Recent Proteomics Platform Publications

Proteogenomic characterization of human colon and rectal cancer.Zhang, B., Wang J., Wang X., Zhu J., Liu Q., Shi Z., Chambers MC, Zimmerman LJ, Shaddox KF, Kim S., Davies SR, Wang S., Wang P., Kinsinger CR, Rivers RC, Rodriguez H., Townsend RR, Ellis MJ, Carr SA, Tabb DL, et al. Nature, 2014/07/20, (2014) Read More / View Supplemental Materials
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Extracellular matrix signatures of human primary metastatic colon cancers and their metastases to liver.Naba, A., Clauser KR, Whittaker CA, Carr SA, Tanabe KK, and Hynes R. O. BMC cancer, 2014/07/18, Volume 14, p.518, (2014) Read More / View Supplemental Materials
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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
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Mycobacterial esx-3 requires multiple components for iron acquisition.Siegrist, MS, Steigedal M., Ahmad R., Mehra A., Dragset MS, Schuster BM, Philips JA, Carr SA, and Rubin EJ mBio, 2014/05/06, Volume 5, Issue 3, (2014) Read More / View Supplemental Materials
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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
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Extracellular matrix signatures of human mammary carcinoma identify novel metastasis promoters.Naba, A., Clauser KR, Lamar JM, Carr SA, and Hynes R. O. eLife, 2014/03/11, Volume 3, p.e01308, (2014) Read More / View Supplemental Materials
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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 D., Mansfield E., Neubert H., Paulovich AG, Reiter L., Vitek O., Aebersold R., et al. Molecular & cellular proteomics : MCP, 2014/03/01, Volume 13, Issue 3, p.907-17, (2014) Read More / View Supplemental Materials
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Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins.Kennedy, JJ, Abbatiello SE, Kim K., Yan P., Whiteaker JR, Lin C., Kim JS, Zhang Y., Wang X., Ivey RG, Zhao L., Min H., Lee Y., Yu MH, Yang EG, Lee C., Wang P., Rodriguez H., Kim Y., Carr SA, et al. Nature methods, 2014/02/01, Volume 11, Issue 2, p.149-55, (2014) Read More / View Supplemental Materials
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Lenalidomide causes selective degradation of IKZF1 and IKZF3 in multiple myeloma cells.Krönke, J., Udeshi ND, Narla A., Grauman P., Hurst SN, McConkey M., Svinkina T., Heckl D., Comer E., Li X., Ciarlo C., Hartman E., Munshi N., Schenone M., Schreiber SL, Carr SA, and Ebert BL Science (New York, N.Y.), 2014/01/17, Volume 343, Issue 6168, p.301-5, (2014) Read More / View Supplemental Materials
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Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defenseKG, Lassen, P Kuballa, KL Conway, KK Patel, CE Becker, JM Peloquin, EJ Villablanca, JM Norman, T Liu, RJ Heath, ML Becker, L Fagbami, H Horn, J Mercer, OH Yilmaz, JJ Jaffe, AF Shamji, AK Bhan, SA Carr, MJ Daly, et al. Molecular & cellular proteomics : MCP, (2014) Read More / View Supplemental Materials
EMRE is an essential component of the mitochondrial calcium uniporter complex.Sancak, Y., Markhard AL, Kitami T., Kovács-Bogdán E., Kamer KJ, Udeshi ND, Carr SA, Chaudhuri D., Clapham DE, Li AA, Calvo SE, Goldberger O., and Mootha VK Science (New York, N.Y.), 2013/12/13, Volume 342, Issue 6164, p.1379-82, (2013) Read More / View Supplemental Materials
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Statistical design for biospecimen cohort size in proteomics-based biomarker discovery and verification studies.Skates, SJ, Gillette MA, LaBaer J., Carr SA, Anderson L., Liebler DC, Ransohoff D., Rifai N., Kondratovich M., Težak Ž., Mansfield E., Oberg AL, Wright I., Barnes G., Gail M., Mesri M., Kinsinger CR, Rodriguez H., and Boja ES Journal of proteome research, 2013/12/06, Volume 12, Issue 12, p.5383-94, (2013) Read More / View Supplemental Materials
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High-resolution mapping reveals a conserved, widespread, dynamic mRNA methylation program in yeast meiosis.Schwartz, S., Agarwala SD, Mumbach MR, Jovanovic M., Mertins P., Shishkin A., Tabach Y., Mikkelsen TS, Satija R., Ruvkun G., Carr SA, Lander E. S., Fink GR, and Regev A. Cell, 2013/12/05, Volume 155, Issue 6, p.1409-21, (2013) Read More / View Supplemental Materials
