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Items: 34

1.

The Retinal Ganglion Cell Transportome Identifies Proteins Transported to Axons and Presynaptic Compartments in the Visual System In Vivo.

Schiapparelli LM, Shah SH, Ma Y, McClatchy DB, Sharma P, Li J, Yates JR 3rd, Goldberg JL, Cline HT.

Cell Rep. 2019 Aug 13;28(7):1935-1947.e5. doi: 10.1016/j.celrep.2019.07.037.

2.

Proteomics INTegrator (PINT): An Online Tool To Store, Query, and Visualize Large Proteomics Experiment Results.

Martínez-Bartolomé S, Bamberger TC, Lavallée-Adam M, McClatchy DB, Yates JR 3rd.

J Proteome Res. 2019 Aug 2;18(8):2999-3008. doi: 10.1021/acs.jproteome.8b00711. Epub 2019 Jul 1.

PMID:
31260318
3.

From Synapse to Function: A Perspective on the Role of Neuroproteomics in Elucidating Mechanisms of Drug Addiction.

Natividad LA, Buczynski MW, McClatchy DB, Yates JR 3rd.

Proteomes. 2018 Dec 9;6(4). pii: E50. doi: 10.3390/proteomes6040050. Review.

4.

Structural Analysis of Hippocampal Kinase Signal Transduction.

McClatchy DB, Yu NK, Martínez-Bartolomé S, Patel R, Pelletier AR, Lavalle-Adam M, Powell SB, Roberto M, Yates JR.

ACS Chem Neurosci. 2018 Dec 19;9(12):3072-3085. doi: 10.1021/acschemneuro.8b00284. Epub 2018 Aug 13.

5.

Quantitative analysis of newly synthesized proteins.

Ma Y, McClatchy DB, Barkallah S, Wood WW, Yates JR 3rd.

Nat Protoc. 2018 Aug;13(8):1744-1762. doi: 10.1038/s41596-018-0012-y.

PMID:
30038347
6.

Quantitative temporal analysis of protein dynamics in cardiac remodeling.

McClatchy DB, Ma Y, Liem DA, Ng DCM, Ping P, Yates JR 3rd.

J Mol Cell Cardiol. 2018 Aug;121:163-172. doi: 10.1016/j.yjmcc.2018.07.126. Epub 2018 Jul 19.

7.

Role of the visual experience-dependent nascent proteome in neuronal plasticity.

Liu HH, McClatchy DB, Schiapparelli L, Shen W, Yates JR 3rd, Cline HT.

Elife. 2018 Feb 7;7. pii: e33420. doi: 10.7554/eLife.33420.

8.

Amyloid Accumulation Drives Proteome-wide Alterations in Mouse Models of Alzheimer's Disease-like Pathology.

Savas JN, Wang YZ, DeNardo LA, Martinez-Bartolome S, McClatchy DB, Hark TJ, Shanks NF, Cozzolino KA, Lavallée-Adam M, Smukowski SN, Park SK, Kelly JW, Koo EH, Nakagawa T, Masliah E, Ghosh A, Yates JR 3rd.

Cell Rep. 2017 Nov 28;21(9):2614-2627. doi: 10.1016/j.celrep.2017.11.009.

9.

S-Nitrosylation of PINK1 Attenuates PINK1/Parkin-Dependent Mitophagy in hiPSC-Based Parkinson's Disease Models.

Oh CK, Sultan A, Platzer J, Dolatabadi N, Soldner F, McClatchy DB, Diedrich JK, Yates JR 3rd, Ambasudhan R, Nakamura T, Jaenisch R, Lipton SA.

Cell Rep. 2017 Nov 21;21(8):2171-2182. doi: 10.1016/j.celrep.2017.10.068.

10.

HILAQ: A Novel Strategy for Newly Synthesized Protein Quantification.

Ma Y, McClatchy DB, Barkallah S, Wood WW, Yates JR 3rd.

J Proteome Res. 2017 Jun 2;16(6):2213-2220. doi: 10.1021/acs.jproteome.7b00005. Epub 2017 May 3.

11.

Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver-Specific LKB1 Knockout Mice.

McClatchy DB, Ma Y, Liu C, Stein BD, Martínez-Bartolomé S, Vasquez D, Hellberg K, Shaw RJ, Yates JR 3rd.

J Proteome Res. 2015 Nov 6;14(11):4815-22. doi: 10.1021/acs.jproteome.5b00653. Epub 2015 Oct 26.

12.

Global quantitative analysis of phosphorylation underlying phencyclidine signaling and sensorimotor gating in the prefrontal cortex.

McClatchy DB, Savas JN, Martínez-Bartolomé S, Park SK, Maher P, Powell SB, Yates JR 3rd.

Mol Psychiatry. 2016 Feb;21(2):205-15. doi: 10.1038/mp.2015.41. Epub 2015 Apr 14.

13.

PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data.

Lavallée-Adam M, Rauniyar N, McClatchy DB, Yates JR 3rd.

J Proteome Res. 2014 Dec 5;13(12):5496-509. doi: 10.1021/pr500473n. Epub 2014 Oct 16.

14.

Direct detection of biotinylated proteins by mass spectrometry.

Schiapparelli LM, McClatchy DB, Liu HH, Sharma P, Yates JR 3rd, Cline HT.

J Proteome Res. 2014 Sep 5;13(9):3966-78. doi: 10.1021/pr5002862. Epub 2014 Aug 25.

15.

Stable isotope labeling in mammals (SILAM).

McClatchy DB, Yates JR 3rd.

