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For: Higgs RE, Knierman MD, Freeman AB, Gelbert LM, Patil ST, Hale JE. Estimating the statistical significance of peptide identifications from shotgun proteomics experiments. J Proteome Res 2007;6:1758-67. [PMID: 17397207 DOI: 10.1021/pr0605320] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Gao Y, Lyu Q, Luo P, Li M, Zhou R, Zhang J, Lyu Q. Applications of Machine Learning to Predict Cisplatin Resistance in Lung Cancer. Int J Gen Med 2021;14:5911-5925. [PMID: 34588799 PMCID: PMC8473573 DOI: 10.2147/ijgm.s329644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/03/2021] [Indexed: 12/25/2022]  Open
2
Keich U, Tamura K, Noble WS. Averaging Strategy To Reduce Variability in Target-Decoy Estimates of False Discovery Rate. J Proteome Res 2019;18:585-593. [PMID: 30560673 DOI: 10.1021/acs.jproteome.8b00802] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
3
Pace MC, Xu G, Fromholt S, Howard J, Crosby K, Giasson BI, Lewis J, Borchelt DR. Changes in proteome solubility indicate widespread proteostatic disruption in mouse models of neurodegenerative disease. Acta Neuropathol 2018;136:919-938. [PMID: 30140941 DOI: 10.1007/s00401-018-1895-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/02/2018] [Indexed: 12/17/2022]
4
Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy. Sci Rep 2018;8:4049. [PMID: 29511296 PMCID: PMC5840295 DOI: 10.1038/s41598-018-21371-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 02/02/2018] [Indexed: 02/08/2023]  Open
5
Liang X, Xia Z, Jian L, Niu X, Link A. An adaptive classification model for peptide identification. BMC Genomics 2015;16 Suppl 11:S1. [PMID: 26578406 PMCID: PMC4652454 DOI: 10.1186/1471-2164-16-s11-s1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
6
Sikdar S, Gill R, Datta S. Improving protein identification from tandem mass spectrometry data by one-step methods and integrating data from other platforms. Brief Bioinform 2015;17:262-9. [PMID: 26141827 DOI: 10.1093/bib/bbv043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Indexed: 01/28/2023]  Open
7
Quantification of cellular NEMO content and its impact on NF-κB activation by genotoxic stress. PLoS One 2015;10:e0116374. [PMID: 25742655 PMCID: PMC4350935 DOI: 10.1371/journal.pone.0116374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/08/2014] [Indexed: 12/28/2022]  Open
8
Keich U, Noble WS. On the importance of well-calibrated scores for identifying shotgun proteomics spectra. J Proteome Res 2014;14:1147-60. [PMID: 25482958 PMCID: PMC4324453 DOI: 10.1021/pr5010983] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
9
Peptide identification based on fuzzy classification and clustering. Proteome Sci 2013;11:S10. [PMID: 24564935 PMCID: PMC3908838 DOI: 10.1186/1477-5956-11-s1-s10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
10
Dumaual CM, Steere BA, Walls CD, Wang M, Zhang ZY, Randall SK. Integrated analysis of global mRNA and protein expression data in HEK293 cells overexpressing PRL-1. PLoS One 2013;8:e72977. [PMID: 24019887 PMCID: PMC3760866 DOI: 10.1371/journal.pone.0072977] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 07/17/2013] [Indexed: 11/19/2022]  Open
11
Kumar S, Zou Y, Bao Q, Wang M, Dai G. Proteomic analysis of immediate-early response plasma proteins after 70% and 90% partial hepatectomy. Hepatol Res 2013;43:876-89. [PMID: 23279269 PMCID: PMC4354878 DOI: 10.1111/hepr.12030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 11/18/2012] [Accepted: 11/20/2012] [Indexed: 02/08/2023]
12
