Mini Symposium and Symposium Registration Foyer, Monterey Room, Hotel Nikko, San Francisco
| Saturday, August 16 | ||
| 3:00 – 5:30 p.m. | ||
| Symposium and Mini Symposium | ||
| Sunday, August 17 | ||
| 7:30 a.m. | Registration Nikko Ballroom Foyer | |
| Mini Symposium on Methods of Protein Quantitation and Dynamics | ||
| Nikko Ballroom | ||
| Chair: Daniel Liebler, Vanderbilt University School of Medicine, Nashville, TN, USA | ||
| 8:30 | MS.1 | Improving the Robustness and Reproducibility of Mass Spectrometry Based Proteomics Michael MacCoss, University of Washington, Seattle, WA, USA |
| 9:30 | MS.2 | SWATH-MS: Principles and Applications to Quantitative Biology Ruedi Aebersold, ETH Zurich, Zurich, Switzerland |
| 10:10 | Coffee Break | |
| 10:50 | MS.3 | Measuring cell signaling and pharmacodynamics using immuno-MRM Jeffrey Whiteaker, Fred Hutchinson Cancer Research Center, Seattle, WA, USA |
| 11:30 | MS.4 | Improving multiplexing limits of parallel reaction monitoring (PRM) through longer one-dimensional chromatography and use of diverse retention time-normalized spectral libraries Anatoly Urisman, University of California, San Francisco, California, USA |
| 12:10 p.m. | Lunch | |
| Chair: Steven A. Carr, The Broad Institute of MIT and Harvard Cambridge, MA, USA | ||
| 1:40 | MS.5 | Recent Advances in HRAM Quantification: Application to Clinical Assays Bruno Domon, Centre de Recherche Public de la Santé (CRP-Santé), Strassen, Luxembourg |
| 2:20 | MS.6 | Expanding Roles of Targeted MS in Biology and Medicine Hasmik Keshishian, The Broad Institute of MIT and Harvard, Cambridge, MA, USA |
| 3:00 | MS.7 | Emerging Approaches to Monitoring Chemotherapeutic Response Arun Wiita, University of California, San Francisco, California, USA |
| 3:40 | MS.8 | Regulation of Protein Acylation by SIRT3 and SIRT5 Bradford Gibson, Buck Institute for Research on Aging, Novato, CA, USA |
| 4:00 p.m. | Symposium Registration Hotel Nikko Ballroom Vestibule, 2nd Floor | |
| 4:00 | Poster Set-up Carmel & Monterey Rooms | |
| 6:00 | Opening Reception Golden Gate Room, 25th Floor | |
| Symposium | ||
| Monday, August 18 | ||
| 7:30 a.m. | Registration Nikko Ballroom Vestibule | |
| Session 1 – Emerging Challenges in Medicine and Biology – Morning | ||
| Nikko Ballroom | ||
| 8:15 | Introduction Ruedi Aebersold, ETH Zurich, Zurich, Switzerland A.L. Burlingame, University of California, San Francisco, CA, USA Steven A. Carr, The Broad Institute of MIT and Harvard Cambridge, MA, USA | |
| Plenary Lecture | ||
| Chair: Arun Wiita, University of California, San Francisco, CA, USA | ||
| 8:30 | 1.1 | Big Data and Human Disease: The New Era Michael Snyder, Stanford University, Stanford, California, USA |
| Chair: Daniel Liebler, Vanderbilt University School of Medicine, Nashville, TN, USA | ||
| 9:30 | 1.2 | Mass spectrometry based draft of the human proteome Bernard Kuster, Technical University Munich, Freising, Germany |
| 10:10 | Coffee Break | |
| 10:30 | 1.3 | Network Approaches to Aggregating Variants and Mutations Trey Ideker, University of California, San Diego, CA, USA |
| 11:10 | 1.4 | Single Cell Network Analysis in 3D Bernd Bodenmiller, University of Zurich, Zurich, Switzerland |
| 11:50 | 1.5 | Spatially-resolved proteomic mapping of living cells (with a focus on mitochondria) using engineered peroxidase reporters Alice Ting, Massachusetts Institute of Technology, Cambridge, MA, USA |
| 12:30 p.m. | Lunch | |
| Session 1 – Afternoon | ||
| Chair: Bradford Gibson, Buck Institute for Research on Aging, Novato, CA, USA | ||
| 2:00 | 2.1 | Use of Personalized Sequence Databases for Peptide MS/MS Spectrum Matching in the Proteogenomic Analysis of 105 TCGA Breast Tumors Karl R. Clauser, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA |
