Source: Molecular & Cellular Proteomics (article, 2019-08-01)
Field: Chemistry — Spectroscopy

Program Schedule All sessions and activities will be held at the Hotel Nikko San Francisco, unless noted otherwise.SATURDAY, AUGUST 174:00 – 6:30 p.m.Registration open Nikko Ballroom Foyer, 3rd FloorSUNDAY, AUGUST 187:30 a.m. – 4:00 p.m.Registration open Nikko Ballroom Foyer, 3rd Floor8:00 a.m.Exhibitor Set-up Nikko Ballroom Foyer, 3rd FloorMINISYMPOSIUM ON DATA-INDEPENDENT ANALYSISNikko Ballroom, 3rd FloorOrganizers: Robert Chalkley, University of California, San Francisco, CA, USA and Hannes Röst, University of Toronto, CanadaPlenary Session8:30MS1Improving the robustness, throughput and comprehensiveness of quantitative proteomics Mike MacCoss, University of Washington, Seattle, WA, USAMorning SessionChair: Robert Chalkley, University of California, San Francisco, CA, USA9:30MS2Complex-centric proteome profiling by SEC-SWATH-MS Isabell Bludau, ETH, Zurich, Switzerland10:10Coffee Break in foyer10:50MS3Aligning label-based discovery and global DIA validation proteomics to explore bacterial virulence phenotypes Stuart Cordwell, University of Sydney, Australia11:30MS4Advanced algorithms to assess and improve quantitative suitability in large DIA datasets Sebastian Vaca Jacome, Broad Institute of MIT and Harvard, Cambridge, MA, USA12:10 p.m.Lunch on ownAfternoon SessionChair: Mike MacCoss, University of Washington, Seattle, WA, USA1:40MS5Parallel accumulation — serial fragmentation combined with data-independent acquisition (diaPASEF) Florian Meier, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany2:20MS6Mobi-DIK (Ion Mobility DIA Analysis Kit): Targeted analysis software for diaPASEF data improves proteome coverage Hannes Röst, University of Toronto, Canada3:00MS7Applications of DIA for PTM research and specific DIA workflows Birgit Schilling, Buck Institute for Research on Aging, Novato, CA, USA3:40MS8Peptide MS/MS prediction for DDA and DIA Mathias Wilhelm, Technical University of Munich, Freising, Germany4:00Poster Set-up – all authors to mount posters on boards Carmel and Monterey Rooms, 3rd Floor4:00 – 6:00 p.m.Exhibits Open Nikko Ballroom Foyer, 3rd Floor6:00Opening Reception Golden Gate Room, 25th FloorMONDAY, AUGUST 197:30 – 4:00 p.m.Registration open Nikko Ballroom Foyer, 3rd Floor8:00 – 1:00 p.m.Exhibits Open Nikko Ballroom Foyer, 3rd FloorSYMPOSIUMNikko Ballroom, 3rd Floor8:15 a.m.Introduction A.L. Burlingame, Steven Carr, and Bernhard KusterPlenary SessionChair: A.L. Burlingame, University of California, San Francisco, CA, USA8:301.1The End of the End: High through-put discovery and analysis of degrons Stephen Elledge, Harvard Medical School, Cambridge, MA, USAMorning SessionChair: Bernhard Kuster, Technical University of Munich, München, Germany9:301.2Drug effects on protein stability and proteostasis Marcus Bantscheff, Glaxo Smith Kline, Heidelberg, Germany10:10Coffee Break in foyer10:301.3Development, use, application of novel TIMS-Tof system Matthias Mann, Max Planck Institute of Biochemistry, Martinsried, Germany11:101.4Lysine-targeted covalent inhibitors and chemoproteomic probes Jack Taunton, University of California, San Francisco, CA, USA11:501.5Mapping proteolysis at the surface of living cells Amy Weeks, University of California, San