421  Sung Kyu Park, John D Venable, Tao Xu, John R Yates III, A quantitative analysis software tool for mass spectrometry.based proteomics., Nature Methods, Mar. 2008

420  Lu B, Motoyama A, Ruse C, Venable J, Yates JR 3rd., Improving protein identification sensitivity by combining MS and MS/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data, Anal Chem. 2008 Mar 15;80(6):2018-25


419  Ashe M, de Bruin RA, Kalashnikova T, McDonald WH, Yates JR 3rd, Wittenberg C., The SBF- and MBF-associated protein Msa1 is required for proper timing of G1-specific transcription in Saccharomyces cerevisiae, J Biol Chem. 2008 Mar 7;283(10):6040-9


418  Dentin R, Hedrick S, Xie J, Yates J 3rd, Montminy M., Hepatic glucose sensing via the CREB coactivator CRTC2, Science. 2008 Mar 7;319(5868):1402-5


417  Diop SB, Bertaux K, Vasanthi D, Sarkeshik A, Goirand B, Aragnol D, Tolwinski NS, Cole MD, Pradel J, Yates JR 3rd, Mishra RK, Graba Y, Saurin AJ, Reptin and Pontin function antagonistically with PcG and TrxG complexes to mediate Hox gene control, EMBO Rep. 2008 Mar;9(3):260-6.


416  Cantin GT, Yi W, Lu B, Park SK, Xu T, Lee JD, Yates JR 3rd, Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis, J Proteome Res. 2008 Mar;7(3):1346-51

415  Chiranand W, McLeod I, Zhou H, Lynn JJ, Vega LA, Myers H, Yates JR 3rd, Lorenz, MC, Gustin MC., CTA4 transcription factor mediates induction of nitrosative stress response in Candida albicans, Eukaryot Cell. 2008 Feb;7(2):268-78


414  Romijn EP, Yates JR 3rd., Analysis of organelles by on-line two-dimensional liquid chromatography-tandem mass spectrometry, Methods Mol Biol. 2008;432:1-16


413  Cravatt BF, Simon GM, Yates JR 3rd., The biological impact of mass-spectrometry-based proteomics, Nature. 2007 Dec 13;450(7172):991-1000.


412  Zhang L, Ding L, Cheung TH, Dong MQ, Chen J, Sewell AK, Liu X, Yates JR 3rd, Han M., Systematic identification of C. elegans miRISC proteins, miRNAs, and mRNA targets by their interactions with GW182 proteins AIN-1 and AIN-2, Mol Cell. 2007 Nov 30;28(4):598-613


411  Delahunty CM, Yates JR 3rd., MudPIT: multidimensional protein identification technology, Biotechniques. 2007 Nov;43(5):563, 565, 567 passim


410  Ahrendt AJ, Tollaksen SL, Lindberg C, Zhu W, Yates JR 3rd, Nevin KP, Babnigg G, Lovley DR, Giometti CS., Steady state protein levels in Geobacter metallireducens grown with iron (III) citrate or nitrate as terminal electron acceptor, Proteomics. 2007 Nov;7(22):4148-57

409  Cass CL, Johnson JR, Califf LL, Xu T, Hernandez HJ, Stadecker MJ, Yates JR 3rd, Williams DL., Proteomic analysis of Schistosoma mansoni egg secretions. Mol Biochem Parasitol. 2007 Oct;155(2):84-93.


407  Lunn ML, Nassirpour R, Arrabit C, Tan J, McLeod I, Arias CM, Sawchenko PE, Yates JR 3rd, Slesinger PA., A unique sorting nexin regulates trafficking of potassium channels via a PDZ domain interaction., Nat Neurosci. 2007 Oct;10(10):1249-59. Epub 2007 Sep 2.


406  Wong CC, Xu T, Rai R, Bailey AO, Yates JR 3rd, Wolf YI, Zebroski H, Kashina A., Global analysis of posttranslational protein arginylation., PLoS Biol. 2007 Oct;5(10):e258.


405  Rexroth S, Wong CC, Park JH, Yates JR 3rd, Barry BA., An activated glutamate residue identified in photosystem II at the interface between the manganese-stabilizing subunit and the D2 polypeptide, J Biol Chem. 2007 Sep 21;282(38):27802-9. Epub 2007 Jul 31.

403  Dentin R, Liu Y, Koo SH, Hedrick S, Vargas T, Heredia J, Yates J 3rd, Montminy, M., Insulin modulates gluconeogenesis by inhibition of the coactivator TORC2., Nature. 2007 Sep 20;449(7160):366-9.


401  Kilburn CL, Pearson CG, Romijn EP, Meehl JB, Giddings TH Jr, Culver BP, Yates JR 3rd, Winey M., New Tetrahymena basal body protein components identify basal body domain structure., J Cell Biol. 2007 Sep 10;178(6):905-12


399  McClatchy DB, Liao L, Park SK, Venable JD, Yates JR., Quantification of the synaptosomal proteome of the rat cerebellum during Genome Res. 2007 Sep;17(9):1378-88.


398  Chen EI, Yates JR., Cancer Proteomics by Quantitative Shotgun Proteomics., Mol Oncol. 2007 Sep;1(2):144-159.


397  Bailey AO, Miller TM, Dong MQ, Vande Velde C, Cleveland DW, Yates JR., RCADiA: simple automation platform for comparative multidimensional protein identification technology., Anal Chem. 2007 Aug 15;79(16):6410-8.


396  Dong MQ, Venable JD, Au N, Xu T, Park SK, Cociorva D, Johnson JR, Dillin A, Yates JR 3rd., Quantitative mass spectrometry identifies insulin signaling targets in C. elegans., Science. 2007 Aug 3;317(5838):660-3.

395  Sanders PR, Cantin GT, Greenbaum DC, Gilson PR, Nebl T, Moritz RL, Yates JR 3rd, Hodder AN, Crabb BS., Identification of protein complexes in detergent-resistant membranes of Plasmodium falciparum schizonts., Mol Biochem Parasitol. 2007 Aug;154(2):148-57.


394  Aronova S, Wedaman K, Anderson S, Yates J 3rd, Powers T., Probing the membrane environment of the TOR kinases reveals functional interactions between TORC1, actin, and membrane trafficking in Saccharomyces cerevisiae., Mol Biol Cell. 2007 Aug;18(8):2779-94.


393  Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H., The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol. 2007 Aug;25(8):887-93. Review.


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


391  Lefkowitz RJ., Functional specialization of beta-arrestin interactions revealed by proteomic analysis. Proc Natl Acad Sci U S A. 2007 Jul 17;104(29):12011-6. Epub 2007 Jul 9.


390  Jung P, Verdoodt B, Bailey A, Yates JR 3rd, Menssen A, Hermeking H. Induction of cullin 7 by DNA damage attenuates p53 function. Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11388-93. Epub 2007 Jun 22.

389  Chen EI, Cociorva D, Norris JL, Yates JR 3rd. Optimization of mass spectrometry-compatible surfactants for shotgun proteomics. J Proteome Res. 2007 Jul;6(7):2529-38. Epub 2007 May 27.


388  Ravnskjaer K, Kester H, Liu Y, Zhang X, Lee D, Yates JR 3rd, Montminy M. Cooperative interactions between CBP and TORC2 confer selectivity to CREB target gene expression. EMBO J. 2007 Jun 20;26(12):2880-9. Epub 2007 May 3.


387  Cantin GT, Shock TR, Park SK, Madhani HD, Yates JR 3rd. Optimizing TiO2-based phosphopeptide enrichment for automated multidimensional liquid chromatography coupled to tandem mass spectrometry. Anal Chem. 2007 Jun 15;79(12):4666-73. Epub 2007 May 25.


386  Efimov A, Kharitonov A, Efimova N, Loncarek J, Miller PM, Andreyeva N, Gleeson P, Galjart N, Maia AR, McLeod IX, Yates JR 3rd, Maiato H, Khodjakov A, Akhmanova A, Kaverina I. Asymmetric CLASP-dependent nucleation of noncentrosomal microtubules at the trans-Golgi network. Dev Cell. 2007 Jun;12(6):917-30.


385  O\'Neill BM, Szyjka SJ, Lis ET, Bailey AO, Yates JR 3rd, Aparicio OM, Romesberg FE. Pph3-Psy2 is a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage. Proc Natl Acad Sci U S A. 2007 May 29;104(22):9290-5. Epub 2007 May 21.


384  Motoyama A, Xu T, Ruse CI, Wohlschlegel JA, Yates JR 3rd. Anion and cation mixed-bed ion exchange for enhanced multidimensional separations of peptides and phosphopeptides. Anal Chem. 2007 May 15;79(10):3623-34. Epub 2007 Apr 6.

383  McClatchy DB, Dong MQ, Wu CC, Venable JD, Yates JR 3rd. 15N metabolic labeling of mammalian tissue with slow protein turnover. J Proteome Res. 2007 May;6(5):2005-10. Epub 2007 Mar 22. McCusker D, Denison C, Anderson S, Egelhofer TA, Yates JR 3rd, Gygi SP, Kellogg DR. Cdk1 coordinates cell-surface growth with the cell cycle. Nat Cell Biol. 2007 May;9(5):506-15. Epub 2007 Apr 8.


382  Venable JD, Wohlschlegel J, McClatchy DB, Park SK, Yates JR 3rd. Relative quantification of stable isotope labeled peptides using a linear ion trap-Orbitrap hybrid mass spectrometer. Anal Chem. 2007 Apr 15;79(8):3056-64. Epub 2007 Mar 17.


381  Liao L, Pilotte J, Xu T, Wong CC, Edelman GM, Vanderklish P, Yates JR 3rd. BDNF induces widespread changes in synaptic protein content and up-regulates components of the translation machinery: an analysis using high-throughput proteomics. J Proteome Res. 2007 Mar;6(3):1059-71.


380  Lu B, Ruse C, Xu T, Park SK, Yates J 3rd. Automatic validation of phosphopeptide identifications from tandem mass spectra. Anal Chem. 2007 Feb 15;79(4):1301-10.


379  Chen EI, Hewel J, Krueger JS, Tiraby C, Weber MR, Kralli A, Becker K, Yates JR 3rd, Felding-Habermann B. Adaptation of energy metabolism in breast cancer brain metastases. Cancer Res. 2007 Feb 15;67(4):1472-86.


378  Toshima J, Toshima JY, Duncan MC, Cope MJ, Sun Y, Martin AC, Anderson S, Yates JR 3rd, Mizuno K, Drubin DG. Negative regulation of yeast Eps15-like Arp2/3 complex activator, Pan1p, by the Hip1R-related protein, Sla2p, during endocytosis. Mol Biol Cell. 2007 Feb;18(2):658-68. Epub 2006 Dec 6.

377  Sun P, Yoshizuka N, New L, Moser BA, Li Y, Liao R, Xie C, Chen J, Deng Q, Yamout M, Dong MQ, Frangou CG, Yates JR 3rd, Wright PE, Han J. PRAK is essential for ras-induced senescence and tumor suppression. Cell. 2007 Jan 26;128(2):295-308.


376  Koch HB, Zhang R, Verdoodt B, Bailey A, Zhang CD, Yates JR 3rd, Menssen A, Hermeking H. Large-scale identification of c-MYC-associated proteins using a combined TAP/MudPIT approach. Cell Cycle. 2007 Jan 15;6(2):205-17. Epub 2007 Jan 20.


375  Schlaitz AL, Srayko M, Dammermann A, Quintin S, Wielsch N, MacLeod I, deRobillard Q, Zinke A, Yates JR 3rd, MüReichert T, Shevchenko A, Oegema K, Hyman AA. The C. elegans RSA complex localizes protein phosphatase 2A to centrosomes and regulates mitotic spindle assembly. Cell. 2007 Jan 12;128(1):115-27.


374  Cociorva D, L Tabb D, Yates JR. Validation of tandem mass spectrometry database search results using DTASelect. Curr Protoc Bioinformatics. 2007 Jan;Chapter 13:Unit 13.4.


373  Min J, Kyung Kim Y, Cipriani PG, Kang M, Khersonsky SM, Walsh DP, Lee JY, Niessen S, Yates JR 3rd, Gunsalus K, Piano F, Chang YT. Forward chemical genetic approach identifies new role for GAPDH in insulin signaling. Nat Chem Biol. 2007 Jan;3(1):55-9. Epub 2006 Nov 19.


372  Sandall S, Severin F, McLeod IX, Yates JR 3rd, Oegema K, Hyman A, Desai A. A Bir1-Sli15 complex connects centromeres to microtubules and is required to sense kinetochore tension. Cell. 2006 Dec 15;127(6):1179-91.

371  Varsano T, Dong MQ, Niesman I, Gacula H, Lou X, Ma T, Testa JR, Yates JR 3rd, Farquhar MG. GIPC is recruited by APPL to peripheral TrkA endosomes and regulates TrkA trafficking and signaling. Mol Cell Biol. 2006 Dec;26(23):8942-52. Epub 2006 Oct 2.


370  Monzo K, Papoulas O, Cantin GT, Wang Y, Yates JR 3rd, Sisson JC. Fragile X mental retardation protein controls trailer hitch expression and cleavage furrow formation in Drosophila embryos. Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18160-5. Epub 2006 Nov 16.


369  Wang X, Venable J, LaPointe P, Hutt DM, Koulov AV, Coppinger J, Gurkan C, Kellner W, Matteson J, Plutner H, Riordan JR, Kelly JW, Yates JR 3rd, Balch WE. Hsp90 cochaperone Aha1 downregulation rescues misfolding of CFTR in cystic fibrosis. Cell. 2006 Nov 17;127(4):803-15.


368  Bashkirova EV, Yates JR 3rd, Heyer WD. Phosphorylation of Rad55 on serines 2, 8, and 14 is required for efficient homologous recombination in the recovery of stalled replication forks. Mol Cell Biol. 2006 Nov;26(22):8396-409. Epub 2006 Sep 11.


367  Sedgwick C, Rawluk M, Decesare J, Raithatha S, Wohlschlegel J, Semchuk P, Ellison M, Yates J 3rd, Stuart D. Saccharomyces cerevisiae Ime2 phosphorylates Sic1 at multiple PXS/T sites but is insufficient to trigger Sic1 degradation. Biochem J. 2006 Oct 1;399(1):151-60.


366  Raffa GD, Wohlschlegel J, Yates JR 3rd, Boddy MN. SUMO-binding motifs mediate the Rad60-dependent response to replicative stress and self-association. J Biol Chem. 2006 Sep 22;281(38):27973-81. Epub 2006 Jul 31.

