"Bioinformatics"},{"key":"3_CR12_3","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1021\/pr0604054","volume":"6","author":"DL Tabb","year":"2007","unstructured":"Tabb, D. L., Fernando, C. G., and Chambers, M. C. (2007) MyriMatch: Highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. Journal of Proteome Research\n                6, 654-61.","journal-title":"Journal of Proteome Research"},{"key":"3_CR13_3","doi-asserted-by":"publisher","first-page":"1454","DOI":"10.1002\/pmic.200300485","volume":"3","author":"J Colinge","year":"2003","unstructured":"Colinge, J., Masselot, A., Giron, M., Dessingy, T., and Magnin, J. (2003) OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics\n                3, 1454-63.","journal-title":"Proteomics"},{"key":"3_CR14_3","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1021\/pr800127y","volume":"7","author":"CY Park","year":"2008","unstructured":"Park, C. Y., Klammer, A. A., Kall, L., MacCoss, M. J., and Noble, W. S. (2008) Rapid and accurate peptide identification from tandem mass spectra. Journal of Proteome Research\n                7, 3022-27.","journal-title":"Journal of Proteome Research"},{"key":"3_CR15_3","doi-asserted-by":"publisher","first-page":"1638","DOI":"10.1074\/mcp.T600050-MCP200","volume":"6","author":"IV Shilov","year":"2007","unstructured":"Shilov, I. V., Seymour, S. L., Patel, A. A., Loboda, A., Tang, W. H., Keating, S. P., Hunter, C. L., Nuwaysir, L. M., and Schaeffer, D. A. (2007) The paragon algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Molecular & Cellular Proteomics\n                6, 1638-55.","journal-title":"Molecular & Cellular Proteomics"},{"key":"3_CR16_3","doi-asserted-by":"publisher","first-page":"4626","DOI":"10.1021\/ac050102d","volume":"77","author":"S Tanner","year":"2005","unstructured":"Tanner, S., Shu, H. J., Frank, A., Wang, L. C., Zandi, E., Mumby, M., Pevzner, P. A., and Bafna, V. (2005) InsPecT: Identification of posttransiationally modified peptides from tandem mass spectra. Analytical Chemistry\n                77, 4626-39.","journal-title":"Analytical Chemistry"},{"key":"3_CR17_3","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1002\/1615-9861(200210)2:10<1406::AID-PROT1406>3.0.CO;2-9","volume":"2","author":"N Zhang","year":"2002","unstructured":"Zhang, N., Aebersold, R., and Schwilkowski, B. (2002) ProbID: A probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics\n                2, 1406-12.","journal-title":"Proteomics"},{"key":"3_CR18_3","doi-asserted-by":"publisher","first-page":"2338","DOI":"10.1021\/pr050264q","volume":"4","author":"R Matthiesen","year":"2005","unstructured":"Matthiesen, R., Trelle, M. B., Hojrup, P., Bunkenborg, J., and Jensen, O. N. (2005) VEMS 3.0: Algorithms and computational tools for tandem mass spectrometry based identification of post-translational modifications in proteins. Journal of Proteome Research\n                4, 2338-47.","journal-title":"Journal of Proteome Research"},{"key":"3_CR19_3","doi-asserted-by":"publisher","first-page":"1977","DOI":"10.1002\/pmic.200300708","volume":"4","author":"J Colinge","year":"2004","unstructured":"Colinge, J., Masselot, A., Cusin, I., Mahe, E., Niknejad, A., Argoud-Puy, G., Reffas, S., Bederr, N., Gleizes, A., Rey, P. A., and Bougueleret, L. (2004) High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics. Proteomics\n                4, 1977-84.","journal-title":"Proteomics"},{"key":"3_CR20_3","doi-asserted-by":"publisher","first-page":"3628","DOI":"10.1093\/bioinformatics\/bth460","volume":"20","author":"J Samuelsson","year":"2004","unstructured":"Samuelsson, J., Dalevi, D., Levander, F., and Rognvaldsson, T. (2004) Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting. Bioinformatics\n                20, 3628-35.","journal-title":"Bioinformatics"},{"key":"3_CR21_3","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1021\/pr070361e","volume":"7","author":"AM Frank","year":"2008","unstructured":"Frank, A. M., Bandeira, N., Shen, Z., Tanner, S., Briggs, S. P., Smith, R. D., and Pevzner, P. A. (2008) Clustering millions of tandem mass spectra. J Proteome Res\n                7, 113-22.","journal-title":"J Proteome Res"},{"key":"3_CR22_3","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1093\/bioinformatics\/bti829","volume":"22","author":"J