Program

Mini Symposium on the Relative Merits of Orthogonal Energy Deposition Modes for Promotion of FragmentationSaturday, August 223:00 p.m.Symposium Registration Hotel Nikko, Olympic Room, 25th FloorSunday, August 23Nikko BallroomChair: A. L. Burlingame, University of California, San Francisco, CA, USA8:30 a.m.MS.1New Technology for the Large-scale Proteomic Comparison of Human Embryonic Stem Cells, Induced Pluripotent Stem Cells, and Somatic Cells Joshua J. Coon, University of Wisconsin, Madison, WI, USA9:30MS.2Electron Capture Dissociation in Radio-Frequency-Free Cell Douglas F. Barofsky, Oregon State University, Corvallis, OR, USA10:10Coffee Break10:50MS.3Decoding the Histone Code by Quantitative Proteomics Benjamin A. Garcia, Princeton University, Princeton, NJ, USA11:30MS.4Data Processing Algorithms for Analysis of High Resolution MSMS Spectra of Peptides with Complex Post-Translational Modifications Shenheng Guan, University of California, San Francisco, CA, USA12:10 p.m.LunchChair: Shenheng Guan, University of California, San Francisco, CA, USA1:40MS.5Use of Electron Transfer Dissociation to Analyze Combinations of Histone Post-Translational Modifications on an LTQ-Orbitrap Shannon Eliuk, University of California, San Francisco, CA, USA2:20MS.6Electron Capture Dissociation for Structural Studies of Integral Membrane Proteins and Their Modifications Julian Whitelegge, University of California, Los Angeles, CA, USA3:00MS.7O-GlcNAcylation: The Post-Translational Modification that Best Highlights the Value of ETD Robert J. Chalkley, University of California, San Francisco, CA, USA3:40MS.8The Use of ECD for Proteomics-wide Identification and Quantification of iso-Asp Residues Roman A. Zubarev, Karolinska Institute, Stockholm, Sweden4:00Symposium Registration Nikko Ballroom Vestibule4:00Poster Set-up Carmel & Monterey Rooms6:00Opening Reception Golden Gate Room, 25th FloorMonday, August 247:30 a.m.Registration Nikko Ballroom VestibuleSession 1Nikko Ballroom8:15Introduction A. L. Burlingame, University of California, San Francisco, CA, USA John Stults, Genentech, Inc., South San Francisco, CA, USAPlenary LectureChair: John Stults, Genentech, Inc., South San Francisco, CA, USA8:301.1Global Analysis of Small Molecule Interactions with Proteins Michael Snyder, Stanford University, Stanford, CA, USAChair: Connie R. Jimenez, VU University Medical Center, Amsterdam, The Netherlands9:301.2Membrane-assisted Sample Preparation for Online ESI-MS Analysis of Biomolecules Juan Astorga-Wells, Karolinska Institute, Stockholm, Sweden and Biomotif AB, Täby, Sweden10:10Coffee Break10:301.3Two-Dimensional Liquid Chromatography Coupled with ESI-MS for Protein Identification and Quantification Jim Langridge, Waters Corporation, Manchester, United Kingdom11:101.4Targeted Proteomic Approaches Provide Insights into Virion Assembly and Chromatin Remodeling during Viral Infection Ilena Cristea, Princeton University, Princeton, NJ, USA11:501.5Confident Assignment of Post-Translational Modifications Using Top-Down Mass Spectrometry Julian Whitelegge, University of California, Los Angeles, CA, USA12:30 p.m.LunchSession 2Chair: Ralph Bradshaw, University of California, San Francisco, CA, USA2:002.1Protein Quantification through Targeted Mass Spectrometry: The Way Out of Biomarker Purgatory? Steven A. Carr, The Broad Institute of MIT and Harvard, Cambridge, MA, USA2:402.2Proteomics Targeted to Sub-Cellular Compartments and Integration with Genomics for Candidate Biomarker Discovery in Colorectal Cancer Connie R. Jimenez, VU