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Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia.Jaffe, JD, Wang Y., Chan HM, Zhang J., Huether R., Kryukov GV, Bhang HE, Taylor JE, Hu M., Englund NP, Yan F., Wang Z., Robert McDonald E 3rd, Wei L., Ma J., Easton J., Yu Z., Debeaumount R., Gibaja V., Venkatesan K., et al. Nature genetics, 2013/11/01, Volume 45, Issue 11, p.1386-91, (2013) Read More / View Supplemental Materials
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Large-scale identification of ubiquitination sites by mass spectrometry.Udeshi, ND, Mertins P., Svinkina T., and Carr SA Nature protocols, 2013/10/01, Volume 8, Issue 10, p.1950-60, (2013) Read More / View Supplemental Materials
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Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium.Ellis, MJ, Gillette M., Carr SA, Paulovich AG, Smith RD, Rodland KK, Townsend RR, Kinsinger C., Mesri M., Rodriguez H., Liebler DC, and Clinical Proteomic Tumor Analysis Consortium(CPTAC) Cancer discovery, 2013/10/01, Volume 3, Issue 10, p.1108-12, (2013) Read More / View Supplemental Materials
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High reliability in respiratory rate assessment in children with respiratory symptomatology in a rural area in MozambiqueLanaspa, M., Valim C., Acacio S., Almendinger K., Ahmad R., Wiegand R., and Bassat Q. Journal of Tropical Pediatrics, 2013/09/25, (2013) Read More / View Supplemental Materials
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
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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
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Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging.Rhee, HW, Zou P., Udeshi ND, Martell JD, Mootha VK, Carr SA, and Ting AY Science (New York, N.Y.), 2013/03/15, Volume 339, Issue 6125, p.1328-31, (2013) Read More / View Supplemental Materials
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Complementary RNA and Protein Profiling Identifies Iron as a Key Regulator of Mitochondrial Biogenesis.Rensvold, JW, Ong SE, Jeevananthan A., Carr SA, Mootha VK, and Pagliarini DJ Cell reports, 2013/01/09, (2013) Read More / View Supplemental Materials
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Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry.Gillette, MA, and Carr SA Nature methods, 2013/01/01, Volume 10, Issue 1, p.28-34, (2013) Read More / View Supplemental Materials
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Magnetic barcode assay for genetic detection of pathogens.Liong, M., Hoang AN, Chung J., Gural N., Ford CB, Min C., Shah RR, Ahmad R., Fernandez-Suarez M., Fortune SM, Toner M., Lee H., and Weissleder R. Nature communications, 2013/01/01, Volume 4, p.1752, (2013) Read More / View Supplemental Materials
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Identification of Trypanosome proteins in plasma from African sleeping sickness patients infected with T. b. rhodesiense.Eyford, BA, Ahmad R., Enyaru JC, Carr SA, and Pearson TW PloS one, 2013/01/01, Volume 8, Issue 8, p.e71463, (2013) Read More / View Supplemental Materials
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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
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Identification of regulators of the innate immune response to cytosolic DNA and retroviral infection by an integrative approach.Lee, MN, Roy M., Ong SE, Mertins P., Villani AC, Li W., Dotiwala F., Sen J., Doench JG, Orzalli MH, Kramnik I., Knipe DM, Lieberman J., Carr SA, and Hacohen N. Nature immunology, 2012/12/23, Volume 14, Issue 2, p.179-85, (2012) Read More / View Supplemental Materials
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H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions.Ku, M., Jaffe JD, Koche RP, Rheinbay E., Endoh M., Koseki H., Carr SA, and Bernstein BE Genome biology, 2012/10/03, Volume 13, Issue 10, p.R85, (2012) Read More / View Supplemental Materials