365  Chu DS, Liu H, Nix P, Wu TF, Ralston EJ, Yates JR 3rd, Meyer BJ. Sperm chromatin proteomics identifies evolutionarily conserved fertility factors. Nature. 2006 Sep 7;443(7107):101-5. Epub 2006 Aug 30.


364  Rosenberg JA, Tomlin GC, McDonald WH, Snydsman BE, Muller EG, Yates JR 3rd, Gould KL. Ppc89 links multiple proteins, including the septation initiation network, to the core of the fission yeast spindle-pole body. Mol Biol Cell. 2006 Sep;17(9):3793-805. Epub 2006 Jun 14.


363  Ruse C, Niessen S, Yates JR 3rd, Muller EG, Bloom K, Odde DJ, Davis TN. Mps1 phosphorylation of Dam1 couples kinetochores to microtubule plus ends at metaphase. Curr Biol. 2006 Aug 8;16(15):1489-501.


362  de Bruin RA, Kalashnikova TI, Chahwan C, McDonald WH, Wohlschlegel J, Yates J 3rd, Russell P, Wittenberg C. Constraining G1-specific transcription to late G1 phase: the MBF-associated corepressor Nrm1 acts via negative feedback. Mol Cell. 2006 Aug;23(4):483-96.


361  Motoyama A, Venable JD, Ruse CI, Yates JR 3rd. Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. Anal Chem. 2006 Jul 15;78(14):5109-18.


360  Karakozova M, Kozak M, Wong CC, Bailey AO, Yates JR 3rd, Mogilner A, Zebroski H, Kashina A. Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science. 2006 Jul 14;313(5784):192-6. Epub 2006 Jun 22.

359  De Craene JO, Coleman J, Estrada de Martin P, Pypaert M, Anderson S, Yates JR 3rd, Ferro-Novick S, Novick P. Rtn1p is involved in structuring the cortical endoplasmic reticulum. Mol Biol Cell. 2006 Jul;17(7):3009-20. Epub 2006 Apr 19.


358  Harashima T, Anderson S, Yates JR 3rd, Heitman J. The kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with the yeast RasGAP neurofibromin homologs Ira1 and Ira2. Mol Cell. 2006 Jun 23;22(6):819-30.


357  Roth AF, Wan J, Bailey AO, Sun B, Kuchar JA, Green WN, Phinney BS, Yates JR 3rd, Davis NG. Global analysis of protein palmitoylation in yeast. Cell. 2006 Jun 2;125(5):1003-13.


356  Okada M, Cheeseman IM, Hori T, Okawa K, McLeod IX, Yates JR 3rd, Desai A, Fukagawa T. The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres. Nat Cell Biol. 2006 May;8(5):446-57. Epub 2006 Apr 16.


355  Foltz DR, Jansen LE, Black BE, Bailey AO, Yates JR 3rd, Cleveland DW. The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol. 2006 May;8(5):458-69. Epub 2006 Apr 16.


354  Wohlschlegel JA, Johnson ES, Reed SI, Yates JR 3rd. Improved identification of SUMO attachment sites using C-terminal SUMO mutants and tailored protease digestion strategies. J Proteome Res. 2006 Apr;5(4):761-70.

353  Kim S, Sorescu DC, Byl O, Yates JT Jr. Perturbation of adsorbed CO by amine derivatives coadsorbed on the gamma-Al2O3 surface: FTIR and first principles studies. J Phys Chem B. 2006 Mar 16;110(10):4742-50.


352  Venable JD, Xu T, Cociorva D, Yates JR 3rd. Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra. Anal Chem. 2006 Mar 15;78(6):1921-9.


351  MartíV, Rodríez-Gabriel MA, McDonald WH, Watt S, Yates JR 3rd, Bäer J, RussellP. Cip1 and Cip2 are novel RNA-recognition-motif proteins that counteract Csx1 function during oxidative stress. Mol Biol Cell. 2006 Mar;17(3):1176-83. Epub 2006 Jan 11.


350  Widlund PO, Lyssand JS, Anderson S, Niessen S, Yates JR 3rd, Davis TN. Phosphorylation of the chromosomal passenger protein Bir1 is required for localization of Ndc10 to the spindle during anaphase and full spindle elongation. Mol Biol Cell. 2006 Mar;17(3):1065-74. Epub 2005 Dec 28.


349  Pebernard S, Wohlschlegel J, McDonald WH, Yates JR 3rd, Boddy MN. The Nse5-Nse6 dimer mediates DNA repair roles of the Smc5-Smc6 complex. Mol Cell Biol. 2006 Mar;26(5):1617-30. Erratum in: Mol Cell Biol. 2006 Apr;26(8):3336.


348  Cao H, Deterding LJ, Venable JD, Kennington EA, Yates JR 3rd, Tomer KB, Blackshear PJ. Identification of the anti-inflammatory protein tristetraprolin as a hyperphosphorylated protein by mass spectrometry and site-directed mutagenesis. Biochem J. 2006 Feb 15;394(Pt 1):285-97.

347  Guelman S, Suganuma T, Florens L, Swanson SK, Kiesecker CL, Kusch T, Anderson S, Yates JR 3rd, Washburn MP, Abmayr SM, Workman JL. Host cell factor and an uncharacterized SANT domain protein are stable components of ATAC, a novel dAda2A/dGcn5-containing histone acetyltransferase complex in Drosophila. Mol Cell Biol. 2006 Feb;26(3):871-82.


346  DR, Harding S, Mitani S, Ruvkun G, Yates JR 3rd, Mello CC. Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways. Cell. 2006 Jan 27;124(2):343-54.


345  Lé S, Zhang L, McDonald WH, Yates J 3rd, Cregg JM, Subramani S. Dynamics of the peroxisomal import cycle of PpPex20p: ubiquitin-dependent localization and regulation. J Cell Biol. 2006 Jan 2;172(1):67-78.


344  Sadygov R, Wohlschlegel J, Park SK, Xu T, Yates JR 3rd. Central limit theorem as an approximation for intensity-based scoring function. Anal Chem. 2006 Jan 1;78(1):89-95.187:


343  Daniel Cociorva, David Tabb, and John R. Yates, III, Validation of Tandem Mass Spectrometry Database earch Results using DTASelect, Current Protocols in Bioinformatics 13.4.1-13.4.14, supplement 16, (2006), John Wiley and Sons,


342  Chen EI, Yates JR., Maspin and tumor metastasis., IUBMB Life. 2006, 58, 25-9.

341  De Craene JO, Coleman J, Estrada de Martin P, Pypaert M, Anderson S, Yates JR 3rd, Ferro-Novick S, Novick P., Rtn1p is involved in structuring the cortical endoplasmic reticulum., Mol Biol Cell. 2006, 17, 3009-20.


340  Martin V, Chahwan C, Gao H, Blais V, Wohlschlegel J, Yates JR 3rd, McGowan CH, Russell P. Sws1 is a conserved regulator of homologous recombination in eukaryotic cells., EMBO J. 2006, 25, 2564-74.


339  Krishnamurthy T, Hewel J, Bonzagni NJ, Dabbs J, Bull RL, Yates JR 3rd., Simultaneous identification and verification of Bacillus anthracis., Rapid Commun Mass Spectrom. 2006, 20, 2053-6.


338  Raffa GD, Wohlschlegel J, Yates JR 3rd, Boddy MN., SUMO-binding motifs mediate the Rad60-dependent response to replicative stress and self-association., J Biol Chem. 2006, 281, 27973-81.


337  Varsano T, Dong MQ, Niesman I, Gacula H, Lou X, Ma T, Testa JR, Yates JR 3rd, Farquhar MG., GIPC is recruited by APPL to Peripheral TrkA Endosomes and Regulates TrkA Trafficking and Signaling., Mol Cell Biol. 2006 Oct 2;


336  Roth AF, Wan J, Green WN, Yates JR, Davis NG., Proteomic identification of palmitoylated proteins., Methods. 2006, 40, 135-42.

335  Emily I. Chen, Johannes Hewel, Joseph S. Krueger, Martin R. Weber, Claire Tiraby, Anastasia Kralli, Katja Becker, John .R. III Yates, and Brunhilde Felding-Habermann, Adaptation of Energy Metabolism in Breast Cancer Brain Metastases, Cancer Research


334  John D. Venable1, James Wohlschlegel1, Dan McClatchy, Sung Kyu Park and John R. Yates III*, Relative Quantification of Stable Isotope Labeled Peptides Using a Linear Ion Trap-Orbitrap Hybrid Mass Spectrometer, Analytical Chemistry


333  Kate Monzo, Ophelia Papoulas, Greg T. Cantin, John R. Yates, III, John C. Sisson, Fragile X mental retardation protein controls trailer hitch expression and cleavage furrow formation in Drosophila embryos, Proc. Natl. Acad. Sci. USA


332  Aaron O. Bailey 1, Timothy M. Miller 2, Don W. Cleveland 2, John R. Yates 1*, RCADIA: Simple Automation Platform For Comparative Multidimensional Protein Identification (Mudpit), Analytical Chemistry


331  Greg T. Cantin1, Teresa R. Shock2, Sung Kyu Park1, Hiten D. Madhani2, and John R. Yates III1*, Optimizing TiO2-based phosphopeptide enrichment for automated multidimensional liquid chromatography coupled to tandem mass spectrometry, Analytical Chemistry


330  Sharsti Sandall; Fedor Severin, Ian X McLeod, John R Yates 3rd, Karen Oegema, Anthony A Hyman, Arshad Desai, A Complex of Sli15-Bir1 (INCENP-Survivin) Connects Centromeres to Microtubules and is the Likely Tension Sensor Controlling Aurora B Activation, Cell (in press)

329  Derek McCusker1, Carilee Denison2, Scott Anderson3, Thea Egelhofer1, John Yates 3rd3, Steve Gygi2 and Douglas Kellogg1, Cdk1 coordinates cell surface growth with the cell cycle


328  Zee-Yong Park1, Rovshan Sadygov2, Judy M. Clark3, John I. Clark3, and John R. Yates, III4, Assigning In vivo Carbamylation and Acetylation In Human Lens Proteins using Tandem Mass Spectrometry and Database Searching, International Journal of Mass Spectrometry (in press)


327  Bingwen Lu1, Cristian Ruse1, Tao Xu, Sung Kyu Park, John Yates III*, Automatic Validation of Phosphopeptide Identifications from Tandem Mass Spectra, Analytical Chemistry


326  Angela J. Ahrendt1, Sandra L. Tollaksen1, Carl Lindberg1, Wenhong Zhu2, John R. Yates III2, Kelly P. Nevin3, Derek Lovley3, and Carol S. Giometti1*, Differential Protein Expression in the Metal-Reducing Bacterium Geobacter metallireducens Grown with Fe(III) Citrate or Nitrate, Applied and Environmental Microbiology


325  Bern, M., Goldberg, D., McDonald, W. H., Yates, J. R., III, Automatic quality assessment of Peptide tandem mass spectra, Bioinformatics, 20 Suppl 1, I49-I54 (2004)


324  Anne-Lore Schlaitz, Martin Srayko, Alexander Dammermann, Sophie Quintin, Natalie Schmalz, Ian MacLeod, Andrea Zinke, John R. Yates III, Andrei Shevchenko, Karen Oegema, Anthony A. Hyman, The RSA protein complex targets Protein Phosphatase 2A to centrosomes and regulates mitotic spindle assembly in Caenorhabditis elegans embryos, Cell

323  Azarian SM, McLeod I, Lillo C, Gibbs D, Yates JR, Williams DS. Related Articles, Links Proteomic analysis of mature melanosomes from the retinal pigmented epithelium. J Proteome Res. 2006, 5, 521-9


322  Daniel R. Foltz, Lars E.T. Jansen, Ben E. Black, Aaron O Bailey, John R. Yates III and Don W. Cleveland, The human CENP-A centromeric nucleosome associated Complex, Nature Cell Biology 2006, 8, 458-69


321  Chantelle Sedgwick, James DeCesare, Matthew Rawluk, Sheetal Raithatha, James Wohlschlegel, Paul Semchuck, Michael Ellison, John Yates III, and David Stuart, Saccharomyces cerevisiae Ime2 phosphorylates Sic1 at multiple PXS/T sites but is insufficient to trigger Sic1 degradation, Biochemical Journal (in press)


320  Bryan M. O Neill, Shawn J. Szyjka, Ewa T. Lis, Aaron O. Bailey, John R. Yates III, Oscar M. Aparicio & Floyd E. Romesberg, Psy2 and Pph3 form a Rad53 phosphatase complex that promotes restart of arrested replication forks, PNAS (in press)


319  Akira Motoyama, John D. Venable, Cristian I. Ruse, and John R. Yates, III, Automated Ultra-high Pressure Multidimensional Protein Identification Technology (MudPIT) for Improved Peptide Identification of Proteomic Samples, Analytical Chemistry 2006, 78, 5109-18

318  Jeffrey R. Johnson, Greg T. Cantin, Bingwen Lu, John D. Venable, Daniel Cociorva, John R. Yates, Reference Library Searching Strategies in Proteomics, Analytical Chemistry (in press)


317  Karine G. Le Roch, Jeffrey R. Johnson, Hugues Ahiboh, David Plouffe, Kerstin Henson, Yingyao Zhou, Choukri Ben Mamoun, John R. Yates, Henri Vial and Elizabeth A. Winzeler. Mode of action of the antimalarial drug T4 revealed by systematic profiling of Plasmodium falciparum Genome Biology


316  Yates JR, Cociorva D, Liao L, Zabrouskov V., Performance of a linear ion trap-Orbitrap hybrid for peptide analysis. Analytical Chemistry 78, 493-500 (2006)


315  Pebernard S, Wohlschlegel J, McDonald WH, Yates JR 3rd, Boddy MN. The nse5-nse6 dimer mediates DNA repair roles of the smc5-smc6 complex. Mol Cell Biol. 26, 1617-30 (2006).


314  Guelman S, Suganuma T, Florens L, Swanson SK, Kiesecker CL, Kusch T, Anderson S, Yates JR 3rd, Washburn MP, Abmayr SM, Workman JL., Host cell factor and an uncharacterized SANT domain protein are stable components of ATAC, a novel dAda2A/dGcn5-containing histone acetyltransferase complex in Drosophila., Mol Cell Biol. 26, 871-82, 2006.