University Medical Center, Amsterdam, The Netherlands3:202.3Towards the Discovery of Biomarkers in Cerebrospinal Fluid by Combining Peptide Ligand Library Treatment and Label Free Protein Quantification on a LTQ-Orbitrap Florence Roux-Dalvai, CNRS IPBS, Toulouse University, FrancePoster Session ACo-Chairs: David Maltby, University of California, San Francisco, CA, USA Shannon Eliuk, University of California, San Francisco, CA, USA4:00Carmel and Monterey RoomsA.1Labeling of Peptide Fragmented Mass Spectra in Proteomic Studies B. Gerrits*, C. Panse, B. Bodenmiller, and R. SchlapbachA.2Exact Quantification of Complex Protein Mixtures Using MeCAT—Metal Coded Tagging R. Ahrends*, U. Bergmann, S. Pieper, B. Neumann, C. Scheler, and M. W. LinscheidA.3On the Reproducibility of a Fractionation Procedure for Fish Muscle Proteomics P. Rodrigues*, T. Silva, F. Jessen, and J. DiasA.4Optimization of Peak Capacity in One and Two-Dimensional NanoLC S. Eeltink, B. Dolman, R. Swart, and G. Tremintin*A.5Improving the Utility of Electron-Transfer Dissociation K. F. Medzihradszky*, S. P. Salas-Castillo, and A. L. BurlingameA.6Enrichment and Characterization of Secreted Glycopeptides Bearing SA1–0Galβ1–3GalNAcα Structures Z. Darula and K. F. Medzihradszky*A.7Enrichment of O-GlcNAc Modified Proteins by the Periodate Oxidation – Hydrazide Resin Capture Approach E. Klement, Z. Lipinszky, Z. Kupihar, A. Udvardy, and K. F. Medzihradszky*A.8Proteome Survey Using Affinity Proteomics and Mass Spectrometry N. Olsson*, C. Wingren, M. Mattsson, P. James, F. Nilsson, and C. A. K. BorrebaeckA.9Sampling the N-terminal Proteome of Human Serum and Plasma P. Wildes* and J. A. WellsA.10Profiling Cell Surface and Secreted Glycoproteins Isolated from Human Thyroid Cancer Cell Lines T.-Y. Yen*, N. Haste, A. Castanieto, A. Arcinas, and B. MacherA.11Chemical Cross-linking in Complex Mixtures M. J. Trnka* and A. L. BurlingameA.12Rapid MRM Assay Development Strategies — Intelligent Software and Acquisition Strategies for Highest Productivity S. Mollah*, M. M. Champion, and C. L. HunterA.13Structural Proteins in the Complex Phage 201phi2-1 S. Weintraub*, J. A. Thomas, K. Hakala, P. Serwer, and S. C. HardiesA.14A Quick Method for Differential PTM Analysis of Hypermodified Proteins by FTICR/ECD/MS/MS and Bioinformatics F. Li*, S. Guan., F. Chu, R. Talroze, and A. L. BurlingameA.15Improved Data Mining by Using TPP-based Analysis Workflows for Searching MS/MS Data A. Quandt*, L. Malstroem, H. Lam, D. Shteynberg, and R. AebersoldA.16Microwave-assisted Phosphoproteomics P. Liu* and W. SandovalA.17Proteome Analysis of Apoplastic Proteins in Rice Shoot Respond to Salt Stress Y. Song, A. L. Burlingame, and Y. Guo*A.18Investigation into the Use of Lys-N Combined with Electron Transfer Dissociation on a Quadrupole Time-of-Flight Mass Spectrometer for Peptide Sequencing J. Langridge*, J. Brown, S. Mohammed, N. Taouatas, I. D. G. Campuzano, and A. J. R. HeckTuesday, August 25Session 3Plenary LectureChair: James Wells, University of California, San Francisco, CA, USANikko Ballroom8:30 a.m.3.1Quantitative Analysis of Proteome Localisation and Dynamics Angus Lamond, Wellcome Trust Biocentre, University of Dundee, Scotland, United KingdomChair: Nevan Krogan, University of California, San Francisco, CA, USA9:303.2Post-Translational Adenosine Monophosphate (AMP) Modification of Proteins Antonious Koller, Stony Brook University, Stony Brook, NY, USA10:10Coffee Break10:303.3Dissecting the Structure of the Human Spliceosome by Looking at Its Pieces Melissa