Langley RJ, Tsalik EL, van Velkinburgh JC, Glickman SW, Rice BJ, Wang C, Chen B, Carin L, Suarez A, Mohney RP, Freeman DH, Wang M, You J, Wulff J, Thompson JW, Moseley MA, Reisinger S, Edmonds BT, Grinnell B, Nelson DR, Dinwiddie DL, Miller NA, Saunders CJ, Soden SS, Rogers AJ, Gazourian L, Fredenburgh LE, Massaro AF, Baron RM, Choi AMK, Corey GR, Ginsburg GS, Cairns CB, Otero RM, Fowler VG, Rivers EP, Woods CW, Kingsmore SF. An integrated clinico-metabolomic model improves prediction of death in sepsis. Sci Transl Med 2013;5:195ra95. [PMID: 23884467 DOI: 10.1126/scitranslmed.3005893] [Citation(s) in RCA: 329] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
13
Granholm V, Noble WS, Käll L. A cross-validation scheme for machine learning algorithms in shotgun proteomics. BMC Bioinformatics 2012;13 Suppl 16:S3. [PMID: 23176259 PMCID: PMC3489528 DOI: 10.1186/1471-2105-13-s16-s3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
14
Cox JM, Troutt JS, Knierman MD, Siegel RW, Qian YW, Ackermann BL, Konrad RJ. Determination of cathepsin S abundance and activity in human plasma and implications for clinical investigation. Anal Biochem 2012;430:130-7. [PMID: 22922382 DOI: 10.1016/j.ab.2012.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/16/2012] [Accepted: 08/16/2012] [Indexed: 11/24/2022]
15
Chen VC, Gouw JW, Naus CC, Foster LJ. Connexin multi-site phosphorylation: mass spectrometry-based proteomics fills the gap. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012;1828:23-34. [PMID: 22421184 DOI: 10.1016/j.bbamem.2012.02.028] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 02/19/2012] [Accepted: 02/28/2012] [Indexed: 10/28/2022]
16
Bell LN, Vuppalanchi R, Watkins PB, Bonkovsky HL, Serrano J, Fontana RJ, Wang M, Rochon J, Chalasani N. Serum proteomic profiling in patients with drug-induced liver injury. Aliment Pharmacol Ther 2012;35:600-12. [PMID: 22403816 PMCID: PMC3654532 DOI: 10.1111/j.1365-2036.2011.04982.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
17
The proteome of normal pancreatic juice. Pancreas 2012;41:186-94. [PMID: 22129531 PMCID: PMC3288545 DOI: 10.1097/mpa.0b013e31822862f6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
18
Sheng Q, Dai J, Wu Y, Tang H, Zeng R. BuildSummary: Using a Group-Based Approach To Improve the Sensitivity of Peptide/Protein Identification in Shotgun Proteomics. J Proteome Res 2012;11:1494-502. [DOI: 10.1021/pr200194p] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
19
Wang M, You J. Mass spectrometry for protein quantification in biomarker discovery. Methods Mol Biol 2012;815:199-225. [PMID: 22130994 DOI: 10.1007/978-1-61779-424-7_16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
20
Zieger MAJ, Gupta MP, Wang M. Proteomic analysis of endothelial cold-adaptation. BMC Genomics 2011;12:630. [PMID: 22192797 PMCID: PMC3270058 DOI: 10.1186/1471-2164-12-630] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 12/22/2011] [Indexed: 02/07/2023]  Open
21
Proteomic Characterization of Cerebrospinal Fluid from Ataxia-Telangiectasia (A-T) Patients Using a LC/MS-Based Label-Free Protein Quantification Technology. INTERNATIONAL JOURNAL OF PROTEOMICS 2011;2011:578903. [PMID: 22084690 PMCID: PMC3200215 DOI: 10.1155/2011/578903] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 03/18/2011] [Indexed: 11/18/2022]
22
van den Toorn HWP, Muñoz J, Mohammed S, Raijmakers R, Heck AJR, van Breukelen B. RockerBox: Analysis and Filtering of Massive Proteomics Search Results. J Proteome Res 2011;10:1420-4. [DOI: 10.1021/pr1010185] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
23
Nesvizhskii AI. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J Proteomics 2010;73:2092-123. [PMID: 20816881 DOI: 10.1016/j.jprot.2010.08.009] [Citation(s) in RCA: 358] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 08/25/2010] [Accepted: 08/25/2010] [Indexed: 12/18/2022]
24