313  Carrozza MJ, Florens L, Swanson SK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex., Biochim Biophys Acta. 1731, 77-87; 2005

312  Lujian Liao*, Tao Xu*, Julie Pilotte , Gerald M. Edelman , Peter Vanderklish , and John R. Yates III*, BDNF increases protein synthesis in a large scale via increasing translation capacity at synapse J. Proteome Research


311  Dawn M. Clifford1, Benjamin A. Wolfe1, Rachel H. Roberts1, W. Hayes McDonald2, John R. Yates III2, and Kathleen L. Gould1*, Mid1 recruits the S. pombe Cdc14-like phosphatase to the contractile ring allowing substrate dephosphorylation, Nature Cell Biology


310  Schneider DA, French S, Bailey AO, Vu L, Dodd J, Yates J, Beyer A, and Nomura M , The RNA Polymerase II elongation complex Spt4p/Spt5p affects transcription elongation by RNA polymerase I. PNAS


309  Liu J, Rivas FV, Wohlschlegel J, Yates JR 3rd, Parker R, Hannon GJ., A role for the P-body component GW182 in microRNA function., Nat Cell Biol. 2005, 7, 1161-6.


308  Chen EI, Hewel J, Brunhilde Felding-Habermann B, Yates JR 3rd., Large Scale Protein Profiling by Combination of Protein Fractionation and Multidimensional Protein Identification Technology (MudPIT)., Mol Cell Proteomics. 5, 53-56 (2005)


307  Page LJ, Suk JY, Huff ME, Lim HJ, Venable J, Yates J, Kelly JW, Balch WE., Metalloendoprotease cleavage triggers gelsolin amyloidogenesis., EMBO J. 2005, 24, 4124-32.

306  Zhu W, Venable J, Giometti CS, Khare T, Tollaksen S, Ahrendt AJ, Yates JR 3rd.Large-scale muLC-MS/MS for silver- and Coomassie blue-stained polyacrylamide gels.. Electrophoresis. 2005, 26, 4495-507.


305  James A. Wohlschlegel1,3, Erica S. Johnson2, Steven I. Reed3, and John R. Yates, III1*, Improved Identification of SUMO Attachment Sites Using C-terminal SUMO Mutants and Tailored Protease Digestion Strategies, J. Proteome Research 2006, 5, 761-770.


304  Ling Qi*, Jose Heredia*, Robert Screaton, Judith Y. Altarejos, Sherry Neissen?, Ian McLeod?, ChongWee Liew?, Rohit Kulkarni?, James Bain?, Christopher Newgard?, Ronald M. Evans, John Yates?, and Marc Montminy?, TRB3 Links the E3 Ubiquitin Ligase COP1 to Lipid Metabolism Science (in press)


303  Wu CC, MacCoss MJ, Mardones G, Finnigan C, Mogelsvang S, Yates JR 3rd, Howell KE., Organellar proteomics reveals Golgi arginine dimethylation., Mol Biol Cell., 15, 2907-19, (2004)


302  Carrozza MJ, Li B, Florens L, Suganuma T, Swanson SK, Lee KK, Shia WJ, Anderson S, Yates J, Washburn MP, Workman JL. Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription. Cell, 123, 581-92 (2005)


301  Sherry Niessen, Ian Mcleod, and John R. Yates III, Identification of Novel Protein Complexes and Protein:Protein Interactions by Mass Spectrometry, Protein-protein Interactions: A Molecular Cloning Manual, eds. Erica Golemis and Peter D. Adams, Cold Spring Harbor Press, Cold Spring Harbor, 2nd Edition, pp 329-354, 2005

300  Joshua A. Rosenberg, Gregory C. Tomlin, W. Hayes McDonald, Brian E. Snydsman, Eric G. Muller, John R. Yates, III, and Kathleen L. Gould, Ppc89p, a novel fission yeast spindle pole body protein required for spindle formation. Mol Biol Cell. 2006,17, 3793-805


299  Marina Karakozova1, Marina Kozak1, Catherine C. L. Wong2, Aaron Bailey2, John R. Yates, III2, and Anna Kashina1*., Arginylation of beta actin regulates actin cytoskeleton and cell motility, Science 2006, 313, 192-6.


298  Adam C. Wilson1, Christine C. Wu3, John R. Yates, III4, and Ming Tan, Chlamydial GroEL auto-regulates its own expression through direct interactions with the HrcA repressor protein., J. Bacteriology 187: 7535-7542, 2005


297  Greg T. Cantin, John D. Venable, Daniel Cociorva, and John R. Yates III, Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway, J. Proteome Research 5, 127-34 (2006)


296  Bianka L. Grosshans1, Anna Andreeva2, Akanksha Gangar2, Sherry Niessen3, John R Yates III3, Patrick Brennwald2 and Peter Novick, The yeast lgl family member Sro7p is an effector of the secretory Rab GTPase Sec4p, J. Cell Biology 172, 55-66 (2006).


295  Heike B. Koch1, Nemone Muster2, John R. Yates III2 and Heiko Hermeking1*Proteome-wide analysis of complexes associated with the c-MYC oncoprotein: evidence for non-transcriptional functions of c-MYC

294  Wolfe BA, McDonald WH, Yates JR 3rd, Gould KL., Phospho-regulation of the Cdc14/Clp1 phosphatase delays late mitotic events in S. pombe., Developmental Cell. 2006, 11, 423-30.


293  Robertus A. M. de Bruin, Tatyana I. Kalashnikova, Charly Chahwan, W. Hayes McDonald, James Wohlschlegel, John Yates, 3rd, Paul Russell and Curt Wittenberg, Constraining G1-specific transcription to late G1-phase: The MBF-associated corepressor Nrm1 acts via negative feedback, Cell (in revision)


292  Anjon Audhya, Francie Hyndman, Ian X. McLeod, Amy S. Maddox, John R. Yates III, Arshad Desai, and Karen Oegema, A complex containing the Sm-protein CAR-1 and the RNA helicase CGH-1 is required for embryonic cytokinesis in C. elegans, Journal of Cell Biology 2005, 171, 267-79.


291  Jennifer R. Schultz-Norton, Hayes McDonald, John R. Yates, and Ann M. Nardulli, Protein Disulfide Isomerase Serves As A Molecular Chaperone To Maintain Estrogen Receptor A Structure And Function, Molecular Endocrinology (in press)


290  S bastien L on, James M. Cregg, John Yates III, and Suresh Subramani, Peroxisomal protein import by the PTS1 and PTS2 pathways:similarities revealed by study of Pichia pastoris Pex20p, J. Cell Biology 172, 67-78 (2006)


289  Masahiro Okada, Iain M. Cheeseman, Tetsuya Hori, Katsuya Okawa, Ian X. McLeod, John R. Yates III, Arshad Desai, and Tatsuo Fukagawa, The CHIP complex is required for the incorporation of newly synthesized CENP-A into centromeres, Nature Cell Biology 8, 446-57 (2006).

288  Ke Hu, Laurence Florens, Jeff Johnson, Martin Fraunholz, Sapna Suravajjala, Camille DiLullo, John Yates, David S Roos, and John M. Murray, Cytoskeletal components of an invasion machine - the apical complex of Toxoplasma gondii, PLoS Pathogens 2, (in press) (2006)


287  Jeffrey K. Huang, Greg R. Phillips, Alejandro D. Roth, Liliana Pedraza, Weisong Shan, Wiam Belkaid, Sha Mi, Asa Fex-Svenningsen, Laurence Florens, John R. Yates III, and David R. Colman, Glial membranes at the CNS node of Ranvier prevent neurite outgrowth, Science 2005, 310, 1813-7.


286  Nadim Jessani, Sherry Niessen, BinQing Q Wei1, Monica Nicolau, Mark Humphrey, Youngran Ji, Wonshik Han, Dong-Young Noh, John R Yates III, Stefanie S Jeffrey & Benjamin F Cravatt, A streamlined platform for high-content functional proteomics of primary human specimens, Nature Methods 2, 691-7 (2005)


285  Widlund, P. O., J. S. Lyssand, S. Anderson, S. Niessen, J. R. Yates, III, and T. N. Davis (2006) Phosphorylation of the chromosomal passenger protein, Bir1, is required for localization of Ndc10 to the spindle during anaphase and full spindle elongation. Mol. Biol. Cell, in press.


284  Toshiaki Harashima, Scott Anderson, John R. Yates III, and Joseph Heitman, The kelch proteins Gpb1 and Gpb2 inhibit Ras activity by stabilizing the Saccharomyces cerevisiae RasGAP neurofibromin homologs Ira1 and Ira2, Molecular Cell (in press)

283  Greg R. Phillips, Laurence Florens, Hidekazu Tanaka, Zin Z. Khaing, Lazar Fidler, John R. Yates III, and David R. Colman, Proteomic Comparison of Two Fractions Derived From the Transsynaptic Scaffold, Journal of Neuroscience 81, 762-775 (2005)


282  Thomas F. Duchaine, James Wohlshlegel, Scott Kennedy, Yanxia Bei, Darryl Conte, KaMing Pang, Dan Brownell, Shohei Mitani, Gary Ruvkun John Yates III, and Craig C. Mello, Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways, Cell 124, 343-54 (2006)


281  Michael J. MacCoss1*, Christine C. Wu2*, Dwight E. Matthews3, and John R. Yates III, Measurement of the Atomic Enrichment of Stable Isotope Labeled Proteins Using High Resolution Mass Spectra of Peptides, Analytical Chemistry 2005;77, 7646-7653


280  Stephanie Cherqui, Sunil M. Kurian, Olivier Schussler, Johannes A. Hewel, John R.Yates III and Daniel R. Salomon, Isolation and angiogenesis by endothelial progenitors in the fetal liver, Stem Cell 2006, 24, (in press)


279  Paul R. Sanders, Paul R. Gilson, Greg T. Cantin, Thomas Nebl, Doron C. Greenbaum, Daniel J. Carucci, Malcolm J. McConville, Louis Schofield, Anthony N. Hodder, John R. Yates III and Brendan S. Crabb, Antigen discovery in Plasmodium falciparum blood-stages by membrane proteomics J. Biological Chemistry 2005, 280, 40169-76.


278  Erin M. Green1, Andrew J. Antczak1, Aaron O. Bailey2, Alexa A. Franco1, Kevin Wu1, John R. Yates 3rd,2, and Paul D. Kaufman3, Replication-Independent Histone Deposition by the HIR Complex and Asf1, Curr Biol. 2005, 15, 2044-9.

277  Alexander Gottschalk, Ruta B. Almedom, Thorsten Schedletzky, Scott D. Anderson, John R. Yates, III, and William R. Schafer, Identification and characterization of novel nicotinic receptor associated proteins in C. elegans, EMBO 24, 2566-78 (2005)


276  Liu H, Du X, Wang M, Huang Q, Ding L, McDonald HW, Yates JR 3rd, Beutler B, Horwitz J, Gong X , Crystallin gamma B-I4F mutant protein binds to alpha -crystallin and affects lens transparency., J Biol Chem. 280, 25071-8 (2005)


275  Martin SG, McDonald WH, Yates JR 3rd, Chang F. Tea4p links microtubule plus ends with the formin for3p in the establishment of cell polarity., Dev Cell., 8, 479-91. (2005)


274  John R. Yates III1, Annalyn Gilchrist2, Kathryn E. Howell3 and John J. M. Bergeron,, Proteomics of organelles and large cellular structures, Nature Reviews Molecular and Cellular Biology 2005, 6, 702-14.


273  Susan E. Francis1, Michelle M. Shimogawa1,2, Beth Graczyk1, Melissa K. Gardner3, Michael Ess1, Cristian Ruse4, Sherry Niessen4, Tennessee J. Yoder1,2, Jeff N. Molk5, Kerry Bloom5, John R. Yates, III4, David J. Odde3, and Trisha N. Davis1,2,*, Mps1 phosphorylation of the kinetochore component Dam1 alters the metaphase kinetochore arrangement by decreasing the affinity of Dam1 for microtubules Current Biology 2006, 16, 1489-501


272  Diana S. Chu1, Hongbin Liu2, 3, John R. Yates III2, Barbara J. Meyer, Sperm Chromatin Proteomics Identifies Evolutionarily Conserved Fertility Factors, Nature 2006, 443, 101-5.

271  Susan Lee1, Frank Comer2, Atsuo Sasaki1, Ian McLeod3, Duong, Yung1, Koichi Okumura4, John R. Yates, III3, Carole Parent2, and Richard A. Firtel1,5, TOR Complex 2 Integrates Chemotaxis and Signal Relay in Dictyostelium Mol Biol Cell. 2005, 16, 4572-83.


270  Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G, Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM, Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proc Natl Acad Sci U S A.102, 2099-104, 2005


269  Lani Keller, Edwin Romijn, Ivan Zamora, John R. Yates 3rd, and Wallace F. Marshall, The Centriole Proteome: Protein Composition Analysis of Isolated Chlamydomonas Basal Bodies Reveals Orthologs of Ciliary Disease Genes, Current Biology 15, 1090-8, (2005)


268  Schirmer EC, Florens L, Guan T, Yates JR, Gerace L., Identification of novel integral membrane proteins of the nuclear envelope with potential disease links using subtractive proteomics., Novartis Found Symp 2005; 264, 63-76.


267  Tripti Khare1, Carol S. Giometti1, Abraham Nunez2, Kelly Nevin2, Wenhong Zhu3, John R. Yates III3, and Derek Lovley2 Differential Protein Expression in the Metal-Reducing Bacterium Geobacter sulfurreducens PCA Grown with Fumarate or Ferric Citrate Proteomics 2006, 6, 632-40.


266  Rovshan Sadygov, James Wohlschlegel, and John R. Yates, III., Central limit theorem as an approximation for intensity-based scoring function. Analytical Chemistry 78, 89-95, (2006)

265  Anselm Sauerwald, Wenhong Zhu, Tiffany A. Major, Herv Roy, Sotiria Palioura, Dieter Jahn, William Whitman, John R. Yates, 3rd, Michael Ibba and Dieter S ll, RNA-dependent cysteine biosynthesis in archaea, Science 307, 1969-1972 (2005)


264  Iain M. Cheeseman, Ian MacLeod, John R. Yates III, Karen Oegema, and Arshad Desai, The CENP-F-like proteins HCP-1 and HCP-2 Target CLASP to Kinetochores to Regulate Microtubule Dynamics, Current Biology, 15, :771-7 (2005)


263  Carnahan, R. H., Feoktistova, A.S., Ren, L., Niessen, S., Yates, Jr., J. R., and Gould, K.L. (2005) Dim1p is required for efficient splicing and export of mRNA for lid1+, a component of the fission yeast Anaphase Promoting Complex. Eukaryot. Cell 4, 577-87 (2005).


