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2014
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 D. R., Zimmerman LJ, Meyer MR, Mesri M., Rodriguez H., Clinical Proteomic Tumor Analysis Consortium(CPTAC), and Paulovich AG Nature methods, 2014/06/27, Volume 11, Issue 7, p.703-4, (2014) Read More / View Supplemental Materials
A framework for installable external tools in Skyline.Broudy, D., Killeen T., Choi M., Shulman N., Mani D. R., Abbatiello SE, Mani D., Ahmad R., Sahu AK, Schilling B., Tamura K., Boss Y., Sharma V., Gibson BW, Carr SA, Vitek O., Maccoss MJ, and Maclean B. Bioinformatics (Oxford, England), 2014/05/09, (2014) Read More / View Supplemental Materials
Abstract
Simplified and Efficient Quantification of Low-abundance Proteins at Very High Multiplex via Targeted Mass Spectrometry.Burgess, MW, Keshishian H., Mani D. R., Gillette MA, and Carr SA Molecular & cellular proteomics : MCP, 2014/04/01, Volume 13, Issue 4, p.1137-49, (2014) Read More / View Supplemental Materials
Abstract
2013
Integrated proteomic analysis of post-translational modifications by serial enrichment.Mertins, P., Qiao JW, Patel J., Udeshi ND, Clauser KR, Mani D. R., Burgess MW, Gillette MA, Jaffe JD, and Carr SA Nature methods, 2013/07/01, Volume 10, Issue 7, p.634-7, (2013) Read More / View Supplemental Materials
Abstract
Design, Implementation, and Multi-Site Evaluation of a System Suitability Protocol for the Quantitative Assessment of Instrument Performance in LC-MRM-MS.Abbatiello, SE, Mani D. R., 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, et al. Molecular & cellular proteomics : MCP, 2013/05/20, (2013) Read More / View Supplemental Materials
Abstract
2012
Refined Preparation and Use of Anti-K- epsilon -GG Antibody Enables Routine Quantification of 10,000s of Ubiquitination Sites in Single Proteomics Experiments.Udeshi, ND, Svinkina T., Mertins P., Kuhn E., Mani D. R., Qiao JW, and Carr SA Molecular & cellular proteomics : MCP, 2012/12/24, (2012) Read More / View Supplemental Materials
Abstract
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., et al. Proceedings of the National Academy of Sciences of the United States of America, 2012/09/04, Volume 109, Issue 36, p.14476-81, (2012) Read More / View Supplemental Materials
Abstract
Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.Udeshi, ND, Mani D. R., Eisenhaure T., Mertins P., Jaffe JD, Clauser KR, Hacohen N., and Carr SA Molecular & cellular proteomics : MCP, 2012/04/14, (2012) Read More / View Supplemental Materials
Abstract
Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics.Mani, D. R., Abbatiello SE, and Carr SA BMC bioinformatics, 2012/01/01, Volume 13 Suppl 16, p.S9, (2012) Read More / View Supplemental Materials
Abstract
iTRAQ labeling is superior to mTRAQ for quantitative global proteomics and phosphoproteomics.Mertins, P., Udeshi ND, Clauser KR, Mani D. R., Patel J., Ong SE, Jaffe JD, and Carr SA Molecular & cellular proteomics : MCP, 2011/12/30, (2012) Read More / View Supplemental Materials
Abstract
2011
Inter-laboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma.Kuhn, E., Whiteaker JR, Mani D. R., Jackson AM, Zhao L., Pope ME, Smith D., Rivera KD, Anderson NL, Skates SJ, Pearson TW, Paulovich AG, and Carr SA Molecular & cellular proteomics : MCP, 2011/12/22, (2011) Read More / View Supplemental Materials
Abstract
Clustering with position-specific constraints on variance: applying redescending M-estimators to label-free LC-MS data analysis.Frühwirth, R., Mani D. R., and Pyne S. BMC bioinformatics, 2011/08/31, Volume 12, p.358, (2011) Read More / View Supplemental Materials
Abstract
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 D. R., Burgess M., Gillette MA, Clauser KR, Shen D., Lewis GD, Farrell LA, Fifer MA, Sabatine MS, Gerszten RE, and Carr SA Nature biotechnology, 2011/06/19, Volume 29, Issue 7, p.635-43, (2011) Read More / View Supplemental Materials
Abstract
2010
Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry.Abbatiello, SE, Mani D. R., Keshishian H., and Carr SA Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.291-305, (2010) Read More / View Supplemental Materials
Abstract
2009
Quantification of cardiovascular biomarkers in patient plasma by targeted mass spectrometry and stable isotope dilution.Keshishian, H., Addona T., Burgess M., Mani D. R., Shi X., Kuhn E., Sabatine MS, Gerszten RE, and Carr SA Molecular & cellular proteomics : MCP, 2009/10/01, Volume 8, Issue 10, p.2339-49, (2009) Read More / View Supplemental Materials
Abstract
Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma.Addona, TA, Abbatiello SE, Schilling B., Skates SJ, Mani D. R., Bunk DM, Spiegelman CH, Zimmerman LJ, Ham AJ, Keshishian H., Hall SC, Allen S., Blackman RK, Borchers CH, Buck C., Cardasis HL, Cusack MP, Dodder NG, Gibson BW, Held JM, et al. Nature biotechnology, 2009/07/01, Volume 27, Issue 7, p.633-41, (2009) Read More / View Supplemental Materials
Abstract
Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry.Kuhn, E., Addona T., Keshishian H., Burgess M., Mani D. R., Lee RT, Sabatine MS, Gerszten RE, and Carr SA Clinical chemistry, 2009/06/01, Volume 55, Issue 6, p.1108-17, (2009) Read More / View Supplemental Materials
Abstract
Identifying the proteins to which small-molecule probes and drugs bind in cells.Ong, SE, Schenone M., Margolin AA, Li X., Do K., Doud MK, Mani D. R., Kuai L., Wang X., Wood JL, Tolliday NJ, Koehler AN, Marcaurelle LA, Golub T. R., Gould RJ, Schreiber SL, and Carr SA Proceedings of the National Academy of Sciences of the United States of America, 2009/03/24, Volume 106, Issue 12, p.4617-22, (2009) Read More / View Supplemental Materials
Abstract
Prediction of high-responding peptides for targeted protein assays by mass spectrometry.Fusaro, VA, Mani D. R., Mesirov J. P., and Carr SA Nature biotechnology, 2009/02/01, Volume 27, Issue 2, p.190-8, (2009) Read More / View Supplemental Materials
Abstract
Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy.Du, J., Bernasconi P., Clauser KR, Mani D. R., Finn SP, Beroukhim R., Burns M., Julian B., Peng XP, Hieronymus H., Maglathlin RL, Lewis TA, Liau LM, Nghiemphu P., Mellinghoff IK, Louis DN, Loda M., Carr SA, Kung AL, and Golub T. R. Nature biotechnology, 2009/01/01, Volume 27, Issue 1, p.77-83, (2009) Read More / View Supplemental Materials
Abstract
2006
PEPPeR, a platform for experimental proteomic pattern recognition.Jaffe, JD, Mani D. R., Leptos KC, Church GM, Gillette MA, and Carr SA Molecular & cellular proteomics : MCP, 2006/10/01, Volume 5, Issue 10, p.1927-41, (2006) Read More / View Supplemental Materials
Abstract
2005
Place of pattern in proteomic biomarker discovery.Gillette, MA, Mani D. R., and Carr SA Journal of proteome research, 2005/1/1, Volume 4, Issue 4, p.1143-54, (2005) Read More / View Supplemental Materials
Abstract
2003
Gene expression-based classification of malignant gliomas correlates better with survival than histological classificationNutt, Catherine L., Mani D. R., Betensky Rebecca A., Tamayo Pablo, Cairncross Gregory J., Ladd Christine, Pohl Ute, Hartmann Christian, McLaughlin Margaret E., Batchelor Tracy T., Black Peter M., von Deimling Andreas, Pomeroy Scott L., Golub Todd R., and Louis David N. Cancer Research, 2003/04/01/, Volume 63, Issue 7, p.1602 - 7, (2003) Read More / View Supplemental Materials
Abstract
Gene expression-based classification of malignant gliomas correlates better with survival than histological classificationNutt, Catherine L., Mani D. R., Betensky Rebecca A., Tamayo Pablo, Cairncross Gregory J., Ladd Christine, Pohl Ute, Hartmann Christian, McLaughlin Margaret E., Batchelor Tracy T., Black Peter M., von Deimling Andreas, Pomeroy Scott L., Golub Todd R., and Louis David N. Cancer Research, 2003/04/01/, Volume 63, Issue 7, p.1602 - 7, (2003) Read More / View Supplemental Materials
Abstract
  • Showing 1-24 of 24 Results