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Shotgun protein sequencing with meta-contig assembly.Guthals, A., Clauser KR, and Bandeira N. Molecular & cellular proteomics : MCP, 2012/10/01, Volume 11, Issue 10, p.1084-96, (2012) Read More / View Supplemental Materials
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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
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ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression.Abdel-Wahab, O., Adli M., LaFave LM, Gao J., Hricik T., Shih AH, Pandey S., Patel JP, Chung YR, Koche R., Perna F., Zhao X., Taylor JE, Park CY, Carroll M., Melnick A., Nimer SD, Jaffe JD, Aifantis I., Bernstein BE, et al. Cancer cell, 2012/08/14, Volume 22, Issue 2, p.180-93, (2012) Read More / View Supplemental Materials
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Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.Wen, Q., Goldenson B., Silver SJ, Schenone M., Dancik V., Huang Z., Wang LZ, Lewis TA, An WF, Li X., Bray MA, Thiollier C., Diebold L., Gilles L., Vokes MS, Moore CB, Bliss-Moreau M., VerPlank L., Tolliday NJ, Mishra R., et al. Cell, 2012/08/03, Volume 150, Issue 3, p.575-89, (2012) Read More / View Supplemental Materials
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Modification site localization scoring: strategies and performance.Chalkley, RJ, and Clauser KR Molecular & cellular proteomics : MCP, 2012/05/01, Volume 11, Issue 5, p.3-14, (2012) Read More / View Supplemental Materials
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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
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Quantitative assessment of ChIP-grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules.Peach, SE, Rudomin EL, Udeshi ND, Carr SA, and Jaffe JD Molecular & cellular proteomics : MCP, 2012/03/23, (2012) Read More / View Supplemental Materials
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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
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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
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Quantitative assessment of ChIP-grade antbodies directed against histone modifications reveals patterns of co-occurring marks on histone protein moleculesPeach, Sally E., Rudomin Emily L., Udeshi Namrata D., Carr Steven A., and Jaffe Jacob D. Molecular & Cellular Proteomics, (2012) Read More / View Supplemental Materials
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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
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The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.Naba, A., Clauser KR, Hoersch S., Liu H., Carr SA, and Hynes R. O. Molecular & cellular proteomics : MCP, 2011/12/09, (2011) Read More / View Supplemental Materials
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Comprehensive proteomic study identifies serpin and cystatin antiproteases as novel correlates of HIV-1 resistance in the cervicovaginal mucosa of female sex workers.Burgener, A., Rahman S., Ahmad R., Lajoie J., Ramdahin S., Mesa C., Brunet S., Wachihi C., Kimani J., Fowke K., Carr S., Plummer F., and Ball TB Journal of proteome research, 2011/11/04, Volume 10, Issue 11, p.5139-49, (2011) Read More / View Supplemental Materials
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A face in the crowd: recognizing peptides through database search.Eng, JK, Searle BC, Clauser KR, and Tabb DL Molecular & cellular proteomics : MCP, 2011/11/01, Volume 10, Issue 11, p.R111.009522, (2011) Read More / View Supplemental Materials
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Mutations in MTFMT underlie a human disorder of formylation causing impaired mitochondrial translation.Tucker, EJ, Hershman SG, Köhrer C., Belcher-Timme CA, Patel J., Goldberger OA, Christodoulou J., Silberstein JM, McKenzie M., Ryan MT, Compton AG, Jaffe JD, Carr SA, Calvo SE, RajBhandary UL, Thorburn DR, and Mootha VK Cell metabolism, 2011/09/07, Volume 14, Issue 3, p.428-34, (2011) Read More / View Supplemental Materials