Methods Mol Biol. 2014;1156:133-46. doi: 10.1007/978-1-4939-0685-7_8.

PMID:
24791985
16.

Census 2: isobaric labeling data analysis.

Park SK, Aslanian A, McClatchy DB, Han X, Shah H, Singh M, Rauniyar N, Moresco JJ, Pinto AF, Diedrich JK, Delahunty C, Yates JR 3rd.

Bioinformatics. 2014 Aug 1;30(15):2208-9. doi: 10.1093/bioinformatics/btu151. Epub 2014 Mar 28.

17.

Stable isotope labeling of mammals (SILAM) for in vivo quantitative proteomic analysis.

Rauniyar N, McClatchy DB, Yates JR 3rd.

Methods. 2013 Jun 15;61(3):260-8. doi: 10.1016/j.ymeth.2013.03.008. Epub 2013 Mar 20.

PMID:
23523555
18.

Comparison of protein expression ratios observed by sixplex and duplex TMT labeling method.

Rauniyar N, Gao B, McClatchy DB, Yates JR 3rd.

J Proteome Res. 2013 Feb 1;12(2):1031-9. doi: 10.1021/pr3008896. Epub 2012 Dec 24.

19.

Dynamics of subcellular proteomes during brain development.

McClatchy DB, Liao L, Lee JH, Park SK, Yates JR 3rd.

J Proteome Res. 2012 Apr 6;11(4):2467-79. doi: 10.1021/pr201176v. Epub 2012 Mar 26.

20.

Differential proteomic analysis of mammalian tissues using SILAM.

McClatchy DB, Liao L, Park SK, Xu T, Lu B, Yates Iii JR.

PLoS One. 2011 Jan 20;6(1):e16039. doi: 10.1371/journal.pone.0016039.

21.

Shotgun protein identification and quantification by mass spectrometry in neuroproteomics.

Lu B, Xu T, Park SK, McClatchy DB, Liao L, Yates JR 3rd.

Methods Mol Biol. 2009;566:229-59. doi: 10.1007/978-1-59745-562-6_16.

PMID:
20058176
22.

Shotgun proteomics in neuroscience.

Liao L, McClatchy DB, Yates JR.

Neuron. 2009 Jul 16;63(1):12-26. doi: 10.1016/j.neuron.2009.06.011.

23.

Quantitative analysis of brain nuclear phosphoproteins identifies developmentally regulated phosphorylation events.

Liao L, McClatchy DB, Park SK, Xu T, Lu B, Yates JR 3rd.

J Proteome Res. 2008 Nov;7(11):4743-55. doi: 10.1021/pr8003198. Epub 2008 Sep 30.

24.

Strategies for shotgun identification of integral membrane proteins by tandem mass spectrometry.

Lu B, McClatchy DB, Kim JY, Yates JR 3rd.

Proteomics. 2008 Oct;8(19):3947-55. doi: 10.1002/pmic.200800120. Review.

PMID:
18780349
25.

Motif-specific sampling of phosphoproteomes.

Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd.

J Proteome Res. 2008 May;7(5):2140-50. doi: 10.1021/pr800147u.

26.

Stable Isotope Labeling of Mammals (SILAM).

McClatchy DB, Yates JR 3rd.

CSH Protoc. 2008 Feb 1;2008:pdb.prot4940. doi: 10.1101/pdb.prot4940.

PMID:
21356771
27.

Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development.

McClatchy DB, Liao L, Park SK, Venable JD, Yates JR.

Genome Res. 2007 Sep;17(9):1378-88. Epub 2007 Aug 3.

28.

Functional specialization of beta-arrestin interactions revealed by proteomic analysis.

Xiao K, McClatchy DB, Shukla AK, Zhao Y, Chen M, Shenoy SK, Yates JR 3rd, Lefkowitz RJ.

Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12011-6. Epub 2007 Jul 9.

29.

15N metabolic labeling of mammalian tissue with slow protein turnover.

McClatchy DB, Dong MQ, Wu CC, Venable JD, Yates JR 3rd.

J Proteome Res. 2007 May;6(5):2005-10. Epub 2007 Mar 22.

30.

Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer.

Venable JD, Wohlschlegel J, McClatchy DB, Park SK, Yates JR 3rd.

Anal Chem. 2007 Apr 15;79(8):3056-64. Epub 2007 Mar 17.

31.

Elongation factor 1A family regulates the recycling of the M4 muscarinic acetylcholine receptor.

McClatchy DB, Fang G, Levey AI.

Neurochem Res. 2006 Jul;31(7):975-88. Epub 2006 Jul 15.

PMID:
16845586
32.

The dynamic relationship between mu and kappa opioid receptors in body temperature regulation.

Chen X, McClatchy DB, Geller EB, Tallarida RJ, Adler MW.

Life Sci. 2005 Dec 12;78(4):329-33. Epub 2005 Oct 28.

PMID:
16257420
33.

Novel interaction between the M4 muscarinic acetylcholine receptor and elongation factor 1A2.

McClatchy DB, Knudsen CR, Clark BF, Kahn RA, Hall RA, Levey AI.

J Biol Chem. 2002 Aug 9;277(32):29268-74. Epub 2002 Jun 4.

34.

Possible mechanism of hypothermia induced by intracerebroventricular injection of orphanin FQ/nociceptin.

Chen X, McClatchy DB, Geller EB, Liu-Chen L, Tallarida RJ, Adler MW.

Brain Res. 2001 Jun 22;904(2):252-8.

PMID:
11406123

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