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 - Tập 6 Số 9 - Trang 1638-1655 - 2007
Ignat V. Shilov, Sean L. Seymour, Alpesh A. Patel, Alex Loboda, Wilfred H. Tang, Sean P. Keating, Christie L. Hunter, Lydia M. Nuwaysir, Daniel Schaeffer

Tóm tắt

Từ khóa


Tài liệu tham khảo

Aebersold, 2003, Mass spectrometry-based proteomics, Nature, 422, 198, 10.1038/nature01511

Sadygov, 2004, Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book, Nat. Methods, 1, 195, 10.1038/nmeth725

Kapp, 2005, An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis, Proteomics, 5, 3475, 10.1002/pmic.200500126

Nesvizhskii, 2005, Interpretation of shotgun proteomic data, Mol. Cell. Proteomics, 4, 1419, 10.1074/mcp.R500012-MCP200

Fricker, 2006, Peptidomics: identification and quantification of endogenous peptides in neuroendocrine tissues, Mass Spectrom. Rev., 25, 327, 10.1002/mas.20079

Hardt, 2005, Toward defining the human parotid gland salivary proteome and peptidome: identification and characterization using 2D SDS-PAGE, ultrafiltration, HPLC, and mass spectrometry, Biochemistry, 44, 2885, 10.1021/bi048176r

Hardt, 2005, Assessing the effects of diurnal variation on the composition of human parotid saliva: quantitative analysis of native peptides using iTRAQ reagents, Anal. Chem., 77, 4947, 10.1021/ac050161r

Geho, 2006, The amplified peptidome: the new treasure chest of candidate biomarkers, Curr. Opin. Chem. Biol., 10, 50, 10.1016/j.cbpa.2006.01.008

Villanueva, 2006, Differential exoprotease activities confer tumor-specific serum peptidome patterns, J. Clin. Investig., 116, 271, 10.1172/JCI26022

Purcell, 2004, Immunoproteomics: mass spectrometry-based methods to study the targets of the immune response, Mol. Cell. Proteomics, 3, 193, 10.1074/mcp.R300013-MCP200

Mann, 1994, Error-tolerant identification of peptides in sequence databases by peptide sequence tags, Anal. Chem., 66, 4390, 10.1021/ac00096a002

Pappin, 1994, Chemistry, mass spectrometry and peptide-mass databases: evolution of methods for the rapid identification and mapping of cellular proteins

Tabb, 2003, GutenTag: high-throughput sequence tagging via an empirically derived fragmentation model, Anal. Chem., 75, 6415, 10.1021/ac0347462

Tanner, 2005, InsPecT: identification of posttranslationally modified peptides from tandem mass spectra, Anal. Chem., 77, 4626, 10.1021/ac050102d

Taylor, 1997, Sequence database searches via de novo peptide sequencing by tandem mass spectrometry, Rapid Commun. Mass Spectrom., 11, 1067, 10.1002/(SICI)1097-0231(19970615)11:9<1067::AID-RCM953>3.0.CO;2-L

Tsur, 2005, Identification of post-translational modifications by blind search of mass spectra, Nat. Biotechnol., 23, 1562, 10.1038/nbt1168

Clauser, 1999, Role of accurate mass measurement (±10 ppm) in protein identification strategies employing MS or MS/MS and database searching, Anal. Chem., 71, 2871, 10.1021/ac9810516

Eng, 1994, 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, 10.1016/1044-0305(94)80016-2

Perkins, 1999, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis, 20, 3551, 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2

Bafna, 2001, SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database, Bioinformatics, 17, S13, 10.1093/bioinformatics/17.suppl_1.S13

Craig, 2004, TANDEM: matching proteins with tandem mass spectra, Bioinformatics, 20, 1466, 10.1093/bioinformatics/bth092

Field, 2002, RADARS, a bioinformatics solution that automates proteome mass spectral analysis, optimises protein identification, and archives data in a relational database, Proteomics, 2, 36, 10.1002/1615-9861(200201)2:1<36::AID-PROT36>3.0.CO;2-W

Colinge, 2003, OLAV: towards high-throughput tandem mass spectrometry data identification, Proteomics, 3, 1454, 10.1002/pmic.200300485

Tang, 2005, Discovering known and unanticipated protein modifications using MS/MS database searching, Anal. Chem., 77, 3931, 10.1021/ac0481046

Chalkley, 2005, Mol. Cell. Proteomics, 4, 1194, 10.1074/mcp.D500002-MCP200

Pappin, 1996, Chemistry, mass spectrometry and peptide-mass databases: evolution of methods for the rapid identification and mapping of cellular proteins, 135

Shevchenko, 2001, Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight Mass spectrometry and BLAST homology searching, Anal. Chem., 73, 1917, 10.1021/ac0013709

Liska, 2005, Error-tolerant EST database searches by tandem mass spectrometry and multiTag software, Proteomics, 5, 4118, 10.1002/pmic.200401262

Sunyaev, 2003, MultiTag: multiple error-tolerant sequence tag search for the sequence-similarity identification of proteins by mass spectrometry, Anal. Chem., 75, 1307, 10.1021/ac026199a

Ma, 2003, PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry, Rapid Commun. Mass Spectrom., 17, 2337, 10.1002/rcm.1196

von Haller, 2003, Mol. Cell. Proteomics, 2, 426, 10.1074/mcp.D300002-MCP200

Chalkley, 2005, Mol. Cell. Proteomics, 4, 1189, 10.1074/mcp.D500001-MCP200

Bradshaw, 2006, Reporting protein identification data: the next generation of guidelines, Mol. Cell. Proteomics, 5, 787, 10.1074/mcp.E600005-MCP200

Carr, 2004, The need for guidelines in publication of peptide and protein identification data, Mol. Cell. Proteomics, 3, 531, 10.1074/mcp.T400006-MCP200

Kerlavage, 2002, The Celera Discovery System, Nucleic Acids Res., 30, 129, 10.1093/nar/30.1.129

Thomas, 2003, PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification, Nucleic Acids Res., 31, 334, 10.1093/nar/gkg115

Creasy, 2002, Error tolerant searching of uninterpreted tandem mass spectrometry data, Proteomics, 2, 1426, 10.1002/1615-9861(200210)2:10<1426::AID-PROT1426>3.0.CO;2-5

Craig, 2003, A method for reducing the time required to match protein sequences with tandem mass spectra, Rapid Commun. Mass Spectrom., 17, 2310, 10.1002/rcm.1198