All sessions and activities will be held at the Hotel Nikko San Francisco, unless noted otherwise.

4:00 – 6:30 p.m.Registration open Nikko Ballroom Foyer, 3rd Floor
7:30 a.m. – 4:00 p.m.Registration open Nikko Ballroom Foyer, 3rd Floor
8:00 a.m.Exhibitor Set-up Nikko Ballroom Foyer, 3rd Floor
Nikko Ballroom, 3rd Floor
Organizers: Robert Chalkley, University of California, San Francisco, CA, USA and Hannes Röst, University of Toronto, Canada
Plenary Session
8:30MS1Improving the robustness, throughput and comprehensiveness of quantitative proteomics
Mike MacCoss, University of Washington, Seattle, WA, USA
Morning Session
Chair: Robert Chalkley, University of California, San Francisco, CA, USA
9:30MS2Complex-centric proteome profiling by SEC-SWATH-MS
Isabell Bludau, ETH, Zurich, Switzerland
10:10Coffee Break in foyer
10:50MS3Aligning label-based discovery and global DIA validation proteomics to explore bacterial virulence phenotypes
Stuart Cordwell, University of Sydney, Australia
11:30MS4Advanced algorithms to assess and improve quantitative suitability in large DIA datasets
Sebastian Vaca Jacome, Broad Institute of MIT and Harvard, Cambridge, MA, USA
12:10 p.m.Lunch on own
Afternoon Session
Chair: Mike MacCoss, University of Washington, Seattle, WA, USA
1:40MS5Parallel accumulation — serial fragmentation combined with data-independent acquisition (diaPASEF)
Florian Meier, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
2:20MS6Mobi-DIK (Ion Mobility DIA Analysis Kit): Targeted analysis software for diaPASEF data improves proteome coverage
Hannes Röst, University of Toronto, Canada
3:00MS7Applications of DIA for PTM research and specific DIA workflows
Birgit Schilling, Buck Institute for Research on Aging, Novato, CA, USA
3:40MS8Peptide MS/MS prediction for DDA and DIA
Mathias Wilhelm, Technical University of Munich, Freising