recent publications

• academic article

  • Lavallee-Adam, M., Rauniyar, N., McClatchy, D. B., Yates III, J. R. PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data Journal of Proteome Research  2014 13:5496-5509  DOI:10.1021/pr500473n  PMID:25177766  PMCID:PMC4258137
  • Schiapparelli, L. M., McClatchy, D. B., Liu, H. H., Sharma, P., Yates III, J. R., Cline, H. T. Direct detection of biotinylated proteins by mass spectrometry Journal of Proteome Research  2014 13:3966-3978  DOI:10.1021/pr5002862  PMID:25117199  PMCID:PMC4156236
  • Rauniyar, N., McClatchy, D. B., Yates, J. R. Stable isotope labeling of mammals (SILAM) for in vivo quantitative proteomic analysis Methods  2013 61:260-268  DOI:10.1016/j.ymeth.2013.03.008  PMID:23523555
  • Rauniyar, N., Gao, B. B., McClatchy, D. B., Yates, J. R. Comparison of protein expression ratios observed by sixplex and duplex TMT labeling method Journal of Proteome Research  2013 12:1031-1039  DOI:10.1021/pr3008896  PMID:23214967  PMCID:PMC3751587
  • McClatchy, D. B., Liao, L., Lee, J. H., Park, S. K., Yates III, J. R. Dynamics of subcellular proteomes during brain development Journal of Proteome Research  2012 11:2467-2479  DOI:10.1021/pr201176v  PMID:22397461  PMCID:PMC3334332
  • McClatchy, D. B., Liao, L. J., Park, S. K., Xu, T., Lu, B. W., Yates, J. R. Differential proteomic analysis of mammalian tissues using SILAM PLoS One  2011 6:e16039  DOI:10.1371/journal.pone.0016039  PMID:21283754  PMCID:PMC3024400
  • Liao, L. J., McClatchy, D. B., Yates, J. R. Shotgun proteomics in neuroscience Neuron  2009 63:12-26  DOI:10.1016/j.neuron.2009.06.011  PMID:19607789  PMCID:PMC2746002
  • Lu, B., Xu, T., Park, S. K., McClatchy, D. B., Liao, L., Yates, J. R., 3rd Shotgun protein identification and quantification by mass spectrometry in neuroproteomics Methods in Molecular Biology  2009 566:229-259  DOI:10.1007/978-1-59745-562-6_16  PMID:20058176
  • Liao, L. J., McClatchy, D. B., Park, S. K., Xu, T., Lu, B. W., Yates, J. R. Quantitative analysis of brain nuclear phosphoproteins identifies developmentally regulated phosphorylation events Journal of Proteome Research  2008 7:4743-4755  DOI:10.1021/pr8003198  PMID:18823140  PMCID:PMC2659596
  • Lu, B. W., McClatchy, D. B., Kim, J. Y., Yates, J. R. Strategies for shotgun identification of integral membrane proteins by tandem mass spectrometry Proteomics  2008 8:3947-3955  DOI:10.1002/pmic.200800120  PMID:18780349
  • Ruse, C. I., McClatchy, D. B., Lu, B. W., Cociorva, D., Motoyama, A., Park, S. K., Yates, J. R. Motif-specific sampling of phosphoproteomes Journal of Proteome Research  2008 7:2140-2150  DOI:10.1021/pr800147u  PMID:18452278  PMCID:PMC2703005
  • McClatchy, D. B., Yates III, J. R. Stable Isotope Labeling of Mammals (SILAM) CSH Protocols  2008 2008  DOI:10.1101/pdb.prot4940  PMID:21356771
  • McClatchy, D. B., Liao, L. J., Park, S. K., Venable, J. D., Yates, J. R. Quantification of the synaptosomal proteome of the rat cerebellum during post-natal development Genome Research  2007 17:1378-1388  DOI:10.1101/gr.6375007  PMID:17675365  PMCID:PMC1950906
  • Xiao, K., McClatchy, D. B., Shukla, A. K., Zhao, Y., Chen, M., Shenoy, S. K., Yates, J. R., Lefkowitz, R. J. Functional specialization of beta-arrestin interactions revealed by proteomic analysis Proceedings of the National Academy of Sciences of the United States of America  2007 104:12011-12016  DOI:10.1073/pnas.0704849104  PMID:17620599  PMCID:PMC1913545
  • Venable, J. D., Wohlschlegel, J., McClatchy, D. B., Park, S. K., Yates, J. R. Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer Analytical Chemistry  2007 79:3056-3064  DOI:10.1021/ac062054i  PMID:17367114  PMCID:PMC3586273
  • McClatchy, D. B., Dong, M. Q., Wu, C. C., Venable, J. D., Yates, J. R. 15N metabolic labeling of mammalian tissue with slow protein turnover Journal of Proteome Research  2007 6:2005-2010  DOI:10.1021/pr060599n  PMID:17375949  PMCID:PMC2527585