| 2:40 | 2.2 | Proteogenomic analysis of human breast cancer connects genetic alterations to phosphorylation networks Philipp Mertins, Broad Institute of MIT and Harvard, Cambridge, MA, USA |
| 3:20 | 2.3 | Proteogenomic Analysis of Human Colon and Rectal Cancer Daniel Liebler, Vanderbilt University School of Medicine, Nashville, TN, USA |
| Poster Session A | ||
| Co-Chairs: Please see Addendum for Chair names and affiliations | ||
| 4:00 | Carmel and Monterey Rooms | |
| A.1 | Lessons learned during eight years of using iTRAQ in the proteomic study of pathology M. Jullig*, M. Middleditch, G. Cooper | |
| A.2 | Whole animal 15N metabolic pulse chase labeling shows which proteins are built to last J. Savas*, B. Toyama, V. Levram-Ellisman, R. Tsien, M. Hetzer, J. Yates | |
| A.3 | Protein evolution through the lens of the sperm proteome T. Karr* | |
| A.4 | MEK and PI3K dual-inhibition elicits pathway-specific and mitochondrial ubiquitination D.J. Bustos*, J. Baughman, L. Phu, T. Dogan, W.F. Forrest, K.P. Hoeflich, D.S. Kirkpatrick | |
| A.5 | Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry A. Barrett*, R.C. Hill, T. Nemkov, A. D'Alessandro, M. Dzieciatkowska, K.C. Hansen | |
| A.6 | Mass Spectrometric Analysis of Endogenous Tau Modifications in Mice G. Knudsen*, M. Morris, S. Maeda, J.C. Trinidad, A. Ianoviciu, A.L. Burlingame, L. Mucke | |
| A.7 | Advances in antibody-based proteomic analysis M.P. Stokes*, H. Gu., C.L. Farnsworth., J.M. Ren, K.A. Lee, J.C. Silva | |
| A.8 | Proteomics versus transcriptomics for the identification of cancer biomarkers: the case of brain-derived metastatic breast cancer cells M.D. Dun, R.J. Chalkley, S. Keene, R.A. Bradshaw, H. Hondermarck* | |
| A.9 | Evolution of separate predation- and defence-evoked venoms in carnivorous cone snails S. Dutertre, A.-H. Jin*, I. Vetter, B. Hamilton, K. Sunagar, V. Lavergne, V. Dutertre, B.G. Fry, A. Antunes, D.J. Venter, P.F. Alewood, R.J. Lewis | |
| A.10 | A Standardized Scoring System for Affinity Purification/Mass Spectrometry Data Xu Li*, B. White, R. Guerra, J. Chen | |
| A.11 | Large Scale Proteomic Characterisation of sites of Proline Hydroxylation in human proteins D. Bensaddek*, S.C. Moser, B. Ortmann, S. Rocha, J.R. Swedlow, A.I. Lamond | |
| A.12 | Using the Exactive Plus EMR mass spectrometer for probing protein-ligand and protein-protein interactions J.B. Johnston*, Ž. Roe-Žurž, M. Trnka, S. Guan, P.R. Ortiz de Montellano, D. Agard, A.L. Burlingame | |
| A.13 | Phoxtrack − an unbiased approach for deciphering proteins that are causative for post-translational modifications S. Sauer*, C. Weidner, C. Fischer, M. Kliem | |
| A.14 | Top Down Venom Analysis with Byonic Software M. Bern*, D. Kletter, D. Fenyo, D. Morgenstern, B. Ueberheide, N. Bern, W. Tang, Y.J. Kil, C. Becker | |
| A.15 | Treatment-induced Apoptotic Peptides as Efficacy Biomarkers in Mouse Models J. Seaman*, J.A. Wells | |
| A.16 | Extracellular Matrix Quantification of Tissue Engineered Scaffolds: Analysis of Rat Lung using the QconCAT Method R.C. Hill*, E.A. Calle, L.E. Niklason, K.C. Hansen | |
| A.17 | Proteomic analysis of the role of the translation initiation factor eIF4E in C. elegans J. Oses-Prieto*, M. Quimis Ponce, Q. Dong, A.L. Burlingame, R.E. Rhoads | |
| Tuesday, August 19 | ||
| Session 2 – Methodologies Enabling New Insights into Biology I – Morning | ||
| Plenary Lecture | ||
| Chair: Steven A. Carr, The Broad Institute of MIT and Harvard, Cambridge, MA, USA | ||
| Nikko Ballroom | ||
| 8:30 a.m. | 3.1 | Systems analysis of mitochondrial pathogenesis Vamsi Mootha, Harvard Medical School, Boston, MA, USA |