262  Herzberg K, Bashkirov VI, Rolfsmeier M, Haghnazari E, McDonald WH, Anderson S, Bashkirova EV, Yates JR 3rd, Heyer WD., Phosphorylation of Rad55 on serines 2, 8, and 14 is required for efficient homologous recombination in the recovery of stalled replication forks., Mol Cell Biol. 2006 Sep 11; [Epub ahead of print]


261  M. Z. Bao, M.A. Schwartz, G. T. Cantin, J. R. Yates, H. Madhani, Phermone dependent destruction of the Tec1 Transcription factor is required for MAP kinase Signaling Specificity in Yeast, Cell, 119, 1-20, (2004)


260  C. Delahunty and J. R. Yates, Making Nano Columns and Tips, Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Wiley Interscience.

259  C. Delahunty and J. R. Yates, Protein Identification using 2-D LC-MS/MS, Methods 35, 248-55 (2005)


258  Geert J.P.L. Kops, Yumi Kim1, Beth A.A. Weaver1, Yinghui Mao1, Ian McLeod, John R. Yates III, Mitsuo Tagaya, Don W. Cleveland, ZW10 Links Mitotic Checkpoint Signaling to the Structural Kinetochore, J. Cell Biology 169, 49-60 (2005).


257  Cristian Ruse and John R. Yates, Mass Spectrometry in Systems Biology, Systems Biology, Springer-Verlag (in press)


256  Flick K, Ouni I, Wohlschlegel JA, Capati C, McDonald WH, Yates JR, Kaiser P., Proteolysis-independent regulation of the transcription factor Met4 by a single Lys 48-linked ubiquitin chain., Nat Cell Biol. 6, 634-41, 2004


255  Loven MA, Davis RE, Curtis CD, Muster N, Yates JR, Nardulli AM., A novel estrogen receptor alpha-associated protein alters receptor-deoxyribonucleic acid interactions and represses receptor-mediated transcription., Mol Endocrinol. 2004, 18, :2649-59.


254  Phillips GR, Anderson TR, Florens L, Gudas C, Magda G, Yates JR 3rd, Colman DR., Actin-binding proteins in a postsynaptic preparation: lasp-1 is a component of central nervous system synapses and dendritic spines., J Neurosci Res. 2004, 78, 38-48

253  Screaton RA, Conkright MD, Katoh Y, Best JL, Canettieri G, Jeffries S, Guzman E, Niessen S, Yates JR 3rd, Takemori H, Okamoto M, Montminy M., The CREB coactivator TORC2 functions as a calcium- and cAMP-sensitive coincidence detector. Cell 2004, 119, 61-74.


252  Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, Grainger M, Yan SF, Williamson KC, Holder AA, Carucci DJ, Yates JR 3rd, Winzeler EA, Global analysis of transcript and protein levels across the Plasmodium falciparum life cycle. Genome Res. 2004, 14, 2308-18.


251  Thomas Kusch, Laurence Florens, W. Hayes MacDonald, Selene K. Swanson, Robert L. Glaser, John R. Yates III, Susan M. Abmayr, Michael P. Washburn, and Jerry L. Workman, Acetylation by Tip60 Is Required for Selective Histone Variant Exchange at DNA Lesions, Science 2004, 306, 2084-7.


250  Heping Cao, Leesa J. Deterding, John D. Venable, Elizabeth A. Kennington, John R. Yates, 3rd, Kenneth B. Tomer And Perry J. Blackshear, Identification of the anti-inflammatory protein tristetraprolin as a hyperphosphorylated protein by mass spectrometry and site-directed mutagenesis, Biochemical Journal 394(Pt 1), 285-97, (2006).


249  Marilyn G. Pray-Grant, Jeremy A. Daniel, David Schieltz, Grant A. Hartzog, C. David Allis, John R. Yates III, and Patrick A. Grant, Chd1 mediates SAGA and SLIK dependent acetylation via chromodomain recognition of methylated histone H3., Nature 433, 434-8, 2005.


248  Florens, L., Liu, X., Wang, Y., Yang, S., Schwartz, O, Peglar, M., Carrucci, D. J., Yates, J. R., Wub, Y., Proteomics reveals novel proteins on the surface of malaria infected erthrocytes, Mol. Biochem., Parasitology 135, 1-11 (2004)

247  J. Venable and J. Yates, Cross correlation algorithm for calculation of peptide molecular weight from tandem mass spectra, Analytical Chemistry 2006, 78, 1921-9


246  Jessani et al, .Carcinoma and stromal enzyme activity profiles associated with breast tumor growth in vivo, PNAS 2004, 101, 13756-61


245  Iain M. Cheeseman1,3, Sherry Niessen2, Scott Anderson2, Francie Hyndman1, John R. Yates III2, Karen Oegema1, and Arshad Desai1,3, A Conserved Protein Network Controls Assembly Of The Outer Kinetochore And Its Ability To Sustain Tension, Genes and Development 2004, 18, 2255-68.


244  Julie L. Kadrmas1, Mark A. Smith1,2, Kathleen A. Clark1,2, Stephen M. Pronovost1, Nemone Muster4, John R. Yates, III4 and Mary C. Beckerle1,2,3,5, Integrin effector PINCH modulates JNK activation during morphogenesis with Ras suppressor RSU-1, Journal of Cell Biology 167, 1019-24, 2004


243  Anne Benzinger1, Nemone Muster2, John Yates III2 and Heiko Hermeking1Targets for tumor suppression by the p53-14-3-3?-pathwayidentified using a combined TAP-MudPIT approach Mol. Cell Proteomics 2005, 4, 785-95.244.


242  W. Hayes McDonald, David L. Tabb, Rovshan G. Sadygov, Michael J. MacCoss, John Venable, Johannes Graumann, Jeff R. Johnson, Daniel Cociorva, John R. Yates III, MS1, MS2, and SQT - three unified, compact, and easily parsed file formats for the storage of shotgun proteomic spectra and identifications, Rapid Communications in Mass Spectrometry2004, 18, 2162-8.

241  Durr E, Yu J, Krasinska KM, Carver LA, Yates JR, Testa JE, Oh P, Schnitzer JE., Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture, Nature Biotechnology, 22, 985-92, 2004


240  John Yates, Mass Spectrometry in Systems Biology, Biotechniques 36, 917-9 (2004)


239  X. Wang, J. Venable. H. McDonald, J. R. Riordan, J. R. Yates, W. E. Balch, The Cystic Fibrosis Protein Network, Science (in revision)


238  Greg T. Cantin and J. R. Yates, III, Strategies for shotgun identification of posttranslational modification by mass spectrometry, J. Chromatography A 1053, 7-14 (2004).


237  Kesti T, McDonald WH, Yates JR 3rd, Wittenberg C., Cell cycle-dependent phosphorylation of the DNA polymerase epsilon subunit, Dpb2, by the Cdc28 cyclin-dependent protein kinase., J Biol Chem. 2004, 279, 14245-55.


236  Robertus A.M. de Bruin, W. Hayes McDonald, Tatyana I. Kalashnikova, John Yates, and Curt Wittenberg, Cln3 Activates G1-Specific Transcription via Phosphorylation of the SBF Bound Repressor Whi5, Cell 117, 887-98 (2004)

235  Rovshan Sadygov, Daniel Cociorva and Yates, J., Database Searching using Tandem Mass Spectra: looking up the answer in the back of the book, Nature Methods, 1, 195-202 (2004)


234  John D. Venable, Mengqui Dong, James Wohlschlegel, Andrew and John R. Yates III, A novel approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nature Methods 1, 39-45, 2004.


233  James A. Wohlschlegel1, Erica S. Johnson2, Steven I. Reed3, and John R. Yates, III1, Global Analysis of Protein Sumoylation in Saccharomyces cerevisiae Journal of Biological Chemistry 2004, 279, 45662-8.


232  Chen E.I.,1* Florens L,2$ Axelrod F.T.,3 Monosov E,3 Barbas CF 3rd,2 Yates J.R. III,2 Felding-Habermann B,1 Smith J.W4 , Molecular analysis of Maspin, a tumor suppressor in breast cancer FASEB J. 2005, 19, 1123-4.


231  Doolan DL, Aguiar JC, Weiss WR, Sette A, Felgner PL, Regis DP, Quinones-Casas P, Yates JR 3rd, Blair PL, Richie TL, Hoffman SL, Carucci DJ. Utilization of genomic sequence information to develop malaria vaccines, J Exp Biol. 2003, 206,:3789-802


230  Reinke A, Anderson S, McCaffery JM, Yates J 3rd, Aronova S, Chu S, Fairclough S, Iverson C, Wedaman KP, Powers T. TOR complex 1 (TORC1) includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in S. cerevisiae., J Biol Chem. 2004, 279, 14752-62.

229  Tobili Y. Sam-Yellowe*, Laurence Florens #, Tongmin Wang*, J. Dale Raine , Daniel J. Carucci , Robert Sinden , and John R. Yates, III, Proteome analysis of rhoptry organelles isolated from Plasmodium merozoites, J. Proteome Research 2004, 3, 995-1001.


228  Sandhya Xirasagar1*, Scott Gustafson1*, Alex B. Merrick2, Kenneth B. Tomer2, Stanley Stasiewicz2, Denny D. Chan1, Kenneth J. Yost III1, John R. Yates III3, Susan Sumner4 Nianqing Xiao1, Michael D. Waters2, CEBS OBJECT MODEL FOR SYSTEMS BIOLOGY DATA, CEBS MAGE SysBio-OM, Bioinformatics 20, 2004-15, 2004


227  Neil Hall,1* Marianna Karras,2 J. Dale Raine,3 Jane M. Carlton,4,5,6 Taco W. A. Kooij,2 Matthew Berriman,1 Laurence Florens,7 Christoph S. Janssen,8 Arnab Pain,1 Georges K. Christophides,9 Keith James,1 Kim Rutherford,1 Barbara Harris,1 David Harris,1 Carol Churcher,1 Michael A. Quail,1 Doug Ormond,1 Jon Doggett,1 Holly E. Trueman,3 Jacqui Mendoza,3 Shelby L. Bidwell,4 Marie-Adele Rajandream,1 Daniel J. Carucci,10 John R. Yates, III,7 Fotis C. Kafatos,9 Chris J. Janse,2 Bart Barrell,1 C. Michael R. Turner,8 Andrew P. Waters,2* Robert E. Sinden3*, A Comprehensive Survey of the Plasmodium Life Cycle by Genomic, Transcriptomic, and Proteomic Analyses, Science 307, 82-86 2005.


226  McDonald WH, Yates JR 3rd.Shotgun proteomics and biomarker discovery., Disease Markers. 2002, 18, 99-105


225  McDonald WH, Yates JR 3rd. Shotgun proteomics: integrating technologies to answer biological questions. Curr Opin Mol Ther. 2003, 5, 302-9.


224  McDonald WH, Pavlova Y, Yates JR 3rd, Boddy MN. Novel essential DNA repair proteins Nse1 and Nse2 are subunits of the fission yeast Smc5-Smc6 complex., J Biol Chem. 2003, 278, 45460-7.

223  Coulon S, Gaillard PH, Chahwan C, McDonald WH, Yates JR 3rd, Russell P.Slx1-Slx4 Are Subunits of a Structure-specific Endonuclease That Maintains Ribosomal DNA in Fission Yeast., Mol Biol Cell. 2004, 15, 71-80.


222  Rodriguez-Gabriel MA, Burns G, McDonald WH, Martin V, Yates JR 3rd, Bahler J, Russell P.RNA-binding protein Csx1 mediates global control of gene expression in response to oxidative stress., EMBO J. 2003, 22, 6256-66.


221  Jeffrey R. Johnson, Laurence Florens , Daniel J. Carucci , and John R. Yates III Proteomics in Malaria, J. Proteome Research 3, 296-306 (2004)


220  Wenhong Zhu , Claudia I. Reich , Gary J. Olsen , Carol S. Giometti , John R. Yates III, Shotgun Proteomics of Methanococcus jannaschii and insights into methanogenesis, J. Proteome Research 3, 538-48 (2004).


219  H. Liu, R. G. Sadygov, J. R. Yates, A model for random sampling and estimation of relative protein abundance in Shotgun Proteomics Analytical Chemistry 76, 4193-201 (2004).


218  J. Yates, Mass Spectral Analysis in Proteomics, Annual Reviews in Biophysics and Biomolecular Structure, Annual Reviews, Palo Alto 2004, 33:297-316.

217  C. Xu and J. Yates, Mass Spectrometry-based Proteomics for Cancer Biology, The Oncogenomics Handbook: Understanding and Treating Cancer in the 21st Century. Humana Press, Totowa, NJ (2005) pages 91-108.


216  Y. H Lin, Z. Y. Park, D. Lin, A. A. Brahmbhatt, Maire-Christine, Rio, J. R. Yates, R. L. Klemke, Requirement of Lasp-1 for Cell Migration Through Regulation of Focal Adhesion Dynamics, J. Cell Biology 165. 421-32 (2004).


215  Jeremy A. Daniel*, Michael S. Torok*, Zu-Wen Sun*, David Schieltz , C. David Allis*, John R. Yates III , and Patrick A. Grant, Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription, J. Biol. Chem. 2004, 279, 1867-71


214  Hongbin Liu, Nicholas Bergman, Brendan Thomason, Shamira Shallom, Alyson Hazen4, Joseph Crossno, Scott Peterson, John Yates, III. & Philip Hanna, Formation and Composition of the Anthrax Endospore, J. Bacteriology 186, 164-78 (2004).


213  Dmitri Leonoudakis*, Lisa R. Conti*, Scott Anderson , Carolyn M. Radeke*, Leah McGuire*, Marvin E. Adams#, Stanley C. Froehner#, John R. Yates III , and Carol A. Vandenberg, Protein Trafficking and Anchoring Complexes Revealed by Proteomic Analysis of Inward Rectifier Potassium Channel (Kir2.x) Associated Protein, J. Biological Chemistry 2004, 279, 22331-46.

212  J. Wohlschlegel and J. Yates, Proteomics: Where s Waldo in Yeast, Nature, 425, 671, 2003.


211  Lorraine B. Anderson, Anthony J. A. Ouellette , Julian Eaton-Rye, Melissa, Michael J. MacCoss, John R. Yates III, and Bridgette A. Barry, Evidence for a post-translational modification in the CP47 subunit of Photosystem II, J. American Chemical Society 2004, 126, 8399-405.