Salmi","year":"2006","unstructured":"Salmi, J., Moulder, R., Filen, J. J., Nevalainen, O. S., Nyman, T. A., Lahesmaa, R., and Aittokallio, T. (2006) Quality classification of tandem mass spectrometry data. Bioinformatics\n                22, 400-6.","journal-title":"Bioinformatics"},{"key":"3_CR23_3","doi-asserted-by":"publisher","first-page":"2470","DOI":"10.1021\/ac026424o","volume":"75","author":"DL Tabb","year":"2003","unstructured":"Tabb, D. L., MacCoss, M. J., Wu, C. C., Anderson, S. D., and Yates, J. R., 3rd (2003) Similarity among tandem mass spectra from proteomic experiments: detection, significance, and utility. Anal Chem\n                75, 2470-7.","journal-title":"Anal Chem"},{"key":"3_CR24_3","doi-asserted-by":"publisher","first-page":"1250","DOI":"10.1016\/j.jasms.2005.04.010","volume":"16","author":"DL Tabb","year":"2005","unstructured":"Tabb, D. L., Thompson, M. R., Khalsa-Moyers, G., VerBerkmoes, N. C., and McDonald, W. H. (2005) MS2Grouper: group assessment and synthetic replacement of duplicate proteomic tandem mass spectra. J Am Soc Mass Spectrom\n                16, 1250-61.","journal-title":"J Am Soc Mass Spectrom"},{"key":"3_CR25_3","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1186\/1471-2105-8-51","volume":"8","author":"JW Wong","year":"2007","unstructured":"Wong, J. W., Sullivan, M. J., Cartwright, H. M., and Cagney, G. (2007) msmsEval: tandem mass spectral quality assignment for high-throughput proteomics. BMC Bioinformatics\n                8, 51.","journal-title":"BMC Bioinformatics"},{"key":"3_CR26_3","doi-asserted-by":"publisher","first-page":"950","DOI":"10.1002\/pmic.200300652","volume":"4","author":"I Beer","year":"2004","unstructured":"Beer, I., Barnea, E., Ziv, T., and Admon, A. (2004) Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics\n                4, 950-60.","journal-title":"Proteomics"},{"key":"3_CR27_3","doi-asserted-by":"publisher","first-page":"5800","DOI":"10.1021\/ac0480949","volume":"77","author":"YY Huang","year":"2005","unstructured":"Huang, Y. Y., Triscari, J. M., Tseng, G. C., Pasa-Tolic, L., Lipton, M. S., Smith, R. D., and Wysocki, V. H. (2005) Statistical characterization of the charge state and residue dependence of low-energy CID peptide dissociation patterns. Analytical Chemistry\n                77, 5800-13.","journal-title":"Analytical Chemistry"},{"key":"3_CR28_3","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1038\/nature07341","volume":"455","author":"LMF Godoy de","year":"2008","unstructured":"de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Frohlich, F., Walther, T. C., and Mann, M. (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature\n                455, 1251-U60.","journal-title":"Nature"},{"key":"3_CR29_3","doi-asserted-by":"publisher","first-page":"1790","DOI":"10.1038\/nprot.2006.317","volume":"1","author":"L McDonald","year":"2006","unstructured":"McDonald, L., and Beynon, R. J. (2006) Positional proteomics: preparation of amino-terminal peptides as a strategy for proteome simplification and characterization. Nature Protocols\n                1, 1790-98.","journal-title":"Nature Protocols"},{"key":"3_CR30_3","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1038\/nmeth811","volume":"2","author":"L McDonald","year":"2005","unstructured":"McDonald, L., Robertson, D. H. L., Hurst, J. L., and Beynon, R. J. (2005) Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nature Methods\n                2, 955-57.","journal-title":"Nature Methods"},{"key":"3_CR31_3","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1021\/pr0705035","volume":"7","author":"J Rodriguez","year":"2008","unstructured":"Rodriguez, J., Gupta, N., Smith, R. D., and Pevzner, P. A. (2008) Does trypsin cut before proline? Journal of Proteome Research\n                7, 300-05.","journal-title":"Journal of Proteome Research"},{"key":"3_CR32_3","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1074\/mcp.T400003-MCP200","volume":"3","author":"JV Olsen","year":"2004","unstructured":"Olsen, J. V., Ong, S. E., and Mann, M. (2004) Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Molecular & Cellular Proteomics\n                3, 608-14.","journal-title":"Molecular & Cellular