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STK33 kinase activity is nonessential in KRAS-dependent cancer cells.Babij, C., Zhang Y., Kurzeja RJ, Munzli A., Shehabeldin A., Fernando M., Quon K., Kassner PD, Ruefli-Brasse AA, Watson VJ, Fajardo F., Jackson A., Zondlo J., Sun Y., Ellison AR, Plewa CA, San MT, Robinson J., McCarter J., Schwandner R., et al. Cancer research, 2011/09/01, Volume 71, Issue 17, p.5818-26, (2011) Read More / View Supplemental Materials
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The genome of the green anole lizard and a comparative analysis with birds and mammals.Alföldi, J., Di Palma F., Grabherr M., Williams C., Kong L., Mauceli E., Russell P., Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S., Shedlock AM, Botka C., Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D., et al. Nature, 2011/08/31, Volume 477, Issue 7366, p.587-91, (2011) Read More / View Supplemental Materials
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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
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Status and prospects for discovery and verification of new biomarkers of cardiovascular disease by proteomics.Gerszten, RE, Asnani A., and Carr SA Circulation research, 2011/08/05, Volume 109, Issue 4, p.463-74, (2011) Read More / View Supplemental Materials
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Quantification of proteins using peptide immunoaffinity enrichment coupled with mass spectrometry.Zhao, L., Whiteaker JR, Pope ME, Kuhn E., Jackson A., Anderson NL, Pearson TW, Carr SA, and Paulovich AG Journal of visualized experiments : JoVE, 2011/07/31, Issue 53, (2011) Read More / View Supplemental Materials
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AAK1 identified as an inhibitor of neuregulin-1/ErbB4-dependent neurotrophic factor signaling using integrative chemical genomics and proteomics.Kuai, L., Ong SE, Madison JM, Wang X., Duvall JR, Lewis TA, Luce CJ, Conner SD, Pearlman DA, Wood JL, Schreiber SL, Carr SA, Scolnick EM, and Haggarty SJ Chemistry & biology, 2011/07/29, Volume 18, Issue 7, p.891-906, (2011) Read More / View Supplemental Materials
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Exoplasmic cysteine Cys384 of the HDL receptor SR-BI is critical for its sensitivity to a small-molecule inhibitor and normal lipid transport activity.Yu, M., Romer KA, Nieland TJ, Xu S., Saenz-Vash V., Penman M., Yesilaltay A., Carr SA, and Krieger M. Proceedings of the National Academy of Sciences of the United States of America, 2011/07/26, Volume 108, Issue 30, p.12243-8, (2011) Read More / View Supplemental Materials
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Selective killing of cancer cells by a small molecule targeting the stress response to ROS.Raj, L., Ide T., Gurkar AU, Foley M., Schenone M., Li X., Tolliday NJ, Golub T. R., Carr SA, Shamji AF, Stern AM, Mandinova A., Schreiber SL, and Lee SW Nature, 2011/07/13, Volume 475, Issue 7355, p.231-4, (2011) Read More / View Supplemental Materials
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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
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Evaluation of large scale quantitative proteomic assay development using peptide affinity-based mass spectrometry.Whiteaker, JR, Zhao L., Abbatiello SE, Burgess M., Kuhn E., Lin C., Pope ME, Razavi M., Anderson NL, Pearson TW, Carr SA, and Paulovich AG Molecular & cellular proteomics : MCP, 2011/04/01, Volume 10, Issue 4, p.M110.005645, (2011) Read More / View Supplemental Materials
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Lipid profiling identifies a triacylglycerol signature of insulin resistance and improves diabetes prediction in humans.Rhee, EP, Cheng S., Larson MG, Walford GA, Lewis GD, McCabe E., Yang E., Farrell L., Fox CS, O'Donnell CJ, Carr SA, Vasan RS, Florez JC, Clish CB, Wang TJ, and Gerszten RE The Journal of clinical investigation, 2011/04/01, Volume 121, Issue 4, p.1402-11, (2011) Read More / View Supplemental Materials
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Metabolite profiles and the risk of developing diabetes.Wang, TJ, Larson MG, Vasan RS, Cheng S., Rhee EP, McCabe E., Lewis GD, Fox CS, Jacques PF, Fernandez C., O'Donnell CJ, Carr SA, Mootha VK, Florez JC, Souza A., Melander O., Clish CB, and Gerszten RE Nature medicine, 2011/04/01, Volume 17, Issue 4, p.448-53, (2011) Read More / View Supplemental Materials