Jurica, University of California, Santa Cruz, CA, USA11:103.4Protein Complexes and Functional Pathways in S. cerevisiae and E. coli Jack Greenblatt, University of Toronto, Ontario, Canada11:503.5N-Terminomics: High Confidence, Broad Dynamic Range Coverage Utilizing Novel Polymers for Proteomics Reveals the Functional State of the Proteome Christopher M. Overall, University of British Columbia, Vancouver, British Columbia, Canada12:30 p.m.LunchSession 4Chair: Charles Craik, University of California, San Francisco, CA, USA2:004.1Activity-based Proteomics: Applications for Enzyme and Inhibitor Discovery Benjamin F. Cravatt III, The Scripps Research Institute, La Jolla, CA, USA2:404.2Global Profiling of Proteolytic Cleavage Sites in Apoptosis Sami Mahrus, University of California, San Francisco, CA, USA3:204.3N-terminal & ‘Genome free’ Proteomics; de novo Sequence Analysis by a Combination of LysN Protein Digestion and Electron Transfer Dissociation Albert J. R. Heck, Netherlands Proteomics Center, Utrecht, The NetherlandsPoster Session BCo-Chairs: Katalin Medzihradszky, University of California, San Francisco, CA, USA Jonathan Trinidad, University of California, San Francisco, CA, USA4:00Carmel and Monterey RoomsB.1Elucidating Methyltransferase Target Amino Acid Residues and Downstream Modification Events by Quantitative Mass Spectrometry S. M. Eliuk*, F. Chu, B. Panning, and A. L. BurlingameB.2Ecotoxicoproteomics to Study Microcystin-LR Effects in Medaka Fish M. Edery*, M. Malécot, K. Mezhoud, A. Marie, D. Praseuth, and S. Puiseux-DaoB.3Analysis of the Death Inducing Signaling Complex (DISC) Using Mass Spectrometry V. Pham*, Z. Jin, R. Pitti, Y. Li, D. Lawrence, A. Ashkenazi, and J. LillB.4Proteome-scale Identification of Mitochondrial Transit Peptide Cleavage Sites E. Crawford* and J. A. WellsB.5Enrichment and Analysis of Phosphopeptides Shaved from Membrane Fraction of Salt-stressed Arabidopsis I.-F. Chang*, J.-L. Hsu, L.-Y. Wang, and S.-Y. WangB.6Identification of Protein-Protein Interactions Using Chemical Cross-linking and CID and ETD Tandem Mass Spectrometry X. Du*, J. Rorie, S. Chowdhury, J. Adkins, G. Anderson, and R. SmithB.7Quantitative 2D-Gel Analysis of Isotope Encoded Proteins Using SERRS Detection G. Knudsen*, B. M. Davis, S. K. Deb, Y. Loethen, R. Gudihal, P. Perera, D. BenAmotz, and V. J. DavissonB.8Global Analysis of Caspase Proteolysis During Inflammation N. Agard* and J. A. WellsB.9Two Mass Spectrometry Based Approaches for the Investigation of the Heparin Interactome A. Ori*, M. C Wilkinson, and D. G. FernigB.10Electron Transfer Dissociation Analysis of the Urinary Peptidome in Pregnancy S. Hart*, R. Blankley, and S. GuanB.11Non-Targeted Characterization of Glycopeptides in Lysosomal Storage Disease Samples C. Dorschel*, R. R. Sprenger, J. M. F. G. Aerts, J. P. C. Vissers, and S. J. GeromanosB.12A Novel Combinatorial Library/Mass Spectrometric Approach for Detection of Autoantibody Signatures to Cancer-Associated O-Glycoprotein Epitopes S. B. Levery*, S. K. Kracun, O. Blixt, E. Clo, K. J. Jensen, and H. ClausenB.13Peak Extraction and Deisotoping of Low-Level MSMS Spectra from Quadrupole/TOF Instruments J. Chen*, J. Trinidad, S. Guan, and A. L. BurlingameB.14Network Analysis of Gcn5 HAT Complexes Refines the Organizational Makeup of the SAGA, SliK (SALSA) and ADA Complexes M. Sardiu*, K. Lee, S. Swanson, J. Workman, L. Florens, and M. P. WashburnB.15Quantitative Label-free Analysis of Complex Protein Mixtures through the MFPaQ Software E. Mouton Barbosa*, D. Bouyssié, A. Gonzalez