210  Eric C. Schirmer, J. R. Yates III, and Larry Gerace, MudPIT: A powerful proteomics tool for discovery, limited primarily by our imagination, Discovery Medicine 3, 38-39 (2003)


209  Rovshan Sadygov, Hongbin Liu, and John R. Yates, Novel Statistical Models for Protein Validation using Tandem Mass Spectral Data and Protein Amino acid sequence databases, Analytical Chemistry 76, 1664-71 (2004)


208  Johannes Graumann, Jae Hong Seol, Leslie Dunipace, W. Hayes McDonald, John R. Yates III, Barbara J. Wold and Raymond J. Deshaies, Applicability of TAP-MudPIT to pathway proteomics in yeast, Molecular and Cellular Proteomics 3, 227-237 (2004).


207  M. P. Washburn, R. R. Ulaszek, and J. R. Yates, Reproducibility of Quantitative Proteomic Analyses of Complex Biological Mixtures by Multi-dimensional Protein identification technology, Analytical Chemistry 75, 5054-5061 (2003).

206  Varsha S. Likhite, Emily I. Cass, Scott D. Anderson, John R. Yates, and Ann M. Nardulli,, Interaction of Estrogen Receptor with 3-Methyladenine DNA Glycosylase Modulates Transcription and DNA Repair, J. Biol. Chem., 2004; 279: 16875 - 16882


205  Sam-Yellowe TY, Florens L, Johnson JR, Wang T, Drazba JA, Le Roch KG, Zhou Y, Batalov S, Carucci DJ, Winzeler EA, Yates JR 3rd, A Plasmodium Gene Family Encoding Maurer\'s Cleft Membrane Proteins: Structural Properties and Expression Profiling, Genome Res. 2004, 14, 1052-9.


204  Tony R. Hazbun, Lars Malmstr m, Scott Anderson, Beth J. Graczyk, Bethany Fox, Michael Riffle, Bryan A. Sundin, J. Derringer Aranda, W. Hayes McDonald, Chun-Hwei Chiu, Brian E. Snydsman, Phillip Bradley, Eric G. D. Muller, Stanley Fields, David Baker, John R. Yates III and Trisha N. Davis, Assigning Function to Yeast Proteins by Integration of Technologies, Molecular Cell 12, 1243-52 (2003)


203  Holly E. Trueman, J. Dale Raine, Laurence Florens, Johannes T. Dessens, Jacqui Mendoza, Cecilia C. Waller, Anthony A. Holder, Jean Langhorne, Daniel J. Carucci, John R. Yates III and Robert E. Sinden, Functional characterisation of an LCCL/lectin-domain containing protein family in Plasmodium berghei. . J. Parasitology 90, 1062-71 (2004)


202  John D. Venable, and John R. Yates III, The Impact of Ion Trap Tandem Mass Spectra Variability on the Identification of Peptides Analytical Chemistry 76, 2928-37 (2004)

201  Stefan Westermann1, Iain M. Cheeseman1, Scott Anderson2, John R. Yates III2, David G. Drubin1, and Georjana Barnes, Molecular Architecture of the Budding Yeast Inner Kinetochore Reveals a Conserved Core of Structural Components J. Cell Biology 163, 215-22 (2003)


200  Christine C. Wu1 , Michael J. MacCoss1 , Kathryn E. Howell2, Dwight E. Matthews3, and John R. Yates, III, Metabolic Labeling of Mammalian Organisms with Stable Isotopes for Quantitative Proteomic Analysis, Analytical Chemistry2004, 76, 4951-9.


199  Rory Geyer, Susan Wee, Scott Anderson, John R. Yates, III, Dieter Wolf, BTB/POZ domain proteins are putative substrate adaptors for cullin 3 ubiquitin ligases, Molecular Cell 12, 783-90 (2003)


198  Irene T. Ling, Laurence Florens, Anton R. Dluzewski, Osamu Kaneko, Munira Grainger, Brian Yim Lim, Tsuboi Takafumi, John M. Hopkins, Jeffrey R. Johnson, Motomi Torii5, Lawrence H. Bannister, John R. Yates, III, Anthony A. Holder and Denise Mattei, The Plasmodium falciparum clag 9 gene encodes a rhoptry protein Molecular Microbiology 52, 107-18 (2004).


197  Eric C. Schrimer, Laurence Florens, Tinglu Guan, John R. Yates III, and Larry Gerace, Novel Membrane Proteins With Potential Disease Links Found By Subtractive Proteomics, Science 301, 1380-1382 (2003)


196  Michael J. MacCoss, Christine C. Wu, Hongbin Liu, Rovshan Sadygov, and John R. Yates III, A Correlation Algorithm for the Automated Analysis of Quantitative Proteomics Data, Analytical Chemistry 75, 6912-6921 (2003)

195  David L. Tabb, Yingying Huang Vicki H. Wysocki John R. Yates, III, Basic residue content influences fragment ion peak intensities in low-energy CID spectra of peptides, Analytical Chemistry 76, 1243-8 (2004)


194  Tabb, D., Saraf, A., Yates, J. R., GutenTag: high throughput sequence tagging via an empirically derived fragmentation model, Analytical Chemistry 75, 6415-6421 (2003).


193  Taylor CF, Paton NW, Garwood KL, Kirby PD, Stead DA, Yin Z, Deutsch EW, Selway L, Walker J, Riba-Garcia I, Mohammed S, Deery MJ, Howard JA, Dunkley T, Aebersold R, Kell DB, Lilley KS, Roepstorff P, Yates JR, Brass A, Brown AJ, Cash P, Gaskell SJ, Hubbard SJ, Oliver SG., A systematic approach to modeling, capturing, and disseminating proteomics experimental data., Nature Biotechnol 21, 247-54 (2003)


192  Tabb, D. L.; Smith, L. L.; Breci, L. A.; Wysocki, V. H.; Lin, D.; Yates, J. R., III; Statistical Characterization of Ion Trap Tandem Mass Spectra from Doubly Charged Tryptic Peptides, Anal. Chem. 75; 1155-1163, (2003)


191  Breci, L. A.; Tabb, D. L.; Yates, J. R., III; Wysocki, V. H., Cleavage N-Terminal to Proline: Analysis of a Database of Peptide Tandem Mass Spectra; Anal. Chem.75, 1963-1971, 2003.


190  W. Hayes McDonald and John R. Yates III, Shotgun Proteomics: Integrating Technologies to Answer Biological Question, Current Opinion in Molecular Therapeutics 5, 302-309 (2003)

189  Karl Willert, Jeff Brown, Esther Danenberg, Andrew Duncan, Irving L. Weissman, Tannishtha Reya, John R. Yates III, and Roel Nusse, Properties of purified biologically active Wnt protein; a lipid modified stem cell growth factor, Nature 423, 448-451 (2003)


188  Rovshan Sadygov and John R. Yates, A hypergeometric probability model for protein identification using tandem mass spectral data and protein sequence databases, Analytical Chemistry 75, 3792-3798 (2003).


187  Bret Cooper, Donna Eckert, Nancy L. Andon, John R. Yates III and Paul A. Haynes, Investigative proteomics: identification of an unknown plant virus from infected plants using mass spectrometry JASMS 14, 736-741 (2003).


186  Christine Wu and Yates, J. R. The application of mass spectrometry to membrane proteomics, Nature Biotechnology 21, 262-7 (2003).


185  Wei Xu, Shilpa Kadam, Helen Cho, Ester M. Banayo, Scott Anderson, John R. Yates III, Beverly M. Emerson & Ronald M. Evans A Methylation-mediator complex in hormone signalling; Genes and Development,18, 144-56 (2004)

184  Gianluca Canettieri, Ianessa Morantte, Ernesto Guzman, Hiroshi Asahara, Stephan Herzig, Scott D. Anderson, John R. Yates III, Marc Montminy Attenuation of a Phosphorylation Dependent Activator by an HDAC:PP1 Complex; Nat Struct Biol. 10, 175-81, (2003)


183  Direct database searching using tandem mass spectra of peptides, J. R. Yates, III, and Hayes McDonald, Cell Biology: A laboratory Handbook, 3rd Edition, Ed. J. E. Celis, Academic Press.


182  Peptide sequencing by tandem mass spectrometry, J. R. Yates, III, Antonius Koller and David Schieltz, Cell Biology: A laboratory Handbook, Second Edition, Ed. J. E. Celis, Academic Press.


181  MacCoss, M. and Yates, J. R., Proteomics: analytical tools and techniques, Current Opinion in Clinical Nutrition and Metabolic Care 4, 369-375, (2001).


180  B. Li, H. L. J., Anderson, S., Yates, J., Stitzer, L., Workman, J. L., The Set2 histone methyltransferase functions through the phosphorylated CTD of RNA polymerase II, J Biol Chem. (2003) 278, 8897-903


179  Skop, A. R., Liu, H., Yates, J. R., Meyer, B. J., Heald, R., Functional proteomic analysis of the mammalian midbody reveals conserved cell division components, Science 305, 61-6 (2004)

178  Andon, N. L., Eckert, D., Koller, A., Yates, J. R., Haynes, P. A., High Throughput Functional Affinity Purification of Mannose Binding Proteins from Oryza sativa Proteomics 3, 1270-8 (2003)


177  Hanjo Lim1@, Lara G. Hays1*, Jimmy Eng1^, Sandra L. Tollaksen2, Carol S. Giometti2, James F. Holden3, Michael W. W. Adams3, Claudia I. Reich4, Gary J. Olsen4, and John R. Yates III1* , Identification of 2D-gel Proteins: A Comparison of MALDI/TOF Peptide Mass Mapping to ? LC-ESI Tandem Mass Spectrometry, J. Am. Soc. Mass Spectrom.14, 957-70 (2003)


176  Kenichi Yamaguchi a, Mar a Ver nica Beligni a, Susana Prieto a, 1, Paul A. Haynes b, W. Hayes McDonald c, John R. Yates III c, and Stephen P. Mayfield a, 2, Proteomic characterization of the Chlamydomonas reinhardtii chloroplast ribosome identifying proteins unique to the 70S ribosome,.J. Biological Chemistry 278, 33774-85 (2003)


175  David l. Tabb, Michael J. MacCoss, Christine C. Wu, Scott D. Anderson, John R. Yates, III, Similarity among tandem mass spectra of proteomic experiments: detection, significance, and utility, Analytical Chemistry 75, 2470-7 (2002)


174  Christine C. Wu, Michael J. MacCoss, Kathryn E. Howell, John R. Yates, III, A novel method for the comprehensive proteomic analysis of membrane proteins: Identification, Modifications, and Topology, Nature Biotechnology 21, 262-7 (2003)


173  Jingping Zhong, Paul A. Haynes, Shiping Zhang, Xinping Yang, Nancy Andon, Antonius Koller, Donna Eckert, John Yates III, Xun Wang, and Paul Budworth, An in vivo system for protein-protein interaction study and its use in characterization of TBP complex in rice, J. Proteome Research 2, 514-22 (2003(

172  Andon NL, Hollingworth S, Koller A, Greenland AJ, Yates JR 3rd, Haynes PA. Proteomic characterization of wheat amyloplasts using identification of proteins by tandem mass spectrometry, Proteomics. 2, 1156-68, (2002).


171  Wenhong Zhu and John R. Yates, Proteome Analysis of Microbes: to gel or not to gel, Applied Genomics and Proteomics 1, 3-12 (2002)


170  Iain Cheeseman, Scott Anderson, Miri Jwa, Erin Green, Jung-seong Kang, John R. Yates, Clarence Chan, David Drubin, Georjana Barnes, Phospho-regulation of Kinetochore-Microtubule attachments by the Aurora kinase Ipl1p, Cell 111, 163-172 (2002).


169  R. Verma, L. Aravind, R. Oania, W. H. McDonald, J. R. Yates III, E.V. Koonin, R. J. Deshaies, Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26S Proteasome, Science 298, 611-5 (2002)


168  Jane M. Carlton*, Samuel V. Angiuoli*, Bernard B. Suh*, Taco Kooij, Mihaela Pertea*, Maria D. Ermolaeva*, Jonathan E. Allen*, Joana C. Silva*, Jeremy D. Selengut*, Hean L. Koo*, Jeremy D. Peterson*, Mihai Pop*, Daniel S. Kosack*, Martin F. Shumway*, Shelby L. Bidwell*, Shamira J. Shallom*, Azadeh Shoaibi*, Leda M. Cummings*, Jennifer K. Cho*, John Quackenbush*, Susan E. van Aken*, Steven B. Riedmuller*, Tamara V. Feldbylum*, Laurence Florens, John R. Yates III, Dale J. Raine, Robert E. Sinden, Michael A. Harris||, Deirdre A. Cunningham, Peter R. Preiser, Lawrence W. Bergman#, Akhil Vaidya#, Leo H. van Lin, Chris J. Janse, Andrew P. Waters, Hamilton O. Smith||, Owen R. White*, Steven L. Salzberg*, J. Craig Venter*, Claire M. Fraser*, Stephen L. Hoffman**, Malcolm J. Gardner*, Daniel J. Carucci**, Whole genome shotgun sequencing of a model rodent malaria parasite and comparative analysis with Plasmodium falciparum, Nature 419, 512-519 (2002)


167  Laurence Florens*, Michael P. Washburn , J. Dale Raine , Robert M. Anthony , Munira Grainger||, J. David Haynes ,**, J. Kathleen Moch , Nemone Muster*, John B. Sacci , , David L. Tabb*, Adam A. Witney , , Dirk Wolters , , Yimin Wu, Malcolm J. Gardner#, Anthony A. Holder||, Robert E. Sinden , John R. Yates III*, and Daniel J. Carucci , A Proteomic View of the Plasmodium falciparum Life Cycle, Nature 419, 520-526 (2002)

166  Doolan DL, Southwood S, Freilich DA, Sidney J, Graber NL, Shatney L, Bebris L, Florens L, Dobano C, Witney AA, Appella E, Hoffman SL, Yates JR 3rd, Carucci DJ, Sette A., Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci U S A, 100, 9952-7 (2003).


165  Claire Delahunty and John R. Yates, III, Identification of Proteins in Complex Mixtures Using Liquid Chromatography and Mass Spectrometry, Current Protocols in Cell Biology 2004


164  Claire Delahunty and John R,. Yates, Proteomics: a shotgun approach without 2-DE gels, Encyclopedia of the Human Genome 2002.


163  Dayin Lin, David Tabb, and John R. Yates, Large-scale protein identification using mass spectrometry, Biochim Biophys Acta. 1646, 1-10(2003).