Francisco, CA, USA12:30 p.m.Lunch on ownAfternoon SessionChair: Anne-Claude Gingras, Lunenfeld-Tanenbaum Research Institute, Toronto, Canada2:001.6Characterization and turnover of RNA-binding proteins: Novel insights into ribosome maintenance Jeroen Krijgsveld, German Cancer Research Center, Heidelberg, Germany2:401.7Deciphering gene expression regulation in health and disease using integrative Omics approaches Michiel Vermeulen, Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands3:201.8Protein interaction networks controlling gene expression programs and beyond Jeffrey A. Ranish, Institute for Systems Biology, Seattle, WA, USA4:00Poster Session A Carmel and Monterey Rooms, 3rd Floor Co-Chairs: Robert Chalkley, University of California, San Francisco, CA, USA Jason Maynard, University of California, San Francisco, CA, USAA.1Dynamic proteomic profiling of the Salmonella-host interplay reveals new modes of action for known and novel virulence factors Jennifer Geddes-McAlister*, Stefanie Vogt, Jennifer Rowland, Sarah Woodward, Arjun Sukumaran, Lilianne Gee, Baerbel Raupach, Brett Finlay, Felix MeissnerA.2Identification of urine-derived diagnostic biomarkers for Tuberculosis Bridget Calder*A.3Microscaled Proteogenomic Methods for Precision Oncology Shankha Satpathy*, Eric Jaehnig, Karsten Krug, Michael Gillette, Alexander Saltzman, Kimberly Holloway, Meenakshi Anurag, Chen Huang, Purba Singh, Beom-Jun Kim, Goerge Miles, Noel Namai, Anna Malovannaya, DR Mani, Chuck Perou, Bing Zhang, Steven Carr, Matthew EllisA.4Reduced proteasome activity in the aging brain results in ribosome stoichiometry loss and aggregation Joanna Kirkpatrick*, Erika Sacramento, Mariateresa Mazzetto, Simone Di Sanzo, Cinzia Caterino, Aleksandar Bartolome, Michele Sanguanini, Nikoletta Papaevgeniou, Maria Lefaki, Dorothee Childs, Eva Terzibasi-Tozzini, Natalie Romanov, Mario Baumgart, Wolfgang Huber, Niki Chondrogianni, Michele Vendruscolo, Alessandro Cellerino, Alessandro OriA.5Affinity Proteomics Reveals Assembly of PPP-type Phosphatase Holoenzyme by PPM1G-B56δ Parveen Kumar*, Prajakta Tathe, Subbareddy MaddikaA.6Targeted Quantification of Incomplete Prohormone Processing Products in Type 1 Diabetes Yinyin Ye*, Adam Swensen, Lian Yi, Yuqian Gao, Emily Sims, Tujin Shi, Carla Greenbaum, Carmella Evans-MolinaA.7Novel methods and reagents for characterization of protein biotinylation sites by peptide-based immunoaffinity enrichment Matthew Stokes*, Yiying Zhu, Matthew Fry, Alissa Nelson, Jian Min Ren, Vicky Yang, Michael Palazzola, Charles Farnsworth, Kimberly LeeA.8Exploring the glycosylation levels of snake venom proteins by mass spectrometry: microheterogeneity determination of sweet spots in toxins of Bothrops snake genus Débora Andrade Silva*, Lívia Rosa-Fernandes, Giuseppe Palmisano, Silvia Travaglia-Cardoso, Solange Toledo Serrano, Martin LarsenA.9Expression of PNPLA3 I148M Variant Alters Lipid Droplet Proteome Mara Monetti*, Jeffrey Culver, Sharath Sasi, Liang Xue, Gregory Tesz, Collin Crowley, Trenton Ross, Thomas Magee, Melissa Miller, Bei Zhang, Kendra BenceA.10Vascular Cell Surface Proteomics In Vivo Dirk Walther*, Elizabeth Gordon, Benjamin Smith, Thomas Cameron, Ru Wei, Peter JuhaszA.11Application of 4C Proteomics and Interactomics in Study of PTM Proteins Involved in Regulation