de Peredo, F. Roux-Dalvai, O. Burlet-Schiltz, and B. MonsarratB.16Pigment Epithelium-derived Factor: A Biomarker of Preeclampsia with a Role in the Pathogenesis of the Syndrome K. Williams*, Y. Zhou, and S. FisherB.17Quantitative Comparison of 13-lined Ground Squirrel Kidney Proteins in Six Stages of Mammalian Hibernation N. M. Heidlebaugh, S. L. Martin, and L. E. Epperson*Wednesday, August 26Session 5Chair: Jonathan Trinidad, University of California, San Francisco, CA, USANikko Ballroom8:30 a.m.5.1Characterization of the Velos, an Enhanced LTQ Orbitrap, for Proteomics Jesper Velgaard Olsen, University of Copenhagen, NNF Center for Protein Research, Copenhagen, Denmark9:105.2Analysis of the Yeast Kinase-Substrate Networks by Quantitative Phosphoproteomics Bernd Bodenmiller, ETH - Swiss Federal Institute of Technology, Zurich, Switzerland9:505.3Quantitative Phosphoproteomics to Define Kinase-Substrate Relationships in Cell Division Judit Villén, Harvard Medical School, Boston, MA, USA10:30Coffee BreakPlenary LectureChair: John Stults, Genentech, Inc., South San Francisco, CA, USA10:505.4Global Analysis of Cdk1 Substrate Phosphorylation Sites in vivo David O. Morgan, University of California, San Francisco, CA, USA11:50 a.m.LunchSession 6Chair: Ilena Cristea, Princeton University, Princeton, NJ, USA1:20p.m.6.1Characterization and Quantification of Phosphosites in the Proteome of Human Primary T-Lymphocytes Emilio Gelpi, Instituto Investigaciones Biomedicas, Barcelona, Spain2:006.2Analysis of Ubiquitin Chain Editing by Quantitative Mass Spectrometry Donald S. Kirkpatrick, Genentech, Inc., South San Francisco, CA, USA2:406.3Age Determination in the Adult Human Brain and Body Using Bomb-Carbon Kirsty L. Spalding, Karolinska Insitute, Stockholm, SwedenPoster Session CCo-Chairs: Robert Chalkley, University of California, San Francisco, CA, USA Nicholas Hertz, University of California, San Francisco, CA, USA3:20Carmel and Monterey RoomsC.1Epitope Tagging of Endogenous Proteins in Human Cells for Discovery of Novel Protein/Protein Interactions T. Waldman*, J.-S. Kim, W. Lane, and F. BunzC.2Quantitative Analysis of the Phosphoproteome of Resting and Activated Human Primary T Cells P. Ruperez*, J. A. Oses-Prieto, Ana Gago, and A. L. BurlingameC.3ATAQS Computational Software Tool for High Throughput Transition Optimization and Validation for SRM M.-Y. Brusniak*, D. Campbell, J. Chen, M. Christiansen, E. Deutsch, C. Kwok, S. Letarte, H. Ramos, P. Picotti, L. Reiter, J. Watts, and R. AebersoldC.4Mass-Spectrometric Identification and Relative Quantification of N-linked Cell Surface Glycoproteins B. Wollscheid*, D. Bausch-Fluck, C. Henderson, R. O'Brien, M. Bibel, R. Schiess, R. Aebersold, and J. D. WattsC.5Chronic Ethanol Feeding Affects Proteasome Interacting Proteins M. P. Bousquet-Dubouch*, S. Nguen, D. Bouyssié, O. Burlet-Schiltz, S. W. French, B. Monsarrat, and F. Bardag-GorceC.6Phosphorylation Dynamics at Synapses in the Central Nervous System J. C. Trinidad*, A. Thalhammer, R. Schoepfer, and A. L. BurlingameC.7Linaclotide, a Novel Peptide Therapeutic Agent in Clinical Development for the Treatment of IBS-C and Chronic Constipation is Digested in the Mouse and Human Small Intestine to Small Peptides M. Kessler*, R. W. Busby, J. D. Wakefield, W. P. Bartolini, P. Germano, A. P. Bryant, C. B. Kurtz, and M. G. CurrieC.8Large Scale Multiplex Stable Isotope Dimethyl Labeling Applied to the Quantitative Analysis of Tyrosine Phosphorylation P. Boersema*, L. Y. Foong, V. Ding, S. Lemeer, S. Mohammed, R. Raijmakers, B. van