McHugh LC, Arthur JW. Harvest: an open-source tool for the validation and improvement of peptide identification metrics and fragmentation exploration. BMC Bioinformatics 2010;11:448. [PMID: 20815925 PMCID: PMC2941693 DOI: 10.1186/1471-2105-11-448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 09/06/2010] [Indexed: 01/21/2023]  Open
25
Renard BY, Timm W, Kirchner M, Steen JAJ, Hamprecht FA, Steen H. Estimating the confidence of peptide identifications without decoy databases. Anal Chem 2010;82:4314-8. [PMID: 20455556 DOI: 10.1021/ac902892j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Bell LN, Lee L, Saxena R, Bemis KG, Wang M, Theodorakis JL, Vuppalanchi R, Alloosh M, Sturek M, Chalasani N. Serum proteomic analysis of diet-induced steatohepatitis and metabolic syndrome in the Ossabaw miniature swine. Am J Physiol Gastrointest Liver Physiol 2010;298:G746-54. [PMID: 20167877 PMCID: PMC3774260 DOI: 10.1152/ajpgi.00485.2009] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
27
Werner SR, Saha JK, Broderick CL, Zhen EY, Higgs RE, Duffin KL, Smith RC. Proteomic analysis of demyelinated and remyelinating brain tissue following dietary cuprizone administration. J Mol Neurosci 2010;42:210-25. [PMID: 20401640 DOI: 10.1007/s12031-010-9354-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
28
Bell LN, Theodorakis JL, Vuppalanchi R, Saxena R, Bemis KG, Wang M, Chalasani N. Serum proteomics and biomarker discovery across the spectrum of nonalcoholic fatty liver disease. Hepatology 2010;51:111-20. [PMID: 19885878 PMCID: PMC2903216 DOI: 10.1002/hep.23271] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
29
Menschaert G, Vandekerckhove TTM, Landuyt B, Hayakawa E, Schoofs L, Luyten W, Van Criekinge W. Spectral clustering in peptidomics studies helps to unravel modification profile of biologically active peptides and enhances peptide identification rate. Proteomics 2009;9:4381-8. [PMID: 19658089 DOI: 10.1002/pmic.200900248] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
30
Salem M, Kenney PB, Rexroad CE, Yao J. Proteomic signature of muscle atrophy in rainbow trout. J Proteomics 2009;73:778-89. [PMID: 19903543 DOI: 10.1016/j.jprot.2009.10.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Revised: 10/13/2009] [Accepted: 10/31/2009] [Indexed: 02/06/2023]
31
Klammer AA, Park CY, Noble WS. Statistical calibration of the SEQUEST XCorr function. J Proteome Res 2009;8:2106-13. [PMID: 19275164 DOI: 10.1021/pr8011107] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
32
Salmi J, Nyman TA, Nevalainen OS, Aittokallio T. Filtering strategies for improving protein identification in high-throughput MS/MS studies. Proteomics 2009;9:848-60. [PMID: 19160393 DOI: 10.1002/pmic.200800517] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
33
Saxena C, Bonacci TM, Huss KL, Bloem LJ, Higgs RE, Hale JE. Capture of Drug Targets from Live Cells Using a Multipurpose Immuno-Chemo-Proteomics Tool. J Proteome Res 2009;8:3951-7. [DOI: 10.1021/pr900277x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
34
Jorrín-Novo JV, Maldonado AM, Echevarría-Zomeño S, Valledor L, Castillejo MA, Curto M, Valero J, Sghaier B, Donoso G, Redondo I. Plant proteomics update (2007–2008): Second-generation proteomic techniques, an appropriate experimental design, and data analysis to fulfill MIAPE standards, increase plant proteome coverage and expand biological knowledge. J Proteomics 2009;72:285-314. [DOI: 10.1016/j.jprot.2009.01.026] [Citation(s) in RCA: 174] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
35
Edwards N, Wu X, Tseng CW. An Unsupervised, Model-Free, Machine-Learning Combiner for Peptide Identifications from Tandem Mass Spectra. Clin Proteomics 2009. [DOI: 10.1007/s12014-009-9024-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
36