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Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease.Bradner, JE, Mak R., Tanguturi SK, Mazitschek R., Haggarty SJ, Ross K., Chang CY, Bosco J., West N., Morse E., Lin K., Shen JP, Kwiatkowski NP, Gheldof N., Dekker J., DeAngelo DJ, Carr SA, Schreiber SL, Golub T. R., and Ebert BL Proceedings of the National Academy of Sciences of the United States of America, 2010/07/13, Volume 107, Issue 28, p.12617-22, (2010) Read More / View Supplemental Materials
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Rictor phosphorylation on the Thr-1135 site does not require mammalian target of rapamycin complex 2.Boulbes, D., Chen CH, Shaikenov T., Agarwal NK, Peterson TR, Addona TA, Keshishian H., Carr SA, Magnuson MA, Sabatini DM, and Sarbassov dos D. Molecular cancer research : MCR, 2010/06/01, Volume 8, Issue 6, p.896-906, (2010) Read More / View Supplemental Materials
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Metabolic signatures of exercise in human plasma.Lewis, GD, Farrell L., Wood MJ, Martinovic M., Arany Z., Rowe GC, Souza A., Cheng S., McCabe EL, Yang E., Shi X., Deo R., Roth FP, Asnani A., Rhee EP, Systrom DM, Semigran MJ, Vasan RS, Carr SA, Wang TJ, et al. Science translational medicine, 2010/05/26, Volume 2, Issue 33, p.33ra37, (2010) Read More / View Supplemental Materials
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Optimizing performance of glycopeptide capture for plasma proteomics.Berven, FS, Ahmad R., Clauser KR, and Carr SA Journal of proteome research, 2010/04/05, Volume 9, Issue 4, p.1706-15, (2010) Read More / View Supplemental Materials
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Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry.Tabb, DL, Vega-Montoto L., Rudnick PA, Variyath AM, Ham AJ, Bunk DM, Kilpatrick LE, Billheimer DD, Blackman RK, Cardasis HL, Carr SA, Clauser KR, Jaffe JD, Kowalski KA, Neubert TA, Regnier FE, Schilling B., Tegeler TJ, Wang M., Wang P., et al. Journal of proteome research, 2010/02/05, Volume 9, Issue 2, p.761-76, (2010) Read More / View Supplemental Materials
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Introduction: Advances in protein analysis for the clinical laboratory.Hortin, GL, Carr SA, and Anderson NL Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.149-51, (2010) Read More / View Supplemental Materials
Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance.Paulovich, AG, Billheimer D., Ham AJ, Vega-Montoto L., Rudnick PA, Tabb DL, Wang P., Blackman RK, Bunk DM, Cardasis HL, Clauser KR, Kinsinger CR, Schilling B., Tegeler TJ, Variyath AM, Wang M., Whiteaker JR, Zimmerman LJ, Fenyo D., Carr SA, et al. Molecular & cellular proteomics : MCP, 2010/02/01, Volume 9, Issue 2, p.242-54, (2010) Read More / View Supplemental Materials
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Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses.Rudnick, PA, Clauser KR, Kilpatrick LE, Tchekhovskoi DV, Neta P., Blonder N., Billheimer DD, Blackman RK, Bunk DM, Cardasis HL, Ham AJ, Jaffe JD, Kinsinger CR, Mesri M., Neubert TA, Schilling B., Tabb DL, Tegeler TJ, Vega-Montoto L., Variyath AM, et al. Molecular & cellular proteomics : MCP, 2010/02/01, Volume 9, Issue 2, p.225-41, (2010) Read More / View Supplemental Materials
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Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration.Regnier, FE, Skates SJ, Mesri M., Rodriguez H., Tezak Z., Kondratovich MV, Alterman MA, Levin JD, Roscoe D., Reilly E., Callaghan J., Kelm K., Brown D., Philip R., Carr SA, Liebler DC, Fisher SJ, Tempst P., Hiltke T., Kessler LG, et al. Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.165-71, (2010) Read More / View Supplemental Materials
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Integration of proteomic-based tools for improved biomarkers of myocardial injury.Gerszten, RE, Carr SA, and Sabatine M. Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.194-201, (2010) Read More / View Supplemental Materials