162  Thomas Sellers and John R. Yates, Applications of Proteomics to Genetic Epidemiology, Genetic Epidemiology 24, 83-89 (2003)


161  Howe L, Kusch T, Muster N, Chaterji R, Yates JR 3rd, Workman JL, Yng1p Modulates the Activity of Sas3p as a Component of the Yeast NuA3 Histone Acetyltransferase Complex, Mol Cell Biol. 14, 5047-53, 2002

160  Michael P. Washburn, Antonius Koller, Guy Oshiro, Ryan R. Ulaszek, David Plouffe, Cosmin Deciu, Elizabeth Winzeler, and John R. Yates, III, Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae., Proc Natl Acad Sci U S A. (2003) 100, 3107-12.


159  Shigeaki Saitoh, Andrei Chabes, W. Hayes McDonald, Lars Thelander, John R. Yates, III, Paul Russell, Cid13 is a cytoplasmic poly (A) polymerase that regulates ribonucleotide reductase mRNA, Cell 109, 563-573 (2002).


158  Michael MacCoss, Christine Wu, and John R. Yates, III, Probability Based Validation of Protein Identifications Using a Modified SEQUEST Algorithm, Analytical Chemistry 74, 5593-5599 (2002).


157  Thomas C. Hunter, Nancy L. Andon, Antonius Koller, John R. Yates III and Paul A. Haynes, The functional proteomics toolbox: methods and applications, J Chromatogr B Analyt Technol Biomed Life Sci. 782, 165-81 (2002)


156  Daniel J. Carucci1, John R. Yates, III2 and Laurence Florens, Exploring the Proteome of Plasmodium, Int J Parasitol. 32, 1539-42, (2002).


155  Toshifumi Inada, Eric Winstall, Salvador Z. Tarun Jr, John R. Yates, III, Dave Schieltz, and Alan B. Sachs, One step affinity purification of the yeast ribosome and its associated proteins and mRNAs, RNA 8, 948-58 (2002)

154  Kenichi Yamaguchi , Susana Prieto, Mar a Ver nica Beligni, Paul A. Haynes, Hayes McDonald, John Yates III, and Stephen P. Mayfield, Proteomic characterization of the small subunit of Chlamydomonas reinhardtii chloroplast ribosome: Identification of a novel S1 domain-containing protein and unusually large orthologues of bacterial S2, S3 and S5, Plant Cell. 14, 2957-74, (2002).


153  Margaret A. Loven, Nemone Muster, John R. Yates and Ann M. Nardulli, A novel estrogen receptor alpha associated protein, template activating factor I beta, inhibits acetylation and transactivation, Molecular Endocrinology 17, 67-78 (2003).


152  Jaekyung Shim, Hanjo Lim, John R.Yates III, Michael Karin, Nuclear export of NF90 is required for interleukin-2 mRNA stabilization, Molecular Cell 10, 1331-1344 (2002).


151  Dongre AR, Kovats S, deRoos P, McCormack AL, Nakagawa T, Paharkova-Vatchkova V, Eng J, Caldwell H, Yates JR 3rd, Rudensky AY. In vivo MHC class II presentation of cytosolic proteins revealed by rapid automated tandem mass spectrometry and functional analyses. Eur J Immunol. (2001) 31(5):1485-94.


150  Carol S. Giometti, Claudia Reich., Sandra Tollaksen, Gyorgy Babnigg, Hanjo Lim, Wenhong Zhu, John Yates III, and Gary Olsen, Global Analysis of a Simple Proteome: Methanococcus jannaschii, J Chromatogr B Analyt Technol Biomed Life Sci. (2002) 782, 227-43.


149  Carol S. Giometti, Tripti Khare, Sandra L. Tollaksen, Alexandre Tsapin, Wenhong Zhu, John R. Yates III, and Kenneth H. Nealson, Analysis of the Shewanella oneidensis Proteome by Two-dimensional Gel Electrophoresis Under Nondenaturing Conditions, Proteomics. 2003, 3, 777-85.

148  Marilyn G. Pray-Grant, David Schieltz, Stacey J. McMahon, Jennifer M. Wood, Erin L. Kennedy, Richard G. Cook, Jerry L. Workman, John R. Yates III and Patrick A. Grant, The novel SLIK (SAGA-Like) histone acetyltransferase complex functions in the yeast retrograde response pathway. Mol Cell Biol. (2002), 22, 8774-86


147  Lim, Hanjo and Yates, John R III (October 2001) Mass Spectrometry: Analysis of Two dimensional Protein Gels. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [doi:10.1038/npg.els.0003110]


146  Cheeseman, I. M., M. Enquist-Newman, et al. (2001). Mitotic spindle integrity and kinetochore function linked by the Duo1p/Dam1p complex. J Cell Biol 152(1): 197-212.


145  Michael J. MacCoss1 , W. Hayes McDonald1 , Anita Saraf1 , Rovshan Sadygov1, Judy M. Clark2, Joseph J. Tasto3, Kathleen L. Gould3, Dirk Wolters4, Michael Washburn5, Avery Weiss6, John I. Clark3 and John R. Yates, III1,5, Shotgun Identification of Protein Modifications from Protein Complexes and Lens Tissue, PNAS 99, 7900-7905 (2002).


144  Boddy, M.N., Gaillard, P.-H.L., McDonald, W.H., Shanahan, P., Yates, J.R., 3rd, and Russell, P. (2001). Mus81-Eme1 are essential components of a Holliday junction resolvase. Cell. 107, 537-548 (2001)

143  Yingying Huang, Vicki H. Wysocki, David L. Tabb, John R. Yates, III, The Influence of Histidine on Cleavage C-terminal to Acidic Residues in Doubly Protonated Tryptic Peptides, Int. J. Mass Spectrom. 219, 233-244 (2002).


142  Lorraine B. Anderson, Melissa Maderia, Anthony J. A. Ouellette, LeeAnn Higgins, Thomas Krick, Hayes McDonald, Mike MacCoss, Hanjo Lim, John R. Yates, III, and Bridgette A. Barry, Post-translational Modifications of Proline and Tryptophanin CP43 of the Photosynthetic Water Oxidizing Complex, Proc Natl Acad Sci U S A. (2002) 99, 14676-81


141  Raymond J. Deshaies, Greg Cope, Svetlana Lyapina, Hayes McDonald, Jae Hong Seol, Andrej Shevchenko, Anna Shevchenko, Rati Verma, and John Yates, Charting the protein \'complexome\' in yeast, Molecular and Cellular Proteomics 1, 3-10, (2002)


140  James F. Holden, Farris L. Poole II, Sandra L. Tollaksen, Carol S. Giometti, Hanjo Lim, John R. Yates III, Michael W. W. Adams Identification of membrane proteins in the hyperthermophilic archaeon Pyrococcus furiosus using proteomics and prediction programs, Comparative and Functional Genomics 2, 275-288 (2001)


139  Eric Mortensen, Hayes McDonald, John R. Yates, III, Douglas R. Kellogg, Cell cycle-dependent assembly of a Gin4-septin complex, Mol Biol Cell. (2002) 13, 2091-105.


138  Rovshan G. Sadygov, Jimmy Eng, Eberhard Durr, Anita Saraf, Hayes McDonald, Michael J. MacCoss, and John R. Yates, III, Code Developments to Improve the Efficiency of Automated MS/MS Spectra Interpretation, Journal of Proteome Research 2, 211-15 (2002)

137  Guy Oshiro, Lisa M. Wodicka, Michael P. Washburn, John R. Yates III, David J. Lockhart, and Elizabeth A. Winzeler, Highly parallel identification of new open reading frames in S. cerevisiae, Genome Research 12, 1210-1220 (2002)


136  A. Koller, M. P. Washburn, B. Markus Lange, N. Andon, C. Deciu,. P. Haynes, L. Hays, D. Schieltz, R. Ulaszek, J. Wei, D. Wolters, J. R. Yates, III; Proteomic survey of metabolic pathways in rice, Proc Natl Acad Sci U S A. (2002) 99, 11969-74


135  M. Washburn, R. Ulaszek, C. Deciu, D. M. Schieltz, J. R. Yates, III, Analysis of quantitative proteomic data generated by multi-dimensional protein identification technology, Anal. Chem. 74, 1650-1657 (2002).


134  Lindstrom DL, Squazzo SL, Muster N, Burckin TA, Wachter KC, Emigh CA, McCleery, JA, Yates JR 3rd, Hartzog GA. Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins., Mol Cell Biol (2003) 23, 1368-78


133  W. Hayes McDonald, Ryoma Ohi, David T. Miyamoto, Timothy J. Mitchison, and John R. Yates III; Comparison of three directly coupled HPLC MS/MS strategies for identification of proteins from complex mixtures: single-dimension LC-MS/MS, 2-phase MudPIT, and 3-phase MudPIT, Int. J. Mass Spectrom. 219, 245-251 (2002).


132  D. Tabb, W. H. McDonald, J. R. Yates, DTASelect and Contrast: Proteomic Tools for Filtering, Summarizing, and Comparing Tandem Mass Spectrometry Results, J. Proteome Research 1, 21-26 (2002)

131  Jizhong Zhou, Carol Giometti, Hanjo Lim, John R. Yates Gene and Protein expression profiles of Shewanella oneidensis during anaerobic growth with different electron acceptors, Omics, 6, 39-60 (2002).


130  Hongbin Liu, Dayin Lin, J. R. Yates, Biotechniques 32, 898-911 (2002).


129  D. Lin, A. Alpert, J. R. Yates, American Genomic/Proteomics Technology 1, 38, 2001.


128  R. Verma, H. McDonald, J. Yates III, and R. J. Deshaies, Selective degradation of ubiquitinated Sic1 by purified 26S proteasome yields fully active S phase cyclin-Cdk, Molecular Cell 8, 439-448, 2001.


127  S. Honey, B. L. Schneider, D. M. Schieltz, J. R. Yates, B. Futcher, A novel multiple affinity purification tag and its use in identification of proteins associated with a cyclin-Cdk complex, Nucleic Acid Research 29, E24, 2001.


126  Shigehiro Osada Ann Sutton Nemone Muster Christine E. Brown John R. Yates III, Rolf Sternglanz, and Jerry L. Workman, The yeast SAS (something about silencing) protein complex contains a MYST-type acetyltransferase and functions with chromatin assembly factor ASF1, Genes and Development 15, 3155-3168 (2001).

125  D. Wolters, M. P. Washburn, J. R. Yates, III, An automated Multidimensional Protein Identification Technology for Shotgun Proteomics, Analytical Chemistry 73, 5683-5690 (2001)


124  Hayes McDonald and John R. Yates, Functional Genomics: Proteomics, 2002 Yearbook of Science and Technology, McGraw-Hill.


123  Hefner Y, Borsch-Haubold AG, Murakami M, Wilde JI, Pasquet S, Schieltz D, Ghomashchi F, Yates JR, Armstrong CG, Paterson A, Cohen P, Fukunaga R, Hunter T, Kudo I, Watson SP, Gelb MH. Serine 727 phosphorylation and activation of cytosolic phospholipase A2 by MNK1-related protein kinases. J Biol Chem. 275, 37542-51 (2000).


122  Todorow, Z., Spang, A., Carmack, E., Yates, J., and Schekman, R. (2000). Active recycling of yeast golgi mannosyltransferase complexes through the endoplasmic reticulum. Proc Natl Acad Sci U S A 97, 13643-13648.


121  Carol S. Giometti, Claudia Reich, Sandra Tollaksen, Gyorgy Babnigg, Hanjo Lim, John Yates III, and Gary Olsen, Structural modifications of Methanococcus jannaschii flagellin proteins revealed by proteome analysis, Proteomics 1, 1033-42 (2001)


120  Dorothea K. Thompson, Alexander S. Beliaev, Carol S. Giometti, Douglas Lies, Kenneth H. Nealson, Hanjo Lim, John Yates III, Craig C. Brandt, James M. Tiedje, and Jizhong Zhou, Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis Using DNA Microarrays and Proteomic Tools, Applied and Environmental Microbiology, 68, 881-92 (2002).

119  M. T. Krahmer, J. J. Waltersm, K. F. Fox, A. Fox, K. E. Creek, L. Pirisi, D. Wunschel, R. D. Smith, D. L. Tabb, J. R. Yates, III, MS for Identification of Single Nucleotide Polymorphisms and MS/MS for Discrimination of Isomeric PCR products, Anal. Chem. 72, 4033-4040 (2000).


118  L. Tabb. J. K. Eng, J. R. Yates, Protein Identification by SEQUEST, Proteome Research: Mass Spectrometry, Ed. Peter James, Springer, Berlin, pp125-142 (2000).


117  S. Bark, N. Muster, J. Yates, G. Siuzdak, High temperature mass mapping using a thermophilic protease. J. American Chemical Society 123, 1774-1775 (2001).


116  K. E. Laidig, W. Chen, Y. Park, K. Park, J. R. Yates, III, R. J. Lamont, M. Hackett, Searching the Porphyromonas gingivalis genome with peptide fragmentation mass spectra in absence of annotations or known open reading frames, The Analyst, 126, 52-7 (2001).


115  M. P. Washburn, D. Wolters, J. R. Yates, III, Large Scale analysis of the yeast proteome via multidimensional protein identification technology Nature Biotechnology 19, 242-247 (2001)


114  H. McDonald and J. R. Yates, III, Proteomic Tools for Cell Biology, Traffic 1, 1-8, 2000.

113  P. Haynes and J. R. Yates, III, Protein Profiling, Comparative and Functional Genomics 17, 81-87 (2000)


112  M. Washburn and J. R. Yates, III, Novel methods of proteome analysis: multidimensional chromatography and mass spectrometry, Proteomics A Current Trends Supplement 27-36, (2000).


111  Proteomic Analysis of Two Functional States of the Golgi Complex in Mammary Epithelial Cells, Christine C. Wu, John R. Yates, III, Margaret C. Neville, and Kathryn E. Howell, Traffic 1, 747-754 (2000).


110  A. Emili, D. M. Schieltz, J. R. Yates, III, L. H. Hartwell, Dynamic interaction of DNA damage checkpoint Rad53 with chromatin assembly factor Asf1, Molecular Cell 7, 13-20 (2001).


109  C.C. Wu, K. E. Howell, M. C. Neville, J. R. Yates, III, J. L. McManaman, Proteomics reveals contribution of endoplasmic reticulum membranes to the lipid secretion process in mammary epithelial cells, Electrophoresis 21, 3470-3482 (2000).


108  R. Verma, S. Chen, R. Feldman, D. Schieltz1, J. Yates2, and R. J. Deshaies Characterization of 26S Proteasomes isolated by a novel one-step method of purification: effect of nucleotides on assembly and composition, Molecular Cellular Biology 11, 3425 (2000).