Proteomic analysis of HCV cirrhosis and HCV-induced HCC: identifying biomarkers for monitoring HCV-cirrhotic patients awaiting liver transplantation. Transplantation 2009;87:143-52. [PMID: 19136905 DOI: 10.1097/tp.0b013e318191c68d] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
37
Differential effects of ethanol in the nucleus accumbens shell of alcohol-preferring (P), alcohol-non-preferring (NP) and Wistar rats: a proteomics study. Pharmacol Biochem Behav 2009;92:304-13. [PMID: 19166871 DOI: 10.1016/j.pbb.2008.12.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 12/15/2008] [Accepted: 12/20/2008] [Indexed: 11/22/2022]
38
Jiang X, Dong X, Ye M, Zou H. Instance Based Algorithm for Posterior Probability Calculation by Target−Decoy Strategy to Improve Protein Identifications. Anal Chem 2008;80:9326-35. [DOI: 10.1021/ac8017229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
39
Käll L, Storey JD, Noble WS. Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics 2008;24:i42-8. [PMID: 18689838 DOI: 10.1093/bioinformatics/btn294] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
40
Kim S, Gupta N, Pevzner PA. Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J Proteome Res 2008;7:3354-63. [PMID: 18597511 PMCID: PMC2689316 DOI: 10.1021/pr8001244] [Citation(s) in RCA: 332] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
41
Saxena C, Zhen E, Higgs RE, Hale JE. An immuno-chemo-proteomics method for drug target deconvolution. J Proteome Res 2008;7:3490-7. [PMID: 18590316 DOI: 10.1021/pr800222q] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
42
Wang M, You J, Bemis KG, Tegeler TJ, Brown DPG. Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008;7:329-39. [PMID: 18579615 DOI: 10.1093/bfgp/eln031] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
43
Shen Y, Tolić N, Hixson KK, Purvine SO, Pasa-Tolić L, Qian WJ, Adkins JN, Moore RJ, Smith RD. Proteome-wide identification of proteins and their modifications with decreased ambiguities and improved false discovery rates using unique sequence tags. Anal Chem 2008;80:1871-82. [PMID: 18271604 PMCID: PMC2600587 DOI: 10.1021/ac702328x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
44
Higgs RE, Knierman MD, Gelfanova V, Butler JP, Hale JE. Label-free LC-MS method for the identification of biomarkers. Methods Mol Biol 2008;428:209-230. [PMID: 18287776 DOI: 10.1007/978-1-59745-117-8_12] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
45
Choi H, Nesvizhskii AI. Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based Proteomics. J Proteome Res 2008;7:254-65. [DOI: 10.1021/pr070542g] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
46
Ackermann BL, Berna MJ, Eckstein JA, Ott LW, Chaudhary AK. Current applications of liquid chromatography/mass spectrometry in pharmaceutical discovery after a decade of innovation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008;1:357-396. [PMID: 20636083 DOI: 10.1146/annurev.anchem.1.031207.112855] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
47
Käll L, Storey JD, MacCoss MJ, Noble WS. Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases. J Proteome Res 2008;7:29-34. [DOI: 10.1021/pr700600n] [Citation(s) in RCA: 472] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
48
Choi H, Ghosh D, Nesvizhskii AI. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J Proteome Res 2007;7:286-92. [PMID: 18078310 DOI: 10.1021/pr7006818] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Choi H, Nesvizhskii AI. False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J Proteome Res 2007;7:47-50. [PMID: 18067251 DOI: 10.1021/pr700747q] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V. Accurate annotation of peptide modifications through unrestrictive database search. J Proteome Res 2007;7:170-81. [PMID: 18034453 DOI: 10.1021/pr070444v] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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