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Items: 46

1.

Correction: Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation.

Hung V, Lam SS, Udeshi ND, Svinkina T, Guzman G, Mootha VK, Carr SA, Ting AY.

Elife. 2019 Aug 5;8. pii: e50707. doi: 10.7554/eLife.50707.

2.

Patterns of substrate affinity, competition, and degradation kinetics underlie biological activity of thalidomide analogs.

Sperling AS, Burgess M, Keshishian H, Gasser JA, Bhatt S, Jan M, Słabicki M, Sellar RS, Fink EC, Miller PG, Liddicoat BJ, Sievers QL, Sharma R, Adams DN, Olesinski EA, Fulciniti M, Udeshi ND, Kuhn E, Letai A, Munshi NC, Carr SA, Ebert BL.

Blood. 2019 Jul 11;134(2):160-170. doi: 10.1182/blood.2019000789. Epub 2019 May 1.

PMID:
31043423
3.

In Situ Peroxidase Labeling and Mass Spectrometry of Alpha-Synuclein in Rat Cortical Neurons.

Sanz R, Ovando-Roche P, Udeshi ND, Carr SA, Chung CY, Khurana V.

Methods Mol Biol. 2019;1948:235-246. doi: 10.1007/978-1-4939-9124-2_18.

PMID:
30771182
4.

Evaluation of Advanced Precursor Determination for Tandem Mass Tag (TMT)-Based Quantitative Proteomics across Instrument Platforms.

Myers SA, Klaeger S, Satpathy S, Viner R, Choi J, Rogers J, Clauser K, Udeshi ND, Carr SA.

J Proteome Res. 2019 Jan 4;18(1):542-547. doi: 10.1021/acs.jproteome.8b00611. Epub 2018 Oct 31.

PMID:
30351145
5.

Lso2 is a conserved ribosome-bound protein required for translational recovery in yeast.

Wang YJ, Vaidyanathan PP, Rojas-Duran MF, Udeshi ND, Bartoli KM, Carr SA, Gilbert WV.

PLoS Biol. 2018 Sep 12;16(9):e2005903. doi: 10.1371/journal.pbio.2005903. eCollection 2018 Sep.

6.

Efficient proximity labeling in living cells and organisms with TurboID.

Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY.

Nat Biotechnol. 2018 Oct;36(9):880-887. doi: 10.1038/nbt.4201. Epub 2018 Aug 20.

7.

Homo-PROTACs for the Chemical Knockdown of Cereblon.

Steinebach C, Lindner S, Udeshi ND, Mani DC, Kehm H, Köpff S, Carr SA, Gütschow M, Krönke J.

ACS Chem Biol. 2018 Sep 21;13(9):2771-2782. doi: 10.1021/acschembio.8b00693. Epub 2018 Sep 5.

PMID:
30118587
8.

Crbn I391V is sufficient to confer in vivo sensitivity to thalidomide and its derivatives in mice.

Fink EC, McConkey M, Adams DN, Haldar SD, Kennedy JA, Guirguis AA, Udeshi ND, Mani DR, Chen M, Liddicoat B, Svinkina T, Nguyen AT, Carr SA, Ebert BL.

Blood. 2018 Oct 4;132(14):1535-1544. doi: 10.1182/blood-2018-05-852798. Epub 2018 Jul 31.

9.

Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry.

Mertins P, Tang LC, Krug K, Clark DJ, Gritsenko MA, Chen L, Clauser KR, Clauss TR, Shah P, Gillette MA, Petyuk VA, Thomas SN, Mani DR, Mundt F, Moore RJ, Hu Y, Zhao R, Schnaubelt M, Keshishian H, Monroe ME, Zhang Z, Udeshi ND, Mani D, Davies SR, Townsend RR, Chan DW, Smith RD, Zhang H, Liu T, Carr SA.

Nat Protoc. 2018 Jul;13(7):1632-1661. doi: 10.1038/s41596-018-0006-9.

10.

The C9orf72-interacting protein Smcr8 is a negative regulator of autoimmunity and lysosomal exocytosis.

Zhang Y, Burberry A, Wang JY, Sandoe J, Ghosh S, Udeshi ND, Svinkina T, Mordes DA, Mok J, Charlton M, Li QZ, Carr SA, Eggan K.