107  Randall S. Taylor, Christine C. Wu, Lara G. Hays, Jimmy K. Eng, John R. Yates, III, Kathryn E. Howell, Proteomics of rat liver Golgi complex: Minor proteins are identified through sequential fractionation, Electrophoresis 21, 3441-3459 (2000).


106  Patricia R. Segarini, James E. Nesbitt, Dongxia Li, Lara G. Hayes, John R. Yates III and David E. Carmichael, The Low Density Lipoprotein Receptor-Related Protein/alpha 2-Macroglobulin Receptor is a Receptor for Connective Tissue Growth Factor (CTGF) J. Biological Chemistry 276, 40659-40667 (2001).


105  Tong, W. and Yates, J. R., Sensitive and High Resolution CE/MS/MS for Protein identification in Complex Mixtures, Chromatographia 53, S-90 (2001).


104  Washburne, M. and Yates, J., Analysis of the Microbial Proteome, Current Opinion in Microbiology 3, 292-297 (2000).


103  Friedman, D. B., Vinh, D., Kern, J., Crawford, D., Steiner, E., Schieltz, D., Yates, III, J., Resing, K., Ahn, N. G., Winey, M., Davis, T. N., Phosphorylation at Spc110p at Msp1p and CDK sites is required for proper interaction with the Tub4p-complex at the centrosome in S. cerevisiae. J. Biological Chemistry 276, 17958-67 (2001).


102  Aird, S. D., Womble, G. C., Yates, J. R., 3rd, Griffin, P. R. Primary structure of gamma-bungarotoxin, a new postsynaptic neurotoxin from venom of Bungarus multicinctus Toxicon 37, 609-625 (1999).

101  Michael Sacher, Jemima Barrowman, David Schieltz, John R. Yates III and Susan Ferro-Novick, Identification and characterization of five new subunits of TRAPP, Eur. J. Cell. Biol. 79, 71-80 (2000)


100  Identifying SNPS expressed in Proteins: rapid identification of amino acid sequence variations by LC/MS/MS with SEQUEST data analysis, C. L. Gatlin, J. K. Eng, S. T. Terashita, J. C. Detter, J. R. Yates, III, Analytical Chemistry 72, 757-763 (2000).


99  The ADA Complex is a Distinct Histone Acetyltransferase Complex in Yeast, P. A. Grant, D. Schieltz, M. G. Pray-Grant, J. R. Yates, III, and J. L. Workman, Molecular and Cellular Biology 19, 6621-6631, 1999.


98  Mass Spectrometry: From Genome and Proteome, J. R. Yates, Trends in Genetics 16, 5-8, 2000.


97  Mgm101p is a novel component of the mitochondrial nucleoid that binds DNA and is required for the repair of oxidatively damaged mitochondrial DNA, S. Meeusen, Q. Tieu, E. Wong, E. Weiss, D. Schieltz, J. R. Yates, III, J. Nunnari, J. Cell Biology 145, 291-304 (1999).


96  Improved methods for structural analysis of protein prenyl groups and associated C-terminal modifications, M. E. Whitten, K. Yokoyama, D. Schieltz F. Ghomashchi, D. Lam, J. R. Yates, K. Palczewski, M. H. Gelb, Methods in Enzymology, 316, 436-51, (2000).

95  Direct analysis of protein complexes, J. R. Yates, A. Link, D. Schieltz, J. Eng, Proteome and Protein Analysis, Eds: Kamp et al., Springer-Verlag, Heidelberg, Germany pp53-64, 1999.


94  Molecular properties of matrilin-3 isolated from human growth cartilage, D. Kleemann-Fischer, G. R. Kleemann, D. Engel, J. R. Yates, III, J.-J. Wu, and D. R. Eyre, Archives of Biochemistry and Biophysics 387, 216-222 (2001).


93  Coronin promotes the rapid assembly and cross-linking of actin filaments and may link the actin and microtubule cytoskeletons in yeast. Goode, B.L., Wong, J.J., Butty, A-C., Peter, M., McCormack, A.L., Yates, J.R., Drubin, D.G., Barnes, G. (1998) J. Cell Biol. 144, 83-98 (1998).


92  Direct analysis of proteins in mixtures: application to protein complexes, J. R. Yates, III, A. J. Link, and D. Schieltz, Protein and Peptide Analysis: Advances in the Use of Mass Spectrometry, Ed. J. R. Chapman, Humana Press, London, England, pp. (2000)


91  The IGF-binding protein-4 protease secreted by human fibroblasts is PAPP-A, J. B. Lawrence, C. Oxvig, M. T. Overgaard, L. Sottrup-Jensen, G. J. Gleich, L. G. Hays, J. R. Yates, C. A. Conover, Proc. Natl. Acad. Sci. USA 96, 3149-3153 (1999).


90  Identification of proteins in complex mixtures by microsolid phase extraction/multistep elution/capillary electrophoresis tandem mass spectrometry, W. Tong, A. Link, J. K. Eng, J. R. Yates, III Analytical Chemistry 71, 2270-2278 (1999)

89  The ATM-related cofactor Tra1 is a component of the purified SAGA complex, P. A. Grant, D. Schieltz, M. G. Pray-Grant, J. R. Yates, III, and J. L. Workman, Molecular Cell 2, 863-867 (1998)


88  Yates, John R (August 2000) Mass Spectrometry in Biology. In: Encyclopedia of Life Sciences. John Wiley & Sons, Ltd: Chichester http://www.els.net/ [doi:10.1038/npg.els.0000999]


87  Direct analysis of protein complexes using mass spectrometry, A. J. Link, J. Eng D. M. Schieltz, E. Carmack, G. Mize, D. R. Morris, B. M. Garvik, J. R. Yates, III, Nature Biotechnology 17, 676-682 (1999)


86  Muchowski, P. J., Hays, L. G., Yates, J. R., 3rd, and Clark, J. I. (1999). ATP and the core alpha-Crystallin domain of the small heat-shock protein alphaB-crystallin. J. Biol. Chem. 274, 30190-5.


85  Mass spectrometric analysis of catechol-histidine adducts from insect cuticle, J. L. Kerwin, F. Turecek, R. Xu, K. J. Kramer, T. L. Hopkins, C. L. Gatlin, J. R. Yates, III, Analytical Biochemistry 268, 229-237 (1999).

84  TRA1: A yeast protein related to human DNA-dependent protein kinase is a component of the ADA/SPT transcriptional regulatory complexes, A. Saleh, D. Schieltz, N. Ting, J. R. Yates, S. P. Lees Miller, and C. J. Brandl, J. Bio. Chem. 273, 26,559-65 (1998).


83  A subset of TAFIIs are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation, P. A. Grant, D. Schieltz, M. G. Pray-Grant, D. J. Steger, J. C. Reese, J. Yates, and J. L. Workman, Cell 94, 45-53 (1998)


82  The septins are required for the mitosis-specific activation of the Gin4 kinase, C. Carroll, R. Altman, D. Schieltz, J. Yates, and D. Kellog, J. Cell Biology 143, 709-717 (1998)


81  The Arp2/3 complex is required for actin dependent mitochondrial motility and inheritance in budding yeast, I. Boldogh, S. L. Karmon, W. D. Nowakowski, L. G. Hays, J. R. Yates, J.and L. A. Pon, PNAS 98, 3162-3167 (2001).


80  The hMre11/hRad50 protein complex and Nijmegen breakage syndrome: Linkage of DNA repair to the cellular DNA damage response, J. P. Carney, R. S. Maser, H. Olivares, E. M. Davis, M. Lebeau, J. R. Yates, III, L. Hays, W. F. Morgan, J. H. J. Petrini, Cell 93, 477-486 (1998)


79  Database Searching using Mass Spectrometry data, J. R. Yates, Electrophoresis 19, 893-900 (1998)

78  Primary structure and function of an A-kinase anchoring protein associated with calcium channels, P. C. Gray, B. D. Johnson, R. E. Westenbroek, L. G. Hays, J. R. Yates, T. Schuer, W. A. Cattarall, and B. J. Murphy, Neuron 20, 1017-1026 (1998).


77  TRAP, A Putative Vesicle Receptor on the cis-Golgi Complex, Michael Sacher, Yu Jiang, Jemima Barrowman, Judy Burston, Li Zhang, David Schieltz, John R. Yates III, Hagai Abeliovich and Susan Ferro-Novick, EMBO J. 17, 2494-2503.


76  Protein identification at the low femtomole level from silver stained gels using MicroLC/MicroESI/MS/MS, T. Gatlin, G. Kleemann, L. Hays, J. Yates, Analytical Biochemistry 263, 93-101 (1998)


75  Method to compare CID spectra of peptides: the potential for library searching and subtractive analysis with MS/MS data, J. Yates, J. Eng Analytical Chemistry 70, 3557-3565 (1998).


74  Mass Spectrometry and the age of the proteome, John R. Yates, III, J. Mass Spectrometry 33, 1-19 (1998).


73  High throughput protein characterization by automated reversed-phase chromatography/electrospray tandem mass spectrometry, Axel Ducret, Inge Van Osteveen, Jimmy K. Eng, John R. Yates, III, Ruedi Aebersold, Protein Science 7, 706-719 (1998).

72  Emerging tandem mass spectrometry techniques for the rapid identification of proteins, Ashok Dongre, Jimmy K. Eng, and John R. Yates, Trends in Biotechnology 15,418-425 (1997).


71  Automated protein identification using micro-column liquid chromatography-tandem mass spectrometry, John R. Yates, III, Edwin Carmack, Lara Hays, Andrew J. Link, and Jimmy K. Eng, Methods in Molecular Biology: 2-D Proteome Analysis Protocols, Ed Andrew J. Link, Humana Press, 1997, v. 112 .pp 553-569.


70  Identifying the major proteome components of Haemophilus influenzae type strain NCTC 8143, Andrew J. Link, Lara Hays, Edwin Carmack, and John R. Yates, III, Electrophoresis 18, 1314-1334 (1997).


69  Matrix-assisted laser desorption ionization/quadrupole ion trap mass spectrometry of peptides; application to the localization of phosphorylation sites on the P protein from Sendai virus, Karen Jonscher and John R. Yates, III, J. Biological Chemistry 272, 1735-1741, 1997.


68  Analysis of Naturally Processed peptides eluted from HLA DRB1*0402 and *0404, James B. Hayden, Ashley L. McCormick, John R. Yates, III, and Michael P. Davey, J. Neuroscience Research 45, 795-902, (1996).


67  Book review, Review of Protein and Peptide Analysis by Mass Spectrometry, Edited by John R. Chapman, Analytica Chimica Acta, 343, 1997, 296

66  Kinetics of folding of the IgG binding domain of peptostreptoccocal protein L, Michelle L. Scalley, Qian Yi, Hongdi Gu, Ashley McCormack, John R. Yates, III, David Baker Biochemistry 36, 3373-82 (1997).


65  Direct analysis of protein mixtures by tandem mass spectrometry, J. R. Yates, A. L. McCormack, D. Schieltz, E. Carmack, and A. Link, J. Protein Chemistry 16, 495-497, 1997.


64  Protein identification by solid-phase microextraction-capillary zone electrophoresis- microelectropray tandem mass spectrometry, D. Figeys, A. Ducret, J. R. Yates, III, R. Aebersold, Nature Biotechnology 14, 1579-1583 (1996).


63  Direct database searching using tandem mass spectra of peptides, J. R. Yates, III, Cell Biology: A laboratory Handbook, Second Edition, Ed. J. E. Celis, Academic Press, Volume 4, pgs 529-538 (1997).


62  Peptide sequencing by tandem mass spectrometry, K. Jonscher and J. R. Yates, III, Cell Biology: A laboratory Handbook, Second Edition, Ed. J. E. Celis, Academic Press, Volume 4, pgs 539-546 (1997).


61  The quadrupole ion trap mass spectrometry: A small solution for a big challenge, K. Jonscher and J. R. Yates, III, Analytical Biochemistry, 244, 1-15, 1997.

60  High throughput analysis of tandem mass spectrometry data for peptides, J. R. Yates, III, E. Carmack, and J. K. Eng, Lab Automation , 2, 28-31 (1997).


59  A strategy for the identification of proteins localized to in subcellular spaces: application to E. coli periplasmic proteins, A. Link, E. Carmack, and J. R. Yates, III, Int. J. Mass Spectrom. Ion Processes 160, 303-316, 1997.


58  The whys and wherefores of quadrupole ion trap mass spectrometry, K. Jonscher and J. R. Yates, III, ABRF Newsletter, 1996 Sept.


57  Protein database searching with MSn spectra of polypeptides, Jimmy K. Eng and John R. Yates, III, in Ultrasensitive Biochemical Diagnostics, Gerald E. Cohn, Steven A. Soper, C. H. Winston Chen, Editors, Proc. SPIE 2680, pp 378-382, (1996).


56  Direct analysis and identification of proteins in mixtures by LC/MS/MS and database searching at the low femtomole level, A. L. McCormack, D. Schieltz, J. K. Eng, B. Goode, S. Yang, G. Barnes, D. Drubin, and J. R. Yates, III, Anal. Chem. 69, 767-776 (1997)


55  Analysis of complex systems by using micro-column LC/ESI/MS/MS, A. Link, J. Eng, J. Yates, American Laboratory 1996, July, 27-30.

54  Future prospects for the analysis of complex biological systems by using micro-column LC/ESI/MS/MS, J. Yates, A. McCormack, A. Link, D. Schieltz, J. Eng, The Analyst 121, 65R-76R (1996).


53  Identification of phosphorylation sites of Human 85 kDa cytosolic phospholipase A2 expressed in insect cells and present in human monocytes, M. G. S. de Carvalho, A. L. McCormack, E. Olson, F. Ghomaschi, M. Gelb, J. Yates, and C. Leslie, J. Biological Chemistry 271, 6987-6997 (1996).


52  Mining Genomes with Mass Spectrometry: J. Yates, A. L. McCormack, and J. Eng, Analytical Chemistry 68, 534A-540A, (1996).


51  Direct database searching with MALDI-PSD spectra of peptides, P. Griffin, M. MacCoss, J. Eng, R. Blevins, J. Aaronson, and J. Yates, Rapid Commun. Mass Spectrom. 9, 1546-1551 (1995).


50  Searching databases by using high energy CID spectra of peptides, J. Yates, J. Eng, C. Klausner, A. L. Burlingame, J. Am. Soc. Mass Spectrom. 7, 1089-1096 (1996).