Proteomics"},{"key":"3_CR33_3","first-page":"1350","volume":"5","author":"JA Siepen","year":"2006","unstructured":"Siepen, J. A., Keevil, E. J., Knight, D., and Hubbard, S. J. (2006) Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics. Molecular & Cellular Proteomics\n                5, 1350.","journal-title":"Molecular & Cellular Proteomics"},{"key":"3_CR34_3","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/ng1159","volume":"34","author":"B Modrek","year":"2003","unstructured":"Modrek, B., and Lee, C. J. (2003) Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and\/or loss. Nature Genetics\n                34, 177-80.","journal-title":"Nature Genetics"},{"key":"3_CR35_3","doi-asserted-by":"publisher","first-page":"1985","DOI":"10.1002\/pmic.200300721","volume":"4","author":"PJ Kersey","year":"2004","unstructured":"Kersey, P. J., Duarte, J., Williams, A., Karavidopoulou, Y., Birney, E., and Apweiler, R. (2004) The International Protein Index: An integrated database for proteomics experiments. Proteomics\n                4, 1985-88.","journal-title":"Proteomics"},{"key":"3_CR36_3","doi-asserted-by":"publisher","first-page":"1963","DOI":"10.1021\/ac026359i","volume":"75","author":"LA Breci","year":"2003","unstructured":"Breci, L. A., Tabb, D. L., Yates, J. R., 3rd, and Wysocki, V. H. (2003) Cleavage N-terminal to proline: analysis of a database of peptide tandem mass spectra. Anal Chem\n                75, 1963-71.","journal-title":"Anal Chem"},{"key":"3_CR37_3","doi-asserted-by":"publisher","first-page":"1243","DOI":"10.1021\/ac0351163","volume":"76","author":"DL Tabb","year":"2004","unstructured":"Tabb, D. L., Huang, Y., Wysocki, V. H., and Yates, J. R., 3rd (2004) Influence of basic residue content on fragment ion peak intensities in low-energy collision-induced dissociation spectra of peptides. Anal Chem\n                76, 1243-8.","journal-title":"Anal Chem"},{"key":"3_CR38_3","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1021\/ac026122m","volume":"75","author":"DL Tabb","year":"2003","unstructured":"Tabb, D. L., Smith, L. L., Breci, L. A., Wysocki, V. H., Lin, D., and Yates, J. R., 3rd (2003) Statistical characterization of ion trap tandem mass spectra from doubly charged tryptic peptides. Anal Chem\n                75, 1155-63.","journal-title":"Anal Chem"},{"key":"3_CR39_3","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1038\/nbt930","volume":"22","author":"JE Elias","year":"2004","unstructured":"Elias, J. E., Gibbons, F. D., King, O. D., Roth, F. P., and Gygi, S. P. (2004) Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat Biotechnol\n                22, 214-9.","journal-title":"Nat Biotechnol"},{"key":"3_CR40_3","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1186\/1471-2105-9-515","volume":"9","author":"A Gehrke","year":"2008","unstructured":"Gehrke, A., Sun, S., Kurgan, L., Ahn, N., Resing, K., Kafadar, K., and Cios, K. (2008) Improved machine learning method for analysis of gas phase chemistry of peptides. BMC Bioinformatics\n                9, 515.","journal-title":"BMC Bioinformatics"},{"key":"3_CR41_3","doi-asserted-by":"publisher","first-page":"325","DOI":"10.1186\/1471-2105-9-325","volume":"9","author":"C Zhou","year":"2008","unstructured":"Zhou, C., Bowler, L. D., and Feng, J. (2008) A machine learning approach to explore the spectra intensity pattern of peptides using tandem mass spectrometry data. BMC Bioinformatics\n                9, 325.","journal-title":"BMC Bioinformatics"},{"key":"3_CR42_3","doi-asserted-by":"publisher","first-page":"5593","DOI":"10.1021\/ac025826t","volume":"74","author":"MJ MacCoss","year":"2002","unstructured":"MacCoss, M. J., Wu, C. C., and Yates, J. R., 3rd (2002) Probability-based validation of protein identifications using a modified SEQUEST algorithm. Anal Chem\n                74, 5593-9.","journal-title":"Anal Chem"},{"key":"3_CR43_3","doi-asserted-by":"publisher","first-page":"5383","DOI":"10.1021\/ac025747h","volume":"74","author":"A Keller","year":"2002","unstructured":"Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS\/MS and database search. Anal Chem\n                74, 5383-92.","journal-title":"Anal Chem"},{"key":"3_CR44_3","doi-asserted-by":"publisher","first-page":"4646","DOI":"10.1021\/ac0341261","volume":"75","author":"AI