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For: Fusaro VA, Mani DR, Mesirov JP, Carr SA. Prediction of high-responding peptides for targeted protein assays by mass spectrometry. Nat Biotechnol. 2009;27:190-198. [PMID: 19169245 DOI: 10.1038/nbt.1524] [Citation(s) in RCA: 228] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 01/03/2009] [Indexed: 12/21/2022]
Number Cited by Other Article(s)
101
Horvatovich P, Végvári Á, Saul J, Park JG, Qiu J, Syring M, Pirrotte P, Petritis K, Tegeler TJ, Aziz M, Fuentes M, Diez P, Gonzalez-Gonzalez M, Ibarrola N, Droste C, De Las Rivas J, Gil C, Clemente F, Hernaez ML, Corrales FJ, Nilsson CL, Berven FS, Bischoff R, Fehniger TE, LaBaer J, Marko-Varga G. In Vitro Transcription/Translation System: A Versatile Tool in the Search for Missing Proteins. J Proteome Res 2015;14:3441-51. [PMID: 26155874 DOI: 10.1021/acs.jproteome.5b00486] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
102
Searle BC, Egertson JD, Bollinger JG, Stergachis AB, MacCoss MJ. Using Data Independent Acquisition (DIA) to Model High-responding Peptides for Targeted Proteomics Experiments. Mol Cell Proteomics 2015;14:2331-40. [PMID: 26100116 DOI: 10.1074/mcp.m115.051300] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 11/06/2022]  Open
103
Mustafa GM, Larry D, Petersen JR, Elferink CJ. Targeted proteomics for biomarker discovery and validation of hepatocellular carcinoma in hepatitis C infected patients. World J Hepatol 2015;7:1312-1324. [PMID: 26052377 PMCID: PMC4450195 DOI: 10.4254/wjh.v7.i10.1312] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/24/2014] [Accepted: 03/09/2015] [Indexed: 02/06/2023]  Open
104
Slade WO, Werth EG, McConnell EW, Alvarez S, Hicks LM. Quantifying reversible oxidation of protein thiols in photosynthetic organisms. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015;26:631-640. [PMID: 25698223 DOI: 10.1007/s13361-014-1073-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 12/18/2014] [Accepted: 12/18/2014] [Indexed: 06/04/2023]
105
Kamita M, Mori T, Sakai Y, Ito S, Gomi M, Miyamoto Y, Harada A, Niida S, Yamada T, Watanabe K, Ono M. Proteomic analysis of ligamentum flavum from patients with lumbar spinal stenosis. Proteomics 2015;15:1622-30. [DOI: 10.1002/pmic.201400442] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/16/2014] [Accepted: 01/08/2015] [Indexed: 02/06/2023]
106
Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Mol Cell Proteomics 2015;14:2357-74. [PMID: 25693799 DOI: 10.1074/mcp.m114.047050] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 11/06/2022]  Open
107
Building high-quality assay libraries for targeted analysis of SWATH MS data. Nat Protoc 2015;10:426-41. [PMID: 25675208 DOI: 10.1038/nprot.2015.015] [Citation(s) in RCA: 220] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
108
Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015;15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
109
Targeted mass spectrometry for the analysis of nutritive modulation of catalase and heme oxygenase-1 expression. J Proteomics 2015;117:58-69. [PMID: 25639505 DOI: 10.1016/j.jprot.2015.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 12/09/2014] [Accepted: 01/13/2015] [Indexed: 12/19/2022]
110
Trötschel C, Poetsch A. Current approaches and challenges in targeted absolute quantification of membrane proteins. Proteomics 2015;15:915-29. [DOI: 10.1002/pmic.201400427] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/05/2014] [Accepted: 12/05/2014] [Indexed: 01/08/2023]
111
Rybina AV, Skvortsov VS, Kopylov AT, Zgoda VG. [A plain method of prediction of visibility of peptides in mass spectrometry with electrospray ionization]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015;60:707-12. [PMID: 25552513 DOI: 10.18097/pbmc20146006707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
112
De Marchi T, Kuhn E, Carr SA, Umar A. Antibody-based capture of target peptides in multiple reaction monitoring experiments. Methods Mol Biol 2015;1293:123-135. [PMID: 26040685 DOI: 10.1007/978-1-4939-2519-3_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