49  Mixture analysis using a hybrid quadrupole mass filter/quadrupole ion trap mass spectrometer, K. Jonscher and J. R. Yates, Analytical Chemistry 68, 659-667, 1996

48  Microcolumn liquid chromatography-electrospray ionization tandem mass spectrometry; Analysis of immunological samples, Biochemical and Biotechnological Applications of Electrospray Ionization Mass Spectrometry, ACS Symposium Series 619, Ed. A. P. Snyder, A. L. McCormack, J. K. Eng, P. DeRoos, A. Rudensky, and J. R. Yates, III (1995), pp207-225


47  Mining Genomes: Correlating tandem mass spectra of modified and unmodified peptides to nucleotide sequences, J. R. Yates, III, J. K. Eng, and A. L. McCormack, Analytical Chemistry 67, 3202-3210 (1995)


46  Localization of the disulfide bond involved in post translational processing of glycosylasparaginase and disrupted by a mutation in the Finnish-type aspartylglycosaminuria, A. L. McCormack, I. Mononen, V. Kaartinen, and J. R. Yates, J. Biological Chemistry 270, 3212-3215 (1995)


45  A method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database, J. R. Yates, III, J. K. Eng, A. L. McCormack, and D. Schieltz, Analytical Chemistry 67,1426-1436 (1995)


44  Peptide sequence analysis on quadrupole mass spectrometers, A. L. McCormack, J. K. Eng, and J. R. Yates, III, Methods: A companion to Methods in Enzymology, Ed. J. E. Shively 6, 274-283 (1994).


43  An approach to correlate MS/MS data to amino acid sequences in a protein database, J. K. Eng, A. L. McCormack, and J. R. Yates, III, J. American Soc. Mass Spectrom. 5, 976-989 (1994).

42  Protein structure analysis by mass spectrometry, J. R. Yates, High resolution separations of biomolecules, Methods in Enzymology, Eds. W. Hancock and B. Karger, vol 271B, 351-377, 1996.


41  Invariant-cognate peptide exchange restores class II dimer stability in HLA-DM mutants, T. Monji, A. L. McCormack, J. R. Yates, III, and D. Pious, J. Immunology 153, 4468-4477 (1994)


40  Protein sequencing by mass spectrometry, J. R. Yates, III, and A. L. McCormack, Encyclopedia of Analytical Science, Ed. A. Townsend, Academic Press, London, 1995, pp. 4220-4226.


39  Sequencing peptides derived from the class II major histocompatibility complex by tandem mass spectrometry, J. R. Yates, III, A. L. McCormack, J. Hayden, M. Davey, Cell Biology: A laboratory Handbook, Ed. J. E. Celis, Academic Press, pg. 380-388 (1994).


38  Peptide mass maps: A highly informative approach to protein identification. J. R. Yates, III, S. Speicher, P. R. Griffin, and T. Hunkapiller, Analytical Biochemistry 214, 397-408 (1993).


37  The analysis of oligonucleotides by negative ion matrix assisted laser desorption mass spectrometry, G. J. Currie and J. R. Yates, III, J. American Soc. Mass Spectrometry, 4, 955-963 (1993).

36  The analysis of peptides and proteins by matrix assisted laser desorption ionization quadrupole ion trap mass spectrometry, K. Jonscher, G. Currie, A. McCormack, and J. R. Yates, III, Rapid Commun. Mass Spectrom. 7, 20-26 (1993),


35  Complete enzymatic deglycosylation of native sex steroid-binding protein (SBP or SHBG) of human and rabbit plasma. Effect on the steroid-binding activity, P. H. Petra, P. R. Griffin, J. R. Yates, III, K. Moore, and W. Zhang, Protein Science 1, 902-909 (1992).


34  Assembly and aggregation properties of synthetic Alzheimer\'s A4/beta amyloid peptide analogs, D. Burdick, B. Soreghan, J. Kosmoski, M. Knauer, A. Henschen, J. R. Yates, III, C. Gotman, and C. Glabe, J. Biological Chemistry 1992, 267, 546-54.


33  Analysis of Proteins by Mass Spectrometry, P. R. Griffin, K. Furer-Jonshur, L. E. Hood, J. R. Yates, III, J. Schwartz, and I Jardine, Techniques in Protein Chemistry III, Ed. R. A. Angeletti, Academic Press, N. Y., 1992, pp. 467-476.


32  Structural analysis of proteins by HPLC-MS and HPLC-MS/MS using Electrospray Ionization on a triple quadrupole mass spectrometer, P. R. Griffin, J. A. Coffman, L. E. Hood, and J. R. Yates, III, Int. J. Mass Spectrom. Ion Processes 1991, 111, 131-149.


31  Aspartylglycosaminuria in the Finnish population: Identification of two point mutations in the heavy chain of glycoasparaginase, I. Mononen, N. Heisterkamp, V. Kaartinen, J. C. Williams, J. R. Yates, III, P. R. Griffin, L. E. Hood, and J. Groffen, Proc. Natl. Acad. Sci. USA 1991, 88, 2941-2945.

30  Leukocyte Glycoasparaginase: Inactivation and Covalent Modification with Diazo-oxonorvaline, V. Kaartinen, J. C. Williams, J. Tomich, J. R. Yates, III, L. E. Hood, and I. Mononen, J. Biological Chemistry 1991, 266, 5860-5869.


29  Computer Aided Interpretation of Low Energy MS/MS Mass Spectra of Peptides, J. R. Yates, III, J. Zhou, P. R. Griffin and L. E. Hood, Techniques in Protein Chemistry II, J. Villafranca, Ed., Academic Press, N. Y., 1990, 477-485.


28  The amino acid sequence of the acidic subunit B-chain of crotoxin, S. Aird, J. R. Yates, III, P. M. Martino, J. Shabanowitz, D. F. Hunt, I. I. Kaiser, Bioc. Biop. Acta 1990, 1040, 217-224.


27  Metabolism-Based Covalent Bonding of the Heme Prosthetic Group to its Apoprotein During the Reductive Debromination of BrCCl3 by Myoglobin, Y. Osawa, B. M. Martin, P. R. Griffin, J. R. Yates, III, D. F. Hunt, A. Murphy, L. Chen, R. J. Cotter, and L. R. Pohl, J. Biological Chemistry 1990, 265, 10340-10346.


26  The complete sequence of the acidic subunit from Mojave toxin determined by Edman degradation and mass spectrometryt, A. L. Bieber, R. R. Becker, R. McParland, D. F. Hunt, J. R. Yates, III, J. Shabanowitz, G. R. Johnson, Biochemical Biophysical Acta 1990, 1037, 413-421.


25  Protein and Oligopeptide Sequence Analysis by Triple Quadrupole and Quadrupole Fourier Transform Mass Spectrometry, D. F. Hunt, J. Shabanowitz, P. R. Griffin, J. R. Yates, III, P. A. Martino, and A. L. McCormack, in Biological Mass Spectrometry , 1990 , A. L. Burlingame and J. A. McCloskey, Eds. (Elsevier Science Publishers, Amsterdam), 337-362.

24  Peptide Sequence Analysis by Triple Quadrupole and Quadrupole Fourier Transform Mass Spectrometry, D. F. Hunt, T. Krishnamurthy, J. Shabanowitz, P. R. Griffin, J. R. Yates, III, P. A. Martino, A. L. McCormack and C. R. Hauer, in Mass Spectrometry of Peptides , D. Desiderio, Ed., CRC Press, 1990.


23  New Instrumentation for Protein Sequence Analysis, D. F. Hunt, J. Shabanowitz, J. R. Yates, III, P. R. Griffin, and N. Z. Zhu, Mass Spectrometry of Biological Materials, B. Larsen and C. McEwen, Eds. Marcel Dekker, Inc., New York, N. Y. 1989, 151-165.


22  Laser Photodissociation Fourier Transform Mass Spectrometry: New Methodology for Sequence Analysis of Oligopeptides and Location of Disulfide Bonds, P. R. Griffin, J. Shabanowitz, J. R. Yates, III, N. Z. Zhu, and D. F. Hunt, Techniques in Protein Chemistry, T. E. Hugli, Ed., Academic Press, N. Y.,1989, 160-167.


21  Sequence Analysis of Protein C-Terminal Proteolytic Fragments, Protein Isolated From 2D-Gels, and Murine Calbindin: New Methodology, J. R. Yates, III, J. Shabanowitz, P. R. Griffin, N. Z. Zhu, and D. F. Hunt, Techniques in Protein Chemistry, T. E. Hugli, Ed., Academic Press, N. Y.,1989, 168-175.


20  Characterization of Standard Test Peptide III, D. F. Hunt, P. R. Griffin, J. R. Yates, III, J. Shabanowitz, J. W. Fox and L. K. Beggerly, Techniques in Protein Chemistry, T. E. Hugli, Ed., Academic Press, N. Y.,1989, 580-588.


19  Protein Sequence Analysis by Tandem Mass Spectrometry, D. F. Hunt, J. Shabanowitz, J. R. Yates, III, P. R. Griffin, and N. Z. Zhu, Methods in Protein Sequence Analysis 1988, B. Wittmann-Liebold, Ed. Springer-Verlag, N. Y., 1989, 183-190.

18  Tandem Quadrupole Fourier Transform Mass Spectrometry, D. Hunt, J. Shabanowitz, J. Yates, P. Griffin, and N-Z. Zhu, Anal. Chim. Acta, 1989, 225, 1-10.


17  Amino Acid Sequencing of a Norwegian Blue-Green Algal Cyclic Peptide By Fast Atom Bombardment Tandem Mass Spectrometric Techniques, T. Krishnamurthy, L. Szafraniec, E. Sarver, D. F. Hunt, J. Shabanowitz, J. R. Yates, III, C. R. Hauer, W. Carmichael, S. Missler and O. Skulberg, Proc. Natl. Acad. Sci. USA 1989, 86, 770-774.


16  Amino Acid Sequence of the 9 kDa Calcium Binding Protein from Mouse Intestine, D. F. Hunt, J. R. Yates, III, J. Shabanowitz, D. Bruns and E. Bruns, J. Biological Chemistry, 1989, 264, 6580-6586.


15  Proteolytic Fragments of the Nicotinic Acetylcholine Receptor Identified by Mass Spectrometry: Implications for Receptor Topography, C. R. Moore, J. R. Yates, III, P. R. Griffin, J. Shabanowitz, P. A. Martino, D. F. Hunt, D. S. Cafiso, Biochemistry 1989, 28, 9184-9191.


14  Peptide Sequence Analysis by Tandem Mass Spectrometry: New Methods and Instrumentation, D. F. Hunt, J. Shabanowitz, J. R. Yates, III, P. R. Griffin, and N. Z. Zhu, The Analysis of Peptides and Proteins, Ed. C. McNeil, John Wiley and Sons, New York, N. Y., 1988, 151-165.


13  Amino Acid Analysis of Mouse Calbindin-9K Isoforms by Tandem Mass Spectrometry, D. E. Bruns, J. R. Yates, III, D. F. Hunt, M. E. Bruns, Proceedings of the 7th Workshop on Vitamin D, Norman et. al., Gruyter, N. Y. 1988.

12  Protein Sequence Analysis by Tandem Mass Spectrometry, J. R. Yates, III, P. R. Griffin, J. Shabanowitz, D. F. Hunt, Advances in Gene Technology: Protein Engineering and Production, Ed. K. Brew, IRL Press, 1988.


11  Peptide Sequence Analysis by Laser Photodissociation Fourier Transform Mass Spectrometry, D. F. Hunt, J. Shabanowitz, and J. R. Yates, III, J. Chem. Soc. Chem. Comm., 548, 1987


10  Sequence Homology in the Metalloproteins: Purple Acid Phosphatase from Beef Spleen and Uteroferrin from Porcine Uterus, D. F. Hunt, J. R. Yates, III, J. Shabanowitz, Nian-Zhou Zhu, T. Zirino, B. A. Averill, S. T. Larroque, J. G. Shewale, R. M. Roberts, and K. Brew, Bioch. Biophys. Res. Comm., 1987, 144, 1154.


9  Tandem Quadrupole-Fourier Transform Mass Spectrometry of Oligopeptides and Small Proteins, D. F. Hunt, J. Shabanowitz, J. R. Yates, III, Nian-Zhou Zhu, D. H. Russell, M. E. Castro, Proc. Natl. Acad. Sci. USA 1987, 84, 620.


8  Proteolytic Fragmentation and Sequencing of the Acetylcholine Receptor from Torpedo using Mass Spectrometry, C. R. Moore, J. R. Yates, D. F. Hunt, D. S. Cafiso, Biophysical J. 1987, 51, 59.


7  Site Directed Chemical Modification of Horse Cytochrome c Results in Changes in Antigenicity Due to Local and Long Range Conformational Perturbations, H. M. Cooper, P. Griffin, J. Shabanowitz, J. R. Yates, III, D. F. Hunt, R. R. Jemmerson, and Y. Paterson, J. Biological Chemistry 1987, 262, 11591.

6  Protein Sequencing by Tandem Mass Spectrometry, D. F. Hunt, J. R. Yates, III, and J. Shabanowitz, Methods in Protein Sequence Analysis 1986, Edited by Kenneth A. Walsh, The Humana Press, 1987, pp. 149-153


5  Tandem Quadrupole-Fourier Transform Mass Spectrometry of Oligopeptides and Small Proteins, D. F. Hunt, J. Shabanowitz, J. R. Yates, III, Nian-Zhou Zhu, D. H. Russell, M. E. Castro, Proc. Natl. Acad. Sci. USA 1987, 84, 620.


4  Protein Sequencing by Tandem Mass Spectrometry, D. F. Hunt, J. R. Yates, III, J. Shabanowitz, S. Winston, C. R. Hauer, Proc. Natl. Acad. Sci. USA 1986, 83, 6233.


3  Tandem Quadrupole-Fourier Transform Mass Spectrometry of Oligopeptides, D. F. Hunt, J. Shabanowitz, J. R. Yates, III, R. T. McIver, R. L. Hunter, J. E. P. Syka, and J. Amy, Analytical Chemistry 1985, 57, 2728,


2  Protein Sequence Analysis using a Combination of Particle Bombardment and Collision Activated Dissociation on a Triple Quadrupole Mass Spectrometer, Jr. Yates, D. F. Hunt, and J. Shabanowitz, in Advances in Mass Spectrometry 1985, Ed. J. F. J. Todd, John Wiley & Sons, New York, pp. 1439-1440.

1  Mixed Gas Chemical Ionization of Peptide Derivatives, J. R. Yates, III and R. J. Anderegg, Biomedical Mass Spectrometry 1983 10, 567