of Arabidopsis Flowering Ning Li*A.12Characterization of Symptomatic Aortic Valve Stenosis Subtypes by DIA-MS Proteome Profiling Christof Lenz*, Lisa Neuenroth, Soeren Brandenburg, Stephan Lehnart, Henning UrlaubA.13Cell-surface proteomic landscape of developing and mature olfactory projection neurons Jiefu Li*, Shuo Han, Hongjie Li, Namrata Udeshi, Tanya Svinkina, D. Mani, Chuanyun Xu, Ricardo Guajardo, Qijing Xie, Tongchao Li, Bing Wu, Anthony Xie, David Luginbuhl, Pornchai Kaewsapsak, Stephen Quake, Steven Carr, Alice Ting, Liqun LuoA.14Breast cancer quantitative proteome and proteogenomic landscape Henrik Johansson*, Fabio Socciarelli, Nathaniel Vacanti, Mads Haugen, Yafeng Zhu, Ioannis Siavelis, Alejandro Fernandez-Woodbridge, Miriam Aure, Bengt Sennblad, Mattias Vesterlund, Rui Branca, Lukas Orre, Mikael Huss, Erik Fredlund, Elsa Beraki, Øystein Garred, Jorrit Boeke, Torill Sauer, Wei Zhao, Silje Nord, Elen Höglander, Daniel Jans, Hjalmar Brismar, Tonje Haukaas, Tone Bathen, Ellen Schlichting, Bjørn Naume, OSBREAC, Torben Luders, Elin Borgen, Vessela Kristensen, Hege Russnes, Ole Christian Lingjærde, Gordon Mills, Kristine Sahlberg, Anne-Lise Børresen-Dale, Janne LehtiöA.15Native Mass Spectrometry Study on the Stoichiometry of Proteasome AAA+ ATPase Nucleotide Binding H. Ewa Witkowska*, Yadong Yu, Haichuan Liu, Zanlin Yu, Yifan ChengA.16Towards Elucidation of Muscle-Specific Receptor Tyrosine Kinase (MuSK) Signaling Pathway by Differential Agonists Hanna Budayeva*, Arundhati Sengupta Ghosh, Lilian Phu, Donald KirkpatrickA.17Multiplexed and Quantitative Assessment of the Cellular Reactive Cysteinome in T cell activation Liang Xue*, Uthpala SeneviratneA.18Enzyme toolkit for selective enrichment and analysis of mucin-domain glycoproteins Stacy Malaker*, Judy Shon, Kayvon Pedram, Nicholas Riley, Carolyn BertozziA.19Functional Metabolomics uncovering the role of Trp–KYN–KA Axis in Intestinal Injury and Repair Di Wang*, Huimin Guo, Zunjian Zhang, Fengguo XuA.20Metabolic Control of OGT Interactome in Hepatocytes Krista Kaasik*, Chin Fen Teo, Robert Chalkey, Alma BurlingameA.21Integrating Phosphoproteomics and Transcriptional Classifiers Reveals “Hidden Signaling” in Multiple Myeloma Including Differential KRAS and NRAS Mutant Effects Yu-Hsiu Lin*, Gregory Way, Benjamin Barwick, Margarette Mariano, Makeba Marcoulis, Ian Ferguson, Christoph Driessen, Lawrence Boise, Casey Greene, Arun WiitaA.22Characterization of KRAS 4B C-Terminal Hypervariable Region using LC/MS James Wilkins*, A.L. BurlingameA.23Rapid, Sensitive and Multiplexed Ubiquitylation Profiling in Cells and Tissues Deepak Mani*, Namrata Udeshi, Philipp Mertins, Shaunt Fereshetian, Jessica Gasser, Shankha Satpathy, Tanya Svinkina, Hasmik Keshishian, Benjamin Ebert, Steven CarrA.24Characterization of a hybrid insulin peptide as an autoantigen in human type 1 diabetes Timothy Wiles*, Rocky Baker, Maki Nakayama, Thomas DelongA.25Improved reproducibility of enrichment and site-assignment of biotinylated peptides using new anti-biotin antibody and its use to investigate redox signaling Meagan Olive*, Namrata Udeshi, Samuel Myers, Steven CarrA.26Proteome-wide analysis of protein stability in E. coli using pulse proteolysis Roman Körner*, Liang Zhao, Giulia Vecchi, Michele Vendruscolo, Manajit Hayer-Hartl, Ulrich