113
Jung S, Danziger SA, Panchaud A, von Haller P, Aitchison JD, Goodlett DR. Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2015;8:231-239. [PMID: 26962293 DOI: 10.4172/jpb.1000374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
114
Muntel J, Boswell SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M. Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA). Mol Cell Proteomics 2014;14:430-40. [PMID: 25473088 DOI: 10.1074/mcp.m114.044321] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
115
Beck TN, Chikwem AJ, Solanki NR, Golemis EA. Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. Physiol Genomics 2014;46:699-724. [PMID: 25096367 PMCID: PMC4187119 DOI: 10.1152/physiolgenomics.00062.2014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/04/2014] [Indexed: 12/22/2022]  Open
116
Demeure K, Duriez E, Domon B, Niclou SP. PeptideManager: a peptide selection tool for targeted proteomic studies involving mixed samples from different species. Front Genet 2014;5:305. [PMID: 25228907 PMCID: PMC4151198 DOI: 10.3389/fgene.2014.00305] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/16/2014] [Indexed: 02/02/2023]  Open
117
Gianazza E, Tremoli E, Banfi C. The selected reaction monitoring/multiple reaction monitoring-based mass spectrometry approach for the accurate quantitation of proteins: clinical applications in the cardiovascular diseases. Expert Rev Proteomics 2014;11:771-88. [PMID: 25400095 DOI: 10.1586/14789450.2014.947966] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
118
Quantitative proteomics at different depths in human articular cartilage reveals unique patterns of protein distribution. Matrix Biol 2014;40:34-45. [PMID: 25193283 DOI: 10.1016/j.matbio.2014.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/20/2014] [Accepted: 08/22/2014] [Indexed: 11/23/2022]
119
Qeli E, Omasits U, Goetze S, Stekhoven DJ, Frey JE, Basler K, Wollscheid B, Brunner E, Ahrens CH. Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data. J Proteomics 2014;108:269-83. [DOI: 10.1016/j.jprot.2014.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 05/14/2014] [Accepted: 05/17/2014] [Indexed: 02/07/2023]
120
Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. Curr Biol 2014;24:1467-1475. [PMID: 24954049 DOI: 10.1016/j.cub.2014.05.044] [Citation(s) in RCA: 184] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 05/01/2014] [Accepted: 05/19/2014] [Indexed: 11/20/2022]
121
Kusebauch U, Deutsch EW, Campbell DS, Sun Z, Farrah T, Moritz RL. Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics. ACTA ACUST UNITED AC 2014;46:13.25.1-13.25.28. [PMID: 24939129 DOI: 10.1002/0471250953.bi1325s46] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
122
Dong Q, Yan X, Kilpatrick LE, Liang Y, Mirokhin YA, Roth JS, Rudnick PA, Stein SE. Tandem mass spectral libraries of peptides in digests of individual proteins: Human Serum Albumin (HSA). Mol Cell Proteomics 2014;13:2435-49. [PMID: 24889059 DOI: 10.1074/mcp.o113.037135] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
123
Mohammed Y, Domański D, Jackson AM, Smith DS, Deelder AM, Palmblad M, Borchers CH. PeptidePicker: A scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments. J Proteomics 2014;106:151-61. [DOI: 10.1016/j.jprot.2014.04.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 01/08/2023]
124
Liu K, Zhang J, Fu B, Xie H, Wang Y, Qian X. Evaluation of empirical rule of linearly correlated peptide selection (ERLPS) for proteotypic peptide-based quantitative proteomics. Proteomics 2014;14:1593-603. [PMID: 24827140 DOI: 10.1002/pmic.201300032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 02/07/2014] [Accepted: 05/09/2014] [Indexed: 11/11/2022]
125
Qiu X, Zhang H, Lai Y. Quantitative targeted proteomics for membrane transporter proteins: method and application. AAPS JOURNAL 2014;16:714-26. [PMID: 24830943 DOI: 10.1208/s12248-014-9607-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/05/2014] [Indexed: 01/04/2023]