| Chair: Anne-Claude Gingras, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ONT, Canada | ||
| 9:30 | 3.2 | PTMomics - Towards comprehensive quantitative analysis of multiple PTMs from biological material. Martin Larsen, University of Southern Denmark, Odense, Denmark |
| 10:10 | Coffee Break | |
| 10:30 | 3.3 | Epigenetic and metabolic regulation by a family of new lysine acylation pathways Yingming Zhao, University of Chicago, Chicago, IL, USA |
| 11:10 | 3.4 | Identification and characterization of caspase substrates that regulate axon degeneration in development and disease Nicholas Hertz, Rockefeller University, New York, NY, USA |
| 11:50 | 3.5 | Proteomics and the functional organization of axons Matthew Rasband, Baylor College of Medicine,Houston, TX, USA |
| 12:30 p.m. | Lunch | |
| Session 2 – Afternoon | ||
| Chair: Bernard Kuster, Technical University Munich, Freising, Germany | ||
| 2:00 | 4.1 | High resolution LC coupled with high resolution MS for in-depth proteomics. Yasushi Ishihama, Kyoto University, Kyoto, Japan |
| 2:40 | 4.2 | NeuCode Mouse and One Hour Proteomes Joshua Coon, University of Wisconsin-Madison, Madison, WI, USA |
| 3:20 | 4.3 | How proteomics big data will transform mass spectrometry data analysis Nuno Bandeira, University of California, San Diego, CA, USA |
| Poster Session B | ||
| Co-Chairs: Please see Addendum for Chair names and affiliations | ||
| 4:00 | Carmel and Monterey Rooms | |
| B.1 | Development of a Proximity Labeling Method to Identify the Protein Targets of Bioactive Small Molecules Z. Hill*, M. Zhuang, J.A. Wells | |
| B.2 | Modelling atherosclerosis: Molecular changes in the ascending aorta of cholesterol-fed rabbits J. Xu*, M. Jüllig, M. Middleditch, G. Cooper | |
| B.3 | Post-translational modification networks V. van Noort* | |
| B.4 | Extracellular Phosphorylation in the Murine Synaptosome J.C. Trinidad*, R. Schoepfer, A.L. Burlingame, K.F. Medzihradszky | |
| B.5 | Using Selective Reaction Monitoring (SRM) mass spectrometry to unmask regulatory feedback loops controlling adipogenesis R. Ahrends*, A. Ota, K.M. Kovary, T. Kudo, B. Ouk Park, M.N. Teruel | |
| B.6 | Application of quantitative and functional phosphoproteomics in study of ethylene signaling Ning Li* | |
| B.7 | Intact N- and O-linked glycopeptide identification from HCD data using Byonic K.F. Medzihradszky*, J. Maynard, K. Kaasik, M. Bern | |
| B.8 | Factors that contribute to the complexity of glycopeptide analysis – besides site-specific heterogeneity K.F. Medzihradszky*, Z. Darula | |
| B.9 | Characterizing qualitative and quantitative global changes in the aging heart using pSMART, a novel acquisition method M.S. Vogelsang*, A. Prakash, D. Sarracino, G. Vadali, S. Peterman | |
| B.10 | Quantitative Site-Specific Profiling S-glutathionylation in Macrophages in Response to Engineered Nanomaterial-induced Oxidative Stress J. Duan*, V.K. Kodali, M.J. Gaffrey, J. Guo, R.K. Chu, D.G. Camp, R.D. Smith, B.Thrall, W.-J. Qian | |
| B.11 | O-GlcNAc regulates SOX2 activity in embryonic stem cells by altering protein-SOX2 interactions S. Myers*, S. Pedadda, T. Freidrich, S. Thomas, G. Krings, M. Lopez, M. Trinidad, B. Panning, A. Burlingame | |
| B.12 | Development of multiplexed assays for oral cancer biomarker verification by peptide immunoaffinity enrichment and targeted mass spectrometry Y.-C. Hsiao*, L.-M. Chi, K.-Y. Chien, Y.-T. Chen, Y.-S. Chang, J.-S. Yu | |
| B.13 | Characterisation of Glycosylation of Paramyxovirus Surface Glycoproteins by Mass Spectrometry C.L. Pegg*, C. Hoogland, S.M. Johnson, C.C. Gonzalez, M.E. Peeples, J.J. Gorman | |
| B.14 | Developing A New In Vivo Cross-linking Mass Spectrometry Platform to Define Protein-Protein Interactions in Living Cells R.M. Kaake, X. Wang, A. Burke, C. Yu, W. Kandur, Y. Yang, E.J. Novtisky, T. Second, J. Duan, A. Kao, S. Guan, D. Vellucci, S.D. Rychnovsky, L. Huang* | |