Genes Dev. 2018 Jul 1;32(13-14):929-943. doi: 10.1101/gad.313932.118. Epub 2018 Jun 27.

11.

Antibodies to biotin enable large-scale detection of biotinylation sites on proteins.

Udeshi ND, Pedram K, Svinkina T, Fereshetian S, Myers SA, Aygun O, Krug K, Clauser K, Ryan D, Ast T, Mootha VK, Ting AY, Carr SA.

Nat Methods. 2017 Dec;14(12):1167-1170. doi: 10.1038/nmeth.4465. Epub 2017 Oct 16.

PMID:
29039416
12.

Phosphorylation coexists with O-GlcNAcylation in a plant virus protein and influences viral infection.

Martínez-Turiño S, Pérez JJ, Hervás M, Navajas R, Ciordia S, Udeshi ND, Shabanowitz J, Hunt DF, García JA.

Mol Plant Pathol. 2018 Jun;19(6):1427-1443. doi: 10.1111/mpp.12626. Epub 2018 Jan 30.

13.

Lysine trimethylation regulates 78-kDa glucose-regulated protein proteostasis during endoplasmic reticulum stress.

Sieber J, Wieder N, Ostrosky-Frid M, Dvela-Levitt M, Aygün O, Udeshi ND, Carr SA, Greka A.

J Biol Chem. 2017 Nov 17;292(46):18878-18885. doi: 10.1074/jbc.M117.797084. Epub 2017 Sep 14.

14.

Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors.

Janouskova H, El Tekle G, Bellini E, Udeshi ND, Rinaldi A, Ulbricht A, Bernasocchi T, Civenni G, Losa M, Svinkina T, Bielski CM, Kryukov GV, Cascione L, Napoli S, Enchev RI, Mutch DG, Carney ME, Berchuck A, Winterhoff BJN, Broaddus RR, Schraml P, Moch H, Bertoni F, Catapano CV, Peter M, Carr SA, Garraway LA, Wild PJ, Theurillat JP.

Nat Med. 2017 Sep;23(9):1046-1054. doi: 10.1038/nm.4372. Epub 2017 Aug 14.

15.

Probing the lithium-response pathway in hiPSCs implicates the phosphoregulatory set-point for a cytoskeletal modulator in bipolar pathogenesis.

Tobe BTD, Crain AM, Winquist AM, Calabrese B, Makihara H, Zhao WN, Lalonde J, Nakamura H, Konopaske G, Sidor M, Pernia CD, Yamashita N, Wada M, Inoue Y, Nakamura F, Sheridan SD, Logan RW, Brandel M, Wu D, Hunsberger J, Dorsett L, Duerr C, Basa RCB, McCarthy MJ, Udeshi ND, Mertins P, Carr SA, Rouleau GA, Mastrangelo L, Li J, Gutierrez GJ, Brill LM, Venizelos N, Chen G, Nye JS, Manji H, Price JH, McClung CA, Akiskal HS, Alda M, Chuang DM, Coyle JT, Liu Y, Teng YD, Ohshima T, Mikoshiba K, Sidman RL, Halpain S, Haggarty SJ, Goshima Y, Snyder EY.

Proc Natl Acad Sci U S A. 2017 May 30;114(22):E4462-E4471. doi: 10.1073/pnas.1700111114. Epub 2017 May 12.

16.

Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation.

Hung V, Lam SS, Udeshi ND, Svinkina T, Guzman G, Mootha VK, Carr SA, Ting AY.

Elife. 2017 Apr 25;6. pii: e24463. doi: 10.7554/eLife.24463. Erratum in: Elife. 2019 Aug 05;8:.

17.

Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells.

Han S, Udeshi ND, Deerinck TJ, Svinkina T, Ellisman MH, Carr SA, Ting AY.

Cell Chem Biol. 2017 Mar 16;24(3):404-414. doi: 10.1016/j.chembiol.2017.02.002. Epub 2017 Feb 23.

18.

In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons.

Chung CY, Khurana V, Yi S, Sahni N, Loh KH, Auluck PK, Baru V, Udeshi ND, Freyzon Y, Carr SA, Hill DE, Vidal M, Ting AY, Lindquist S.