126
Wei J, Ding C, Zhang J, Mi W, Zhao Y, Liu M, Fu T, Zhang Y, Ying W, Cai Y, Qin J, Qian X. High-throughput absolute quantification of proteins using an improved two-dimensional reversed-phase separation and quantification concatemer (QconCAT) approach. Anal Bioanal Chem 2014;406:4183-93. [PMID: 24760396 DOI: 10.1007/s00216-014-7784-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/14/2014] [Accepted: 03/21/2014] [Indexed: 11/24/2022]
127
Chen Y, Ray WK, Helm RF, Melville SB, Popham DL. Levels of germination proteins in Bacillus subtilis dormant, superdormant, and germinating spores. PLoS One 2014;9:e95781. [PMID: 24752279 PMCID: PMC3994143 DOI: 10.1371/journal.pone.0095781] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/31/2014] [Indexed: 12/24/2022]  Open
128
Liang SY, Wu SW, Pu TH, Chang FY, Khoo KH. An adaptive workflow coupled with Random Forest algorithm to identify intact N-glycopeptides detected from mass spectrometry. Bioinformatics 2014;30:1908-16. [DOI: 10.1093/bioinformatics/btu139] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
129
Hawkridge AM. Practical Considerations and Current Limitations in Quantitative Mass Spectrometry-based Proteomics. QUANTITATIVE PROTEOMICS 2014. [DOI: 10.1039/9781782626985-00001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
130
Kelchtermans P, Bittremieux W, De Grave K, Degroeve S, Ramon J, Laukens K, Valkenborg D, Barsnes H, Martens L. Machine learning applications in proteomics research: how the past can boost the future. Proteomics 2014;14:353-66. [PMID: 24323524 DOI: 10.1002/pmic.201300289] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 09/24/2013] [Accepted: 10/14/2013] [Indexed: 01/22/2023]
131
Beretov J, Wasinger VC, Graham PH, Millar EK, Kearsley JH, Li Y. Proteomics for breast cancer urine biomarkers. Adv Clin Chem 2014;63:123-67. [PMID: 24783353 DOI: 10.1016/b978-0-12-800094-6.00004-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
132
Ebhardt HA. Selected reaction monitoring mass spectrometry: a methodology overview. Methods Mol Biol 2014;1072:209-22. [PMID: 24136525 DOI: 10.1007/978-1-62703-631-3_16] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
133
Higdon R, Stewart E, Stanberry L, Haynes W, Choiniere J, Montague E, Anderson N, Yandl G, Janko I, Broomall W, Fishilevich S, Lancet D, Kolker N, Kolker E. MOPED enables discoveries through consistently processed proteomics data. J Proteome Res 2013;13:107-13. [PMID: 24350770 DOI: 10.1021/pr400884c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
134
Schliekelman P, Liu S. Quantifying the effect of competition for detection between coeluting peptides on detection probabilities in mass-spectrometry-based proteomics. J Proteome Res 2013;13:348-61. [PMID: 24313442 DOI: 10.1021/pr400034z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
135
Fujimoto GM, Monroe ME, Rodriguez L, Wu C, MacLean B, Smith RD, MacCoss MJ, Payne SH. Accounting for population variation in targeted proteomics. J Proteome Res 2013;13:321-3. [PMID: 24320210 DOI: 10.1021/pr4011052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
136
Shi T, Gao Y, Quek SI, Fillmore TL, Nicora CD, Su D, Zhao R, Kagan J, Srivastava S, Rodland KD, Liu T, Smith RD, Chan DW, Camp DG, Liu AY, Qian WJ. A highly sensitive targeted mass spectrometric assay for quantification of AGR2 protein in human urine and serum. J Proteome Res 2013;13:875-82. [PMID: 24251762 DOI: 10.1021/pr400912c] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
137
Lin D, Alborn WE, Slebos RJC, Liebler DC. Comparison of protein immunoprecipitation-multiple reaction monitoring with ELISA for assay of biomarker candidates in plasma. J Proteome Res 2013;12:5996-6003. [PMID: 24224610 PMCID: PMC3864264 DOI: 10.1021/pr400877e] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
138