| B.15 | High-resolution Orbitrap characterization of preferential chain pairing in co-expressed bispecific antibody production by MS under native and acidic conditions L. Schachner*, J. Zhou, L. McCarty, D. Ellerman, M. Dillon, C. Spiess, J. Lill, P. Carter, W. Sandoval | |
| B.16 | Controlling low rates of cell differentiation through noise and ultra-high feedback R. Ahrends, A. Ota, K.M. Kovary, T. Kudo, B. Ouk Park, .M.N. Teruel* | |
| Wednesday, August 20 | ||
| Session 3 – Methodologies Enabling New Insights into Biology II – Morning | ||
| Chair: Averil Ma, University of California, San Francisco, California, USA | ||
| Nikko Ballroom | ||
| 8:30 a.m. | 5.1 | Resolving sites of protein palmitoylation using quantitative proteomics Mark Collins, The University of Sheffield, England, UK |
| 9:10 | 5.2 | A novel comprehensive discovery approach for SUMO modified proteins. Elizabeth Komives, University of California, San Diego, CA, USA |
| 9:50 | 5.3 | NeuCode Mass Spectrometry Unveils New Roles for Ubiquitin Machinery in Metabolic Homeostasis. Josh Baughman, Genentech, Inc., South San Francisco, CA, USA |
| 10:30 | Coffee Break | |
| Plenary Lecture | ||
| Chair: Gerald Hart, Johns Hopkins University School of Medicine, Baltimore, MD, USA | ||
| 10:50 | 5.4 | Functional Glycomics - Defining Glycan Recognition by Proteins Richard Cummings, Emory University, Atlanta, GA, USA |
| 11:50 a.m. | Lunch | |
| Session 3 – Afternoon | ||
| Chair: Ruedi Aebersold, ETH Zurich, Zurich, Switzerland | ||
| 1:20 pm | 6.1 | Dynamic profiling of the protein life cycle reveals two distinct strategies for controlling differential expression of immune and housekeeping protein levels in response to pathogens. Marko Jovanovic, The Broad Institute of MIT and Harvard, Cambridge, MA, USA |
| 2:00 | 6.2 | High-Throughput Proteomic Mapping of Protein Interaction Networks: Toward a Global View of the Human Interactome Edward L. Huttlin, Harvard Medical School, Boston, MA, USA |
| Poster Session C | ||
| Co-Chairs: Please see Addendum for Chair names and affiliations | ||
| 2:40 | Carmel and Monterey Rooms | |
| C.1 | Non-biased identification and kinetic analysis of Caspase-2 and Caspase-6 proteolytic substrates in cell lysate O. Julien*, M. Zhuang, A. Wiita, J.A. Wells | |
| C.2 | Sensitive Isoform-specific Quantification of ERK Phosphorylation Dynamics and Stoichiometry in Human Cells by PRISM-SRM W. Qian*, T. Shi, Y. Gao, M.J. Gaffrey, T.L. Fillmore, C.D. Nicora, W.B. Chrisler, M.A. Gritsenko, R.D. Smith, D.G. Camp, T. Liu, K.D. Rodland, S.H. Wiley | |
| C.3 | Comprehensive Proteomic Dissection of the Battle Between Human Respiratory Syncytial Virus and Host Cells J. Gorman*, K. Dave, E. Norris, M. Headlam, T. Singh, K. Chappell, A. Bukreyev, U. Buchholz, P. Collins | |
| C.4 | Improved Peak Detection and Deconvolution of Native Protein Complex Electrospray Mass Spectra J. Lu*, M. Trnka, S. Guan, A.L. Burlingame | |
| C.5 | Targeted proteomic analysis reveals potential saliva biomarker for recurrence monitoring of oral cavity squamous cell carcinoma L.C.J. Chu*, Y.-T. Chen, J.-S. Yu, Y.-S. Chang | |
| C.6 | In vivo cross-linking combined with Affinity-Purification Mass Spectrometry and label-free quantification to study human proteasome complexes: Composition, subcellular distribution, and preferential subcomplexes associations. B. Fabre, T. Lambour, L. Garrigues, T. Menneteau, M. Ducoux, F. Amalric, B. Monsarrat, M.-P. Bousquet-Dubouch, O. Burlet-Schiltz* | |