Cell Syst. 2017 Feb 22;4(2):242-250.e4. doi: 10.1016/j.cels.2017.01.002. Epub 2017 Jan 25.

19.

Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts.

Loh KH, Stawski PS, Draycott AS, Udeshi ND, Lehrman EK, Wilton DK, Svinkina T, Deerinck TJ, Ellisman MH, Stevens B, Carr SA, Ting AY.

Cell. 2016 Aug 25;166(5):1295-1307.e21. doi: 10.1016/j.cell.2016.07.041.

20.

Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2.

Hung V, Udeshi ND, Lam SS, Loh KH, Cox KJ, Pedram K, Carr SA, Ting AY.

Nat Protoc. 2016 Mar;11(3):456-75. doi: 10.1038/nprot.2016.018. Epub 2016 Feb 11.

21.

Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase.

Chen CL, Hu Y, Udeshi ND, Lau TY, Wirtz-Peitz F, He L, Ting AY, Carr SA, Perrimon N.

Proc Natl Acad Sci U S A. 2015 Sep 29;112(39):12093-8. doi: 10.1073/pnas.1515623112. Epub 2015 Sep 11.

22.

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):183-188. doi: 10.1038/nature14610. Epub 2015 Jul 1.

23.

Deep, Quantitative Coverage of the Lysine Acetylome Using Novel Anti-acetyl-lysine Antibodies and an Optimized Proteomic Workflow.

Svinkina T, Gu H, Silva JC, Mertins P, Qiao J, Fereshetian S, Jaffe JD, Kuhn E, Udeshi ND, Carr SA.

Mol Cell Proteomics. 2015 Sep;14(9):2429-40. doi: 10.1074/mcp.O114.047555. Epub 2015 May 7.

24.

Building the Connectivity Map of epigenetics: chromatin profiling by quantitative targeted mass spectrometry.

Creech AL, Taylor JE, Maier VK, Wu X, Feeney CM, Udeshi ND, Peach SE, Boehm JS, Lee JT, Carr SA, Jaffe JD.

Methods. 2015 Jan 15;72:57-64. doi: 10.1016/j.ymeth.2014.10.033. Epub 2014 Nov 6.

25.

Prostate cancer. Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer.

Theurillat JP, Udeshi ND, Errington WJ, Svinkina T, Baca SC, Pop M, Wild PJ, Blattner M, Groner AC, Rubin MA, Moch H, Prive GG, Carr SA, Garraway LA.

Science. 2014 Oct 3;346(6205):85-89. doi: 10.1126/science.1250255. Epub 2014 Oct 2.

26.

An unbiased approach to identify endogenous substrates of "histone" deacetylase 8.

Olson DE, Udeshi ND, Wolfson NA, Pitcairn CA, Sullivan ED, Jaffe JD, Svinkina T, Natoli T, Lu X, Paulk J, McCarren P, Wagner FF, Barker D, Howe E, Lazzaro F, Gale JP, Zhang YL, Subramanian A, Fierke CA, Carr SA, Holson EB.

ACS Chem Biol. 2014 Oct 17;9(10):2210-6. doi: 10.1021/cb500492r. Epub 2014 Aug 11.

27.

Proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric APEX tagging.

Hung V, Zou P, Rhee HW, Udeshi ND, Cracan V, Svinkina T, Carr SA, Mootha VK, Ting AY.

Mol Cell. 2014 Jul 17;55(2):332-41. doi: 10.1016/j.molcel.2014.06.003. Epub 2014 Jul 4.

28.

Quantitative-proteomic comparison of alpha and Beta cells to uncover novel targets for lineage reprogramming.

Choudhary A, Hu He K, Mertins P, Udeshi ND, Dančík V, Fomina-Yadlin D, Kubicek S, Clemons PA, Schreiber SL, Carr SA, Wagner BK.

PLoS One. 2014 Apr 23;9(4):e95194. doi: 10.1371/journal.pone.0095194. eCollection 2014.

29.

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, Ebert BL.

Science. 2014 Jan 17;343(6168):301-5. doi: 10.1126/science.1244851. Epub 2013 Nov 29.

30.

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, Mootha VK.

Science. 2013 Dec 13;342(6164):1379-82. doi: 10.1126/science.1242993. Epub 2013 Nov 14.

