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Items: 1 to 20 of 31

1.

Using the CPTAC Assay Portal to Identify and Implement Highly Characterized Targeted Proteomics Assays.

Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Boja E, Carr SA, Chan DW, Chen X, Chen J, Davies SR, Ellis MJ, Fenyö D, Hiltke T, Ketchum KA, Kinsinger C, Kuhn E, Liebler DC, Liu T, Loss M, MacCoss MJ, Qian WJ, Rivers R, Rodland KD, Ruggles KV, Scott MG, Smith RD, Thomas S, Townsend RR, Whiteley G, Wu C, Zhang H, Zhang Z, Rodriguez H, Paulovich AG.

Methods Mol Biol. 2016;1410:223-36. doi: 10.1007/978-1-4939-3524-6_13.

PMID:
26867747
2.

Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS.

Krönke J, Fink EC, Hollenbach PW, MacBeth KJ, Hurst SN, Udeshi ND, Chamberlain PP, Mani DR, Man HW, Gandhi AK, Svinkina T, Schneider RK, McConkey M, Järås M, Griffiths E, Wetzler M, Bullinger L, Cathers BE, Carr SA, Chopra R, Ebert BL.

Nature. 2015 Jul 9;523(7559):183-8. doi: 10.1038/nature14610. Epub 2015 Jul 1.

PMID:
26131937
3.

Multiplexed, Quantitative Workflow for Sensitive Biomarker Discovery in Plasma Yields Novel Candidates for Early Myocardial Injury.

Keshishian H, Burgess MW, Gillette MA, Mertins P, Clauser KR, Mani DR, Kuhn EW, Farrell LA, Gerszten RE, Carr SA.

Mol Cell Proteomics. 2015 Sep;14(9):2375-93. doi: 10.1074/mcp.M114.046813. Epub 2015 Feb 27.

PMID:
25724909
4.

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma.

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.

Mol Cell Proteomics. 2015 Sep;14(9):2357-74. doi: 10.1074/mcp.M114.047050. Epub 2015 Feb 18.

PMID:
25693799
5.

CPTAC Assay Portal: a repository of targeted proteomic assays.

Whiteaker JR, Halusa GN, Hoofnagle AN, Sharma V, MacLean B, Yan P, Wrobel JA, Kennedy J, Mani DR, Zimmerman LJ, Meyer MR, Mesri M, Rodriguez H; Clinical Proteomic Tumor Analysis Consortium (CPTAC), Paulovich AG.

Nat Methods. 2014 Jul;11(7):703-4. doi: 10.1038/nmeth.3002. No abstract available.

6.

A framework for installable external tools in Skyline.

Broudy D, Killeen T, Choi M, Shulman N, Mani DR, Abbatiello SE, Mani D, Ahmad R, Sahu AK, Schilling B, Tamura K, Boss Y, Sharma V, Gibson BW, Carr SA, Vitek O, MacCoss MJ, MacLean B.

Bioinformatics. 2014 Sep 1;30(17):2521-3. doi: 10.1093/bioinformatics/btu148. Epub 2014 May 9.

7.

Ischemia in tumors induces early and sustained phosphorylation changes in stress kinase pathways but does not affect global protein levels.

Mertins P, Yang F, Liu T, Mani DR, Petyuk VA, Gillette MA, Clauser KR, Qiao JW, Gritsenko MA, Moore RJ, Levine DA, Townsend R, Erdmann-Gilmore P, Snider JE, Davies SR, Ruggles KV, Fenyo D, Kitchens RT, Li S, Olvera N, Dao F, Rodriguez H, Chan DW, Liebler D, White F, Rodland KD, Mills GB, Smith RD, Paulovich AG, Ellis M, Carr SA.

Mol Cell Proteomics. 2014 Jul;13(7):1690-704. doi: 10.1074/mcp.M113.036392. Epub 2014 Apr 9.

8.

Simplified and efficient quantification of low-abundance proteins at very high multiplex via targeted mass spectrometry.

Burgess MW, Keshishian H, Mani DR, Gillette MA, Carr SA.

Mol Cell Proteomics. 2014 Apr;13(4):1137-49. doi: 10.1074/mcp.M113.034660. Epub 2014 Feb 11.

9.

Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach.

Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S.

Mol Cell Proteomics. 2014 Mar;13(3):907-17. doi: 10.1074/mcp.M113.036095. Epub 2014 Jan 17.

10.