HartlA.27The case for mass spectrometry-based proteomics and phospho-proteomics in personalized cancer medicine Sophia Doll*, Fabian Coscia, Alberto Santos, Philipp Nuhn, Philipp Geyer, Matthias MannA.28Characterization of the Sin3 HDAC complex interaction network Mark Adams*, Charles Banks, Janet Thornton, Cassandra Kempf, Sayem Miah, Laurence Florens, Michael WashburnA.29Proteogenomics of melanoma cell lines and xenografts identifies amino acid variants with a potential to rewire signal transduction networks Marisa Schmitt*, Nicolas Nalpas, Tobias Sinnberg, Heike Niessner, Claus Garbe, Boris MacekA.30Integration of the deep learning prediction tool Prosit into Skyline for high-accuracy, on-demand fragment intensity and iRT prediction Tobias Rohde*, Tobias Schmidt, Bernhard Kuster, Michael MacCoss, Mathias Wilhelm, Brendan MacLeanA.31Exploring mechanisms of immune suppression promoted by cancer-associated fibroblasts in lung squamous cell carcinoma Carlo Ramil*, Handan Xiang, Josephine Hai, Chunsheng Zhang, Huijun Wang, Amanda Watkins, Roshi Afshar, Peter Georgiev, Xuelei Song, Dongyu Sun, Andrey Loboda, Yanlin Jia, Lily Moy, Philip Brandish, An ChiA.32Changes in prooncogenic and immune response proteins during development of cervical cancer through quantitative proteomics Jose Hernandez-Hernandez*, Gonzalo Soto-Fuenzalida, Rosa Lopez-Sanchez, Sergio Encarnacion-Guevara, Juan Martinez-Ledesma, Rocio Ortiz-Lopez, Luis Villela-Martinez, Victor Treviño-AlvaradoA.33Elucidating Changes in O-GlcNAcylation in Pancreatic Cancer Talieh Zomorrodinia*, Jason Maynard, Krista Kaasik, Alma BurlingameA.34In vivo investigation of kigelia africana leaf as possible therapeutic option for gastric ulcer disease Oladayo Apalowo*, Babatunde Adekola, Funke Asaolu, Vincent Oriyomi, Gbenga Ogunleye, Oladayo Areola, Olusegun BabalolaA.35Formation of N-GlcNAc proteins is upregulated upon inhibition of proteasome activity in Ngly1-KO cells Jason Maynard*, Haruhiko Fujihira, Gabby Dolgonos, Tadashi Suzuki, Alma BurlingameA.36Unbiased Proteomics and Network Propagation Reveals Cancer Drug Targets Mehdi Bouhaddou*, Neil Bhola, Rachel O'Keefe, Margaret Soucheray, Hua Li, Tian Zhu, Kelechi Nwachuku, Toni Brand, Gordon Mills, Dan Johnson, Danielle Swaney, Jennifer Grandis, Nevan KroganA.37Tuning residence time with lysine-targeted, reversible covalent probes Tangpo Yang*, Adolfo Cuesta, Xiaobo Wan, Jack TauntonA.38Characterizing and Targeting the Hypoxic T Cell Surfaceome to Promote Immune Function in Cancer James Byrnes*, Lisa Kirkemo, Amy Weeks, James WellsA.39Twins Labeling Derivatization-based LC-MS/MS Strategy for absolute quantification of modified metabolites Wei Li*, Zunjian Zhang, Fengguo XuA.40A Chemoproteomics Workflow for the Global Analysis of Acyl-CoA Signaling Networks Michaella Levy*, David Montgomery, Mihaela Sardiu, Abigail Thorpe, Steve Fox, Qishan Lin, Thorkell Andresson, Laurence Florens, Michael Washburn, Jordan MeierA.41Proteomics insights into the role of PknG in mycobacterial physiology and pathogenesis Rosario Durán*, Analía Lima, Magdalena Gil, Bernardina Rivera, Jessica Rossello, Annemarie Wehenkel, María Lisa, Pedro AlzariA.42Pushing the limits: Boosting sensitivity of PRM assays for the detection of very low abundant proteins in complex samples Alexander