31.

Large-scale identification of ubiquitination sites by mass spectrometry.

Udeshi ND, Mertins P, Svinkina T, Carr SA.

Nat Protoc. 2013 Oct;8(10):1950-60. doi: 10.1038/nprot.2013.120. Epub 2013 Sep 19.

32.

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.

33.

O-GlcNAc modification of the coat protein of the potyvirus Plum pox virus enhances viral infection.

Pérez Jde J, Udeshi ND, Shabanowitz J, Ciordia S, Juárez S, Scott CL, Olszewski NE, Hunt DF, García JA.

Virology. 2013 Aug 1;442(2):122-31. doi: 10.1016/j.virol.2013.03.029. Epub 2013 Apr 29.

34.

Proteomic mapping of mitochondria in living cells via spatially restricted enzymatic tagging.

Rhee HW, Zou P, Udeshi ND, Martell JD, Mootha VK, Carr SA, Ting AY.

Science. 2013 Mar 15;339(6125):1328-1331. doi: 10.1126/science.1230593. Epub 2013 Jan 31.

35.

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.

36.

Identification and origin of N-linked β-D-N-acetylglucosamine monosaccharide modifications on Arabidopsis proteins.

Kim YC, Jahren N, Stone MD, Udeshi ND, Markowski TW, Witthuhn BA, Shabanowitz J, Hunt DF, Olszewski NE.

Plant Physiol. 2013 Jan;161(1):455-64. doi: 10.1104/pp.112.208900. Epub 2012 Nov 8.

37.

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.

38.

Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules.

Peach SE, Rudomin EL, Udeshi ND, Carr SA, Jaffe JD.

Mol Cell Proteomics. 2012 May;11(5):128-37. doi: 10.1074/mcp.M111.015941. Epub 2012 Mar 21.

39.

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.

40.

O-GlcNAcylation of the Plum pox virus capsid protein catalyzed by SECRET AGENT: characterization of O-GlcNAc sites by electron transfer dissociation mass spectrometry.

Kim YC, Udeshi ND, Balsbaugh JL, Shabanowitz J, Hunt DF, Olszewski NE.

Amino Acids. 2011 Mar;40(3):869-76. doi: 10.1007/s00726-010-0706-0. Epub 2010 Jul 31.

41.

Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.

Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW.

Sci Signal. 2010 Jan 12;3(104):ra2. doi: 10.1126/scisignal.2000526.

42.

Enrichment and site mapping of O-linked N-acetylglucosamine by a combination of chemical/enzymatic tagging, photochemical cleavage, and electron transfer dissociation mass spectrometry.

Wang Z, Udeshi ND, O'Malley M, Shabanowitz J, Hunt DF, Hart GW.

Mol Cell Proteomics. 2010 Jan;9(1):153-60. doi: 10.1074/mcp.M900268-MCP200. Epub 2009 Aug 19.

43.

A PGC-1alpha-O-GlcNAc transferase complex regulates FoxO transcription factor activity in response to glucose.

Housley MP, Udeshi ND, Rodgers JT, Shabanowitz J, Puigserver P, Hunt DF, Hart GW.

J Biol Chem. 2009 Feb 20;284(8):5148-57. doi: 10.1074/jbc.M808890200. Epub 2008 Dec 22.

44.

Methods for analyzing peptides and proteins on a chromatographic timescale by electron-transfer dissociation mass spectrometry.

Udeshi ND, Compton PD, Shabanowitz J, Hunt DF, Rose KL.

Nat Protoc. 2008;3(11):1709-17. doi: 10.1038/nprot.2008.159.

45.

O-GlcNAc regulates FoxO activation in response to glucose.

Housley MP, Rodgers JT, Udeshi ND, Kelly TJ, Shabanowitz J, Hunt DF, Puigserver P, Hart GW.

J Biol Chem. 2008 Jun 13;283(24):16283-92. doi: 10.1074/jbc.M802240200. Epub 2008 Apr 17.

46.

Analysis of proteins and peptides on a chromatographic timescale by electron-transfer dissociation MS.

Udeshi ND, Shabanowitz J, Hunt DF, Rose KL.

FEBS J. 2007 Dec;274(24):6269-76. Epub 2007 Nov 16. Review.

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