Identification of apolipoprotein D as a cardioprotective gene using a mouse model of lethal atherosclerotic coronary artery disease.

Tsukamoto K, Mani DR, Shi J, Zhang S, Haagensen DE, Otsuka F, Guan J, Smith JD, Weng W, Liao R, Kolodgie FD, Virmani R, Krieger M.

Proc Natl Acad Sci U S A. 2013 Oct 15;110(42):17023-8. doi: 10.1073/pnas.1315986110. Epub 2013 Sep 30.

11.

Integrated proteomic analysis of post-translational modifications by serial enrichment.

Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.

Nat Methods. 2013 Jul;10(7):634-7. doi: 10.1038/nmeth.2518. Epub 2013 Jun 9.

12.

Design, implementation and multisite evaluation of a system suitability protocol for the quantitative assessment of instrument performance in liquid chromatography-multiple reaction monitoring-MS (LC-MRM-MS).

Abbatiello SE, Mani DR, Schilling B, Maclean B, Zimmerman LJ, Feng X, Cusack MP, Sedransk N, Hall SC, Addona T, Allen S, Dodder NG, Ghosh M, Held JM, Hedrick V, Inerowicz HD, Jackson A, Keshishian H, Kim JW, Lyssand JS, Riley CP, Rudnick P, Sadowski P, Shaddox K, Smith D, Tomazela D, Wahlander A, Waldemarson S, Whitwell CA, You J, Zhang S, Kinsinger CR, Mesri M, Rodriguez H, Borchers CH, Buck C, Fisher SJ, Gibson BW, Liebler D, Maccoss M, Neubert TA, Paulovich A, Regnier F, Skates SJ, Tempst P, Wang M, Carr SA.

Mol Cell Proteomics. 2013 Sep;12(9):2623-39. doi: 10.1074/mcp.M112.027078. Epub 2013 May 20.

13.

Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.

Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.

Mol Cell Proteomics. 2013 Mar;12(3):825-31. doi: 10.1074/mcp.O112.027094. Epub 2012 Dec 24.

14.

Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics.

Mani DR, Abbatiello SE, Carr SA.

BMC Bioinformatics. 2012;13 Suppl 16:S9. doi: 10.1186/1471-2105-13-S16-S9. Epub 2012 Nov 5.

15.

Functional analysis of receptor tyrosine kinase mutations in lung cancer identifies oncogenic extracellular domain mutations of ERBB2.

Greulich H, Kaplan B, Mertins P, Chen TH, Tanaka KE, Yun CH, Zhang X, Lee SH, Cho J, Ambrogio L, Liao R, Imielinski M, Banerji S, Berger AH, Lawrence MS, Zhang J, Pho NH, Walker SR, Winckler W, Getz G, Frank D, Hahn WC, Eck MJ, Mani DR, Jaffe JD, Carr SA, Wong KK, Meyerson M.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14476-81. doi: 10.1073/pnas.1203201109. Epub 2012 Aug 20.

16.

Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.

Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.

Mol Cell Proteomics. 2012 May;11(5):148-59. doi: 10.1074/mcp.M111.016857. Epub 2012 Apr 14.

17.

iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.

Mertins P, Udeshi ND, Clauser KR, Mani DR, Patel J, Ong SE, Jaffe JD, Carr SA.

Mol Cell Proteomics. 2012 Jun;11(6):M111.014423. doi: 10.1074/mcp.M111.014423. Epub 2011 Dec 30.

18.

Interlaboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma.

Kuhn E, Whiteaker JR, Mani DR, Jackson AM, Zhao L, Pope ME, Smith D, Rivera KD, Anderson NL, Skates SJ, Pearson TW, Paulovich AG, Carr SA.

Mol Cell Proteomics. 2012 Jun;11(6):M111.013854. doi: 10.1074/mcp.M111.013854. Epub 2011 Dec 22.

19.

Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis.

Frühwirth R, Mani DR, Pyne S.

BMC Bioinformatics. 2011 Aug 31;12:358. doi: 10.1186/1471-2105-12-358.

20.

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease.

Addona TA, Shi X, Keshishian H, Mani DR, Burgess M, Gillette MA, Clauser KR, Shen D, Lewis GD, Farrell LA, Fifer MA, Sabatine MS, Gerszten RE, Carr SA.

Nat Biotechnol. 2011 Jun 19;29(7):635-43. doi: 10.1038/nbt.1899.

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