Nesvizhskii","year":"2003","unstructured":"Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem\n                75, 4646-58.","journal-title":"Anal Chem"},{"key":"3_CR45_3","doi-asserted-by":"publisher","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","volume":"25","author":"SF Altschul","year":"1997","unstructured":"Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res\n                25, 3389-402.","journal-title":"Nucleic Acids Res"},{"key":"3_CR46_3","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1074\/mcp.M600469-MCP200","volume":"6","author":"BM Balgley","year":"2007","unstructured":"Balgley, B. M., Laudeman, T., Yang, L., Song, T., and Lee, C. S. (2007) Comparative evaluation of tandem MS search algorithms using a target-decoy search strategy. Mol Cell Proteomics\n                6, 1599-608.","journal-title":"Mol Cell Proteomics"},{"key":"3_CR47_3","doi-asserted-by":"crossref","unstructured":"Jones, A. R., Siepen, J.A., Hubbard, S.J., Paton, N.W. (2009) Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines. Proteomics\n                9, 1220-9.","DOI":"10.1002\/pmic.200800473"},{"key":"3_CR48_3","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1021\/pr070540w","volume":"7","author":"BC Searle","year":"2008","unstructured":"Searle, B. C., Turner, M., and Nesvizhskii, A. I. (2008) Improving sensitivity by probabilistically combining results from multiple MS\/MS search methodologies. J Proteome Res\n                7, 245-53.","journal-title":"J Proteome Res"},{"key":"3_CR49_3","first-page":"87","volume":"367","author":"AI Nesvizhskii","year":"2007","unstructured":"Nesvizhskii, A. I. (2007) Protein identification by tandem mass spectrometry and sequence database searching. Methods Mol Biol\n                367, 87-119.","journal-title":"Methods Mol Biol"},{"key":"3_CR50_3","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1021\/pr700747q","volume":"7","author":"H Choi","year":"2008","unstructured":"Choi, H., and Nesvizhskii, A. I. (2008) False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J Proteome Res\n                7, 47-50.","journal-title":"J Proteome Res"},{"key":"3_CR51_3","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1021\/pr700600n","volume":"7","author":"L Kall","year":"2008","unstructured":"Kall, L., Storey, J. D., MacCoss, M. J., and Noble, W. S. (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J Proteome Res\n                7, 29-34.","journal-title":"J Proteome Res"},{"key":"3_CR52_3","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1021\/pr700739d","volume":"7","author":"L Kall","year":"2008","unstructured":"Kall, L., Storey, J. D., MacCoss, M. J., and Noble, W. S. (2008) Posterior error probabilities and false discovery rates: two sides of the same coin. J Proteome Res\n                7, 40-4.","journal-title":"J Proteome Res"},{"key":"3_CR53_3","doi-asserted-by":"publisher","first-page":"3354","DOI":"10.1021\/pr8001244","volume":"7","author":"S Kim","year":"2008","unstructured":"Kim, S., Gupta, N., and Pevzner, P. A. (2008) Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res\n                7, 3354-63.","journal-title":"J Proteome Res"},{"key":"3_CR54_3","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1038\/nmeth1088","volume":"4","author":"AI Nesvizhskii","year":"2007","unstructured":"Nesvizhskii, A. I., Vitek, O., and Aebersold, R. (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nature Methods\n                4, 787-97.","journal-title":"Nature Methods"},{"key":"3_CR55_3","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1021\/pr025556v","volume":"2","author":"J Peng","year":"2003","unstructured":"Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., and Gygi, S. P. (2003) Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC\/LC-MS\/MS) for large-scale protein analysis: the yeast proteome. J Proteome Res\n                2, 43-50.","journal-title":"J Proteome Res"},{"key":"3_CR56_3","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1021\/pr700728t","volume":"7","author":"DL Tabb","year":"2008","unstructured":"Tabb, D. L. (2008) What\u2019s driving false discovery rates? J Proteome Res\n                7, 45-6.","journal-title":"J Proteome