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Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics.Rodriguez, H., Tezak Z., Mesri M., Carr SA, Liebler DC, Fisher SJ, Tempst P., Hiltke T., Kessler LG, Kinsinger CR, Philip R., Ransohoff DF, Skates SJ, Regnier FE, Anderson NL, Mansfield E., and Workshop Participants Clinical chemistry, 2010/02/01, Volume 56, Issue 2, p.237-43, (2010) Read More / View Supplemental Materials
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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
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A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint.van Vugt, MA, Gardino AK, Linding R., Ostheimer GJ, Reinhardt HC, Ong SE, Tan CS, Miao H., Keezer SM, Li J., Pawson T., Lewis TA, Carr SA, Smerdon SJ, Brummelkamp TR, and Yaffe MB PLoS biology, 2010/01/26, Volume 8, Issue 1, p.e1000287, (2010) Read More / View Supplemental Materials
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ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth.Markljung, E., Jiang L., Jaffe JD, Mikkelsen TS, Wallerman O., Larhammar M., Zhang X., Wang L., Saenz-Vash V., Gnirke A., Lindroth AM, Barrés R., Yan J., Strömberg S., De S., Pontén F., Lander E. S., Carr SA, Zierath JR, Kullander K., et al. PLoS biology, 2009/12/01, Volume 7, Issue 12, p.e1000256, (2009) Read More / View Supplemental Materials
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Empirical Bayes analysis of quantitative proteomics experiments.Margolin, AA, Ong SE, Schenone M., Gould R., Schreiber SL, Carr SA, and Golub T. R. PloS one, 2009/10/14, Volume 4, Issue 10, p.e7454, (2009) Read More / View Supplemental Materials
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Proteomic and genetic approaches identify Syk as an AML target.Hahn, CK, Berchuck JE, Ross KN, Kakoza RM, Clauser K., Schinzel AC, Ross L., Galinsky I., Davis TN, Silver SJ, Root DE, Stone RM, DeAngelo DJ, Carroll M., Hahn WC, Carr SA, Golub T. R., Kung AL, and Stegmaier K. Cancer cell, 2009/10/06, Volume 16, Issue 4, p.281-94, (2009) Read More / View Supplemental Materials
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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
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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
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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
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Directed sample interrogation utilizing an accurate mass exclusion-based data-dependent acquisition strategy (AMEx).Rudomin, EL, Carr SA, and Jaffe JD Journal of proteome research, 2009/06/01, Volume 8, Issue 6, p.3154-60, (2009) Read More / View Supplemental Materials
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Plk1 self-organization and priming phosphorylation of HsCYK-4 at the spindle midzone regulate the onset of division in human cells.Burkard, ME, Maciejowski J., Rodriguez-Bravo V., Repka M., Lowery DM, Clauser KR, Zhang C., Shokat KM, Carr SA, Yaffe MB, and Jallepalli PV PLoS biology, 2009/05/05, Volume 7, Issue 5, p.e1000111, (2009) Read More / View Supplemental Materials
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A human proteome detection and quantitation project.Anderson, NL, Anderson NG, Pearson TW, Borchers CH, Paulovich AG, Patterson SD, Gillette M., Aebersold R., and Carr SA Molecular & cellular proteomics : MCP, 2009/05/01, Volume 8, Issue 5, p.883-6, (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
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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
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Protein quantitation through targeted mass spectrometry: the way out of biomarker purgatory?Carr, SA, and Anderson L. Clinical chemistry, 2008/11/01, Volume 54, Issue 11, p.1749-52, (2008) Read More / View Supplemental Materials
Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification.Jaffe, JD, Keshishian H., Chang B., Addona TA, Gillette MA, and Carr SA Molecular & cellular proteomics : MCP, 2008/10/01, Volume 7, Issue 10, p.1952-62, (2008) Read More / View Supplemental Materials