Sheynkman GM, Shortreed MR, Frey BL, Scalf M, Smith LM. Large-scale mass spectrometric detection of variant peptides resulting from nonsynonymous nucleotide differences. J Proteome Res 2013;13:228-40. [PMID: 24175627 DOI: 10.1021/pr4009207] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
139
Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring. Clin Proteomics 2013;10:16. [PMID: 24207061 PMCID: PMC3827840 DOI: 10.1186/1559-0275-10-16] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Accepted: 10/22/2013] [Indexed: 01/22/2023]  Open
140
Zhao Y, Brasier AR. Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways. Methods 2013;61:313-22. [PMID: 23410677 PMCID: PMC3763905 DOI: 10.1016/j.ymeth.2013.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Revised: 01/30/2013] [Accepted: 02/01/2013] [Indexed: 01/12/2023]  Open
141
Shi T, Sun X, Gao Y, Fillmore TL, Schepmoes AA, Zhao R, He J, Moore RJ, Kagan J, Rodland KD, Liu T, Liu AY, Smith RD, Tang K, Camp DG, Qian WJ. Targeted quantification of low ng/mL level proteins in human serum without immunoaffinity depletion. J Proteome Res 2013;12:3353-61. [PMID: 23763644 DOI: 10.1021/pr400178v] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
142
Percy AJ, Chambers AG, Yang J, Borchers CH. Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma. Proteomics 2013;13:2202-15. [DOI: 10.1002/pmic.201200316] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/06/2013] [Accepted: 03/26/2013] [Indexed: 12/28/2022]
143
van den Broek I, Niessen WM, van Dongen WD. Bioanalytical LC–MS/MS of protein-based biopharmaceuticals. J Chromatogr B Analyt Technol Biomed Life Sci 2013;929:161-79. [DOI: 10.1016/j.jchromb.2013.04.030] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 04/15/2013] [Accepted: 04/20/2013] [Indexed: 12/18/2022]
144
Zhao Y, Tian B, Edeh CB, Brasier AR. Quantitation of the dynamic profiles of the innate immune response using multiplex selected reaction monitoring-mass spectrometry. Mol Cell Proteomics 2013;12:1513-29. [PMID: 23418394 PMCID: PMC3675810 DOI: 10.1074/mcp.m112.023465] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 01/23/2013] [Indexed: 11/06/2022]  Open
145
Colangelo CM, Chung L, Bruce C, Cheung KH. Review of software tools for design and analysis of large scale MRM proteomic datasets. Methods 2013;61:287-98. [PMID: 23702368 DOI: 10.1016/j.ymeth.2013.05.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 05/06/2013] [Accepted: 05/11/2013] [Indexed: 12/13/2022]  Open
146
Warwood S, Byron A, Humphries MJ, Knight D. The effect of peptide adsorption on signal linearity and a simple approach to improve reliability of quantification. J Proteomics 2013;85:160-4. [PMID: 23665148 PMCID: PMC3694305 DOI: 10.1016/j.jprot.2013.04.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/10/2013] [Accepted: 04/29/2013] [Indexed: 11/19/2022]
147
Sandin M, Teleman J, Malmström J, Levander F. Data processing methods and quality control strategies for label-free LC-MS protein quantification. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013;1844:29-41. [PMID: 23567904 DOI: 10.1016/j.bbapap.2013.03.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/18/2013] [Accepted: 03/08/2013] [Indexed: 12/20/2022]
148
Liebler DC, Zimmerman LJ. Targeted quantitation of proteins by mass spectrometry. Biochemistry 2013;52:3797-806. [PMID: 23517332 PMCID: PMC3674507 DOI: 10.1021/bi400110b] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Scheubert K, Hufsky F, Böcker S. Computational mass spectrometry for small molecules. J Cheminform 2013;5:12. [PMID: 23453222 PMCID: PMC3648359 DOI: 10.1186/1758-2946-5-12] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/01/2013] [Indexed: 12/29/2022]  Open
150
Thézénas ML, Huang H, Njie M, Ramaprasad A, Nwakanma DC, Fischer R, Digleria K, Walther M, Conway DJ, Kessler BM, Casals-Pascual C. PfHPRT: A New Biomarker Candidate of Acute Plasmodium falciparum Infection. J Proteome Res 2013;12:1211-22. [DOI: 10.1021/pr300858g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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