Schmidt*, Emmanuelle Lezan, Erik Ahrné, Thomas BockA.43Discovery of a common target of natural products through combination of chemical genomics and proteomics Haijun Guo, Yang Yang, Jieren Deng, Mankin Wong, Qian ZhaoA.44Developing a reversible covalent protein/ peptide capture technology for low abundance proteomics Brendan M. Floyd, Cecil J. Howard II, Jagannath Swaminathan, James L. Reuther, Edward M. Marcotte, Eric V. AnslynTUESDAY, AUGUST 208:00 – 1:00 p.m.Exhibits Open Nikko Ballroom Foyer, 3rd FloorSYMPOSIUMNikko Ballroom, 3rd Floor8:30 a.m.Flash Talks: Poster presenters will be invited to give 1 min. “flash” talks on their work.Chair: Angus Lamond School of Life Sciences, University of Dundee, Dundee, Scotland10:10 a.m.Coffee Break in foyerMorning SessionChair: Don Kirkpatrick, Genentech, Inc.10:302.1The growing molecular complexity of ribosome biology Maria Barna, Stanford University, Stanford, CA, USA11:102.2Deciphering cellular organization using protein thermal stability and solubility Mikhail M. Savitski, European Molecular Biology Laboratory, Heidelberg, Germany11:502.3A proteomics view of mTOR signaling in humans Anne-Claude Gingras, Lunenfeld–Tanenbaum Research Institute, Toronto, Canada12:30 p.m.Lunch on ownAfternoon SessionChair: Bernhard Kuster, Technical University of Münich, München, Germany2:302.4New Ub profiling approaches and applications Namrata Udeshi, Broad Institute of MIT and Harvard, Cambridge, MA, USA3:102.5Proteomic exploration of lysine acetylation signaling Chuna Choudhary, University of Copenhagen, Copenhagen, Denmark3:502.6Characterization of complexes and organelles Kathryn Lilley, University of Cambridge, United Kingdom4:30Poster Session B Carmel and Monterey Rooms, 3rd FloorChairs: Michael Trnka, University of California, San Francisco, CA, USA and Nancy Phillips, University of California, San Francisco, CA, USAB.1Identification and Quantification Method for UCN2 by LC/MS/MS from Plasma/Serum from Mouse Disease Models Shakey Quazi*, Wei Zheng, Olivier BezyB.2Integrating de novo sequencing with sequence database and spectral library search for in-depth analysis of DIA data with PEAKS Paul Shan*, Xin Chen, Clark Chen, Julia HopkinsB.3High-Throughput PEAKS Workflow for Large Scale Quantitative Proteomics using PEAKS Online X Jonathan Krieger*, Julia Hopkins, Lei Xin, Baozhen ShanB.4TAILS identifies candidate substrates and biomarkers of ADAMTS7, a therapeutic protease target in coronary artery disease Charlie Mundorff*, Daniel Lai, Nadine Elowe, Hasmik Keshishian, Alessandro Arduini, Bryan MacDonald, Steven CarrB.5Role of the Particle for Arrangement of Quaternary structure (PAQosome) in assembly/maturation of human protein complexes and networks Benoit Coulombe*, Philippe Cloutier, Maxime Pinard, Christian Poitras, Analysis of peptides from B cells and cells in J. Lawrence of the is by the proteins and and of and T cells Lawrence proteomics to novel of the proteome inhibition in cancer cells Silvia Mark Paul Angus Paul analysis of Interactome proteome profiling to and in Philipp Matthias Mann, and of using Yafeng Zhu, Janne Rui Branca, profiling reveals activity in Nevan novel profiling mass to improve prediction Amanda Daniel Ting, Michael Jennifer capture and of proteins for profiling Nancy Juan Robert Chalkley, Alma