Res"},{"key":"3_CR57_3","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1021\/ac801664q","volume":"81","author":"G Wang","year":"2009","unstructured":"Wang, G., Wu, W. W., Zhang, Z., Masilamani, S., and Shen, R. F. (2009) Decoy methods for assessing false positives and false discovery rates in shotgun proteomics. Anal Chem\n                81, 146-59.","journal-title":"Anal Chem"},{"key":"3_CR58_3","doi-asserted-by":"publisher","first-page":"1419","DOI":"10.1074\/mcp.R500012-MCP200","volume":"4","author":"AI Nesvizhskii","year":"2005","unstructured":"Nesvizhskii, A. I., and Aebersold, R. (2005) Interpretation of shotgun proteomic data: the protein inference problem. Mol Cell Proteomics\n                4, 1419-40.","journal-title":"Mol Cell Proteomics"},{"key":"3_CR59_3","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1002\/rcm.1741","volume":"19","author":"CL Chepanoske","year":"2005","unstructured":"Chepanoske, C. L., Richardson, B. E., von Rechenberg, M., and Peltier, J. M. (2005) Average peptide score: a useful parameter for identification of proteins derived from database searches of liquid chromatography\/tandem mass spectrometry data. Rapid Commun Mass Spectrom\n                19, 9-14.","journal-title":"Rapid Commun Mass Spectrom"},{"key":"3_CR60_3","doi-asserted-by":"publisher","first-page":"3363","DOI":"10.1002\/rcm.2203","volume":"19","author":"I Shadforth","year":"2005","unstructured":"Shadforth, I., Dunkley, T., Lilley, K., Crowther, D., and Bessant, C. (2005) Confident protein identification using the average peptide score method coupled with search-specific, ab initio thresholds. Rapid Commun Mass Spectrom\n                19, 3363-8.","journal-title":"Rapid Commun Mass Spectrom"},{"key":"3_CR61_3","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1186\/1471-2164-10-61","volume":"10","author":"JC Wright","year":"2009","unstructured":"Wright, J. C., Sugden, D., Francis-McIntyre, S., Riba-Garcia, I., Gaskell, S. J., Grigoriev, I. V., Baker, S. E., Beynon, R. J., and Hubbard, S. J. (2009) Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger. BMC Genomics\n                10, 61.","journal-title":"BMC Genomics"},{"issue":"Suppl 2","key":"3_CR62_3","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1002\/pmic.200600549","volume":"6","author":"CF Taylor","year":"2006","unstructured":"Taylor, C. F. (2006) Minimum reporting requirements for proteomics: a MIAPE primer. Proteomics\n                6 Suppl 2, 39-44.","journal-title":"Proteomics"},{"key":"3_CR63_3","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1038\/nbt1329","volume":"25","author":"CF Taylor","year":"2007","unstructured":"Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P. A., Julian, R. K., Jr., Jones, A. R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E. W., Dunn, M. J., Heck, A. J., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T. A., Patterson, S. D., Ping, P., Seymour, S. L., Souda, P., Tsugita, A., Vandekerckhove, J., Vondriska, T. M., Whitelegge, J. P., Wilkins, M. R., Xenarios, I., Yates, J. R., 3rd, and Hermjakob, H. (2007) The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol\n                25, 887-93.","journal-title":"Nat Biotechnol"},{"key":"3_CR64_3","doi-asserted-by":"publisher","first-page":"2769","DOI":"10.1002\/pmic.200700152","volume":"7","author":"JA Mead","year":"2007","unstructured":"Mead, J. A., Shadforth, I. P., and Bessant, C. (2007) Public proteomic MS repositories and pipelines: available tools and biological applications. Proteomics\n                7, 2769-86.","journal-title":"Proteomics"}],"container-title":["Methods in Molecular Biology","Proteome Bioinformatics"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-60761-444-9_3.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,1]],"date-time":"2021-05-01T18:09:10Z","timestamp":1619892550000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-1-60761-444-9_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,12,5]]},"ISBN":["9781607614432","9781607614449"],"references-count":64,"URL":"https:\/\/doi.org\/10.1007\/978-1-60761-444-9_3","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"type":"print","value":"1064-3745"},{"type":"electronic","value":"1940-6029"}],"subject":[],"published":{"date-parts":[[2009,12,5]]}}}