| C.7 | Proteomic mapping of living cells with an evolved peroxidase reporter, and application to mitochondrial and endoplasmic reticulum proteomes. S. Lam*, V. Hung, J.D. Martell, N.D. Udeshi, V.K. Mootha, S.A. Carr, A.Y. Ting | |
| C.8 | Optimization of Glycopeptide Enrichment using Lectin Weak Affinity Chromatography J. Maynard*, K. Kaasik, A.L. Burlingame | |
| C.9 | Single Cell Proteomic Analysis of the Cell Cycle K. Kovary*, M. Teruel | |
| C.10 | In-Depth Identification of Protein Sequence Variants and Posttranslational Modifications in 10 Human Cell Lines A.J. Cesnik*, M.R. Shortreed, G.M. Sheynkman, B.L. Frey, L.M. Smith | |
| C.11 | Expanding the Role of TAK1 in Immune and Inflammatory Response Through Chemical Genetics R. Levin*, N. Hertz, J. Gordan, A.L. Burlingame, K. Shokat | |
| C.12 | Investigating HIV-mediated dynamics of Cullin RING E3 ligases and ubiquitination by targeted proteomics R. Huttenhain*, J.R. Johnson, D. Crosby, L. Satkamp, T.L. Johnson, W. Newton, N.J. Krogan | |
| C.13 | Validating plasma-based biomarkers for ovarian cancer using targeted proteomics R. Hüttenhain*, M. Choi, C.-Y. Chang, D. Dinulescu, O. Vitek, E. Nimèus-Malmström, R. Aebersold | |
| C.14 | Interaction Proteomics of the exocytosis machinery – an essential role for septin dynamics E. Tokhtaeva, J. Capri, E. Marcus, J. Whitelegge*, V. Khuzakhmetova, E. Bukharaeva, N. Deiss-Yehiely, L. Dada, G. Sachs, O. Vagin | |
| C.15 | Site-specific N-Glycosylation Mapping for Glycopeptides in the Presence of Other Unknown Post-translational Modifications B. Wang*, D. Salom, K. Palczewski, M.R. Chance | |
| C.16 | Protein interaction networks involved in lineage specific transcriptional programs P. Samavarchi-Tehrani*, J.-P. Lambert, B. Larsen, M. Tucholska, A.-C. Gingras | |
| CONFERENCE DINNER | ||
| 6:00 | Reception Foyer, Nikko Ballroom | |
| 7:00 | Conference Dinner Nikko Ballroom | |
| Thursday, August 21 | ||
| Session 4 – Methodologies Enabling New Insights into Biology III – Morning | ||
| Chair: Odile Burlet-Schiltz, Institute of Pharmacology and Structural Biology (IPBS), CNRS, Toulouse, France | ||
| Nikko Ballroom | ||
| 8:30 a.m. | 7.1 | Proteomic Advances for Epigenetics Research Ben Garcia, University of Pennsylvania Medical School, Philadelphia, PA, USA |
| 9:10 | 7.2 | Dissecting the role of the extracellular matrix in cancer progression: a proteomics-based approach. Alexandra Naba, Massachusetts Institute of Technology, Cambridge, MA, USA |
| 9:50 | 7.3 | Signaling interactome dynamics in health and disease Anne-Claude Gingras, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ONT, Canada |
| 10:30 | Coffee Break | |
| 11:00 | 7.4 | Structure of RNA polymerase II – Mediator holoenzyme investigated through an integrated mass spectrometry and electron microscopy approach Michael Trnka, University of California, San Francisco, CA, USA |
| 11:40 a.m. | Lunch | |
| Session 4 – Afternoon | ||
| Chair: A.L. Burlingame, University of California, San Francisco, California, USA | ||
| 1:40 p.m. | 8.1 | Photo-cross-linking and high-resolution mass spectrometry for assignement of RNA-binding sites in RNA-binding proteins. Henning Urlaub, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany |
| 2:20 | 8.2 | Cellular Immune Response versus Viral Immune Evasion: Lessons from Proteomics Ileana Cristea, Princeton University, New Jersey, USA |
| 3:00 | 8.3 | Genetic Variability and the Quantitative Proteome Ruedi Aebersold, ETH Zurich, Zurich, Switzerland |
| MCP Plenary Lecture | ||
| Chair: Ralph A. Bradshaw, University of California, San Francisco, California, USA | ||
| 3:40 | 8.4 | The interplay between protein phosphorylation and protein ubiquitylation in regulating the innate immune system Sir Philip Cohen, University of Dundee, Scotland, GB |
| 4:40 | Closing Remarks | |
| 5:00 | Adjourn | |