a of the proteome the into the inhibitors proteasome by proteostasis Arun Ian Ferguson, Margarette Mariano, Paul Wang, Jason in Multiple of the and Emily Melissa Thomas and of a Targeted to the of and to Michael Adam Hasmik Keshishian, Eric Steven Carr, Benjamin Profiling of from High Cancer and Reveals Novel Eric Karsten Krug, Liu, Paul Michael DR Mani, Steven Steven Carr, Michael of Quantitative Phosphoproteomics in the Study of Yang*, Ning the with and David proteomics of and proteins Zhang, Lin, Alice of the during the immune response profiling as a novel tool to the of on the proteome Sarah Jose Analysis to Proteins in Particle by Method and Analysis of the – an in Thomas Juan Shi, Wang, Alma Burlingame, in proteome in cells Kumar*, of by Juan Chen, Burlingame, Adam of factors on the brain Liu, Alice Ting, Steven peptide sequencing and sensitivity of database search results and de novo Wu, Steven proteome profiling potential biomarkers of disease Philipp Geyer, Alberto Santos, Sophia Stephan Matthias Matthias of as a for the and Paul Emily Adam Thomas Michael Ian Matthew Nathaniel Donald of Type and Targeting the Cell Surface Proteome of Hypoxic Pancreatic Cancer Lisa James Assessment of in Targeted Proteomics using of for a signaling network in Arabidopsis Kim, Zhu, Alice Ting, Xu, a for the of peptides from mass Eric Melissa of protein interaction networks Xu, Mark Nevan DIA to Workflow selective for and Yang*, Juan Alma Burlingame, of sites of Arabidopsis with enrichment and mass the role of protein in of gene regulation and cell Juan A. Steven M. Jack M. Alma L. Burlingame, Maria results from samples for proteomics M. Benjamin A. J. enrichment of proteins cell and Maria – all authors to posters from boards Carmel and Monterey Rooms, 3rd AUGUST – 1:00 p.m.Exhibits Open Nikko Ballroom Foyer, 3rd FloorSYMPOSIUMNikko Ballroom, 3rd SessionChair: Steven Carr, Broad Institute of MIT and Harvard, Cambridge, MA, for cancer Matthew of USAMorning SessionChair: Bernhard Kuster, Technical University of Munich, München, to insights from proteomics and Laboratory, WA, Break in for proteomic profiling of large human Robert Medical Center, MA, of lung Michael Gillette, Broad Institute of MIT and Harvard, Cambridge, MA, on ownAfternoon SessionChair: Nicholas human cell proteome in health and disease Angus University of Dundee, United through University of structure and by biotinylation of at the at for AUGUST Ballroom, 3rd SessionChair: Steven Carr, Broad Institute of MIT and Harvard, Cambridge, MA, with molecular Janne Institute, and disease University of of mechanisms of activity and to with a quantitative Adam Cancer Institute, MA, Break in mass and the structure of a novel in complex with the ribosome Michael Trnka, University of California, San Francisco, CA, on ownAfternoon SessionChair: University of profiling of improves prediction Broad Institute of MIT and Harvard, MA, novel open peptides to the Broad Institute of MIT and Harvard, MA, is a of University of CanadaPlenary SessionChair: University of and for the development of personalized cancer Cancer Center, Molecular and Cellular Proteomics Schedule ; Computer science ; Operating system Advanced Proteomics Techniques and Applications ; Bioinformatics and Genomic Networks ; Cell Image Analysis Techniques