Breukelen, J. Boekhorst, A. B. H. Choo, and A. J. R. HeckC.9Structural Characterization of Novel Components from the Venom of the Mexican Scorpion Vaejovis mexicanus smithi by Electron Capture Dissociation and Electron Transfer Dissociation S. P. Salas-Castillo*, K. F. Medzihradszky, S. Guan, and A. L. BurlingameC.10Proteomics Analysis Reveals a New Player Involved in DNA Repair and/or Replication J. M. Gilmore*, M. E. Sardiu, S. Venkatesh, B. Stutzman, and M. P. WashburnC.11Quantitative Comparison of the Shigella dysenteriae Proteome Assessed by Two Label-Free Global Profiling Methods, APEX and 2D Gels S. Kuntumalla*, J. C. Braisted, S.-T. Huang, P. P. Parmar, D. J. Clark, H. Alami, Q. Zhang, A. Donohue-Rolfe, S. Tzipori, R. D. Fleischmann, S. N. Peterson, and R. PieperC.12Characterization of Protein Kinase C-catalyzed CYP3A4 Phosphorylation by LC Tandem Mass Spectrometry Y. Q. Wang*, S. Guan, A. L. Burlingame, and M. A. CorreiaC.13Analysis of H5N1 Influenza Hemagglutinin Glycosylation by LC/MS/MS Utilizing Hydrazide Capture SPE and HILIC Separation of Intact Glycopeptides T. A. Blake*, T. L. Williams, J. L. Pirkle, and J. R. BarrC.14Mapping the Chromatin Structure Controlling Life Cycle Progression of the Human Malaria Parasite A. Saraf*, S. Cervantes, L. Florens, and K. Le RochC.15Developing Optimized Sensitivity for Proteomic Characterization of Minimal Numbers J. A. Oses-Prieto*, D. Maltby, and A. L. BurlingameC.16A Proteomics Approach to Overcoming Bacterial Drug Resistance: The Ribosomal QconCAT J. Barber, Z. Al-majdoub*, and S. GaskellC.17Proteomic Analysis of the Venom from the Mexican Scorpion Centruroides limpidus limpidus C. V. Ferreira Batista*, O. Villa-Hernández, L. Hernández Orihuela, V. Pando, and L. D. Possani6:00ReceptionJulia Morgan Ballroom7:00Conference DinnerJulia Morgan BallroomThursday, August 27Session 7Chair: Emilio Gelpi, Instituto de Investigaciones Biomedica, Barcelona, SpainNikko Ballroom8:30 a.m.7.1Signaling to Transcription Networks in Nerve Injury Response Michael Fainzilber, Weizmann Institute of Science, Rehovot, Israel9:107.2Regulation of Neuronal Protein Levels at Subcellular Sites Distant from the Cell Body Jeffery L. Twiss, A.I. duPont Hospital for Children, Wilmington, DE, USA9:507.3Organelle Proteomics: Linking Axonal Transport to Nerve Regeneration Valeria Cavalli, Hope Center for Neurological Diseases, Washington University, St. Louis, MO, USA10:30Coffee Break11:007.4Quantitative Phosphoproteomics Identifies Sites in K-Cl Co-Transporters that Regulate Cell Volume and Neuronal Excitation Jesse J. Rinehart, Yale University, New Haven, CT, USA11:40 a.m.LunchSession 8Chair: Pete Wildes, University of California, San Francisco, CA, USA1:40 p.m.8.1A Proteomics Approach to Overcoming Bacterial Drug Resistance: The Ribosomal QconCAT Jill Barber, University of Manchester, Manchester, United Kingdom2:208.2Quantitative Proteomics Analysis of C/EBPα Transcription Factor Complexes in Leukemia Jarrod A. Marto, Dana-Farber Cancer Institute, Harvard Medical Center, Boston, MA, USA3:008.3Rapid, Near Proteome-wide, Quantitative Analysis of Aneuploid Budding Yeast Noah Dephoure, Harvard Medical School, Boston, MA, USAPlenary LectureChair: A. L. Burlingame, University of California, San Francisco, CA, USA3:408.4Advancing Epigenetics Research by Proteomics: Technologies, Applications and Perspectives. Ole Nørregaard Jensen, University of Southern Denmark, Odense, Denmark4:40Closing Remarks5:00Adjourn

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