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Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury.Lewis, GD, Wei R., Liu E., Yang E., Shi X., Martinovic M., Farrell L., Asnani A., Cyrille M., Ramanathan A., Shaham O., Berriz G., Lowry PA, Palacios IF, Taşan M., Roth FP, Min J., Baumgartner C., Keshishian H., Addona T., et al. The Journal of clinical investigation, 2008/10/01, Volume 118, Issue 10, p.3503-12, (2008) Read More / View Supplemental Materials
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A mitochondrial protein compendium elucidates complex I disease biology.Pagliarini, DJ, Calvo SE, Chang B., Sheth SA, Vafai SB, Ong SE, Walford GA, Sugiana C., Boneh A., Chen WK, Hill DE, Vidal M., Evans JG, Thorburn DR, Carr SA, and Mootha VK Cell, 2008/07/11, Volume 134, Issue 1, p.112-23, (2008) Read More / View Supplemental Materials
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Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity.Shaham, O., Wei R., Wang TJ, Ricciardi C., Lewis GD, Vasan RS, Carr SA, Thadhani R., Gerszten RE, and Mootha VK Molecular systems biology, 2008/01/01, Volume 4, p.214, (2008) Read More / View Supplemental Materials
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Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution.Keshishian, H., Addona T., Burgess M., Kuhn E., and Carr SA Molecular & cellular proteomics : MCP, 2007/12/01, Volume 6, Issue 12, p.2212-29, (2007) Read More / View Supplemental Materials
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Proteomic screen defines the Polo-box domain interactome and identifies Rock2 as a Plk1 substrate.Lowery, DM, Clauser KR, Hjerrild M., Lim D., Alexander J., Kishi K., Ong SE, Gammeltoft S., Carr SA, and Yaffe MB The EMBO journal, 2007/05/02, Volume 26, Issue 9, p.2262-73, (2007) Read More / View Supplemental Materials
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PRAS40 is an insulin-regulated inhibitor of the mTORC1 protein kinase.Sancak, Y., Thoreen CC, Peterson TR, Lindquist RA, Kang SA, Spooner E., Carr SA, and Sabatini DM Molecular cell, 2007/03/23, Volume 25, Issue 6, p.903-15, (2007) Read More / View Supplemental Materials
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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
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The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.Lamb, J., Crawford ED, Peck D., Modell JW, Blat IC, Wrobel MJ, Lerner J., Brunet JP, Subramanian A., Ross KN, Reich M., Hieronymus H., Wei G., Armstrong SA, Haggarty SJ, Clemons PA, Wei R., Carr SA, Lander E. S., and Golub T. R. Science (New York, N.Y.), 2006/09/29, Volume 313, Issue 5795, p.1929-35, (2006) Read More / View Supplemental Materials
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mSin1 is necessary for Akt/PKB phosphorylation, and its isoforms define three distinct mTORC2s.Frias, MA, Thoreen CC, Jaffe JD, Schroder W., Sculley T., Carr SA, and Sabatini DM Current biology : CB, 2006/09/19, Volume 16, Issue 18, p.1865-70, (2006) Read More / View Supplemental Materials
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Protein biomarker discovery and validation: the long and uncertain path to clinical utility.Rifai, N., Gillette MA, and Carr SA Nature biotechnology, 2006/08/01, Volume 24, Issue 8, p.971-83, (2006) Read More / View Supplemental Materials
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Systematic identification of human mitochondrial disease genes through integrative genomics.Calvo, S., Jain M., Xie X., Sheth SA, Chang B., Goldberger OA, Spinazzola A., Zeviani M., Carr SA, and Mootha VK Nature genetics, 2006/05/01, Volume 38, Issue 5, p.576-82, (2006) Read More / View Supplemental Materials
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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
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Mapping posttranslational modifications of proteins by MS-based selective detection: application to phosphoproteomics.Carr, SA, Annan RS, and Huddleston MJ Methods in enzymology, 2005/01/01, Volume 405, p.82-115, (2005) Read More / View Supplemental Materials
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Selective detection of glycopeptides on ion trap mass spectrometers.Sullivan, B., Addona TA, and Carr SA Analytical chemistry, 2004/06/01, Volume 76, Issue 11, p.3112-8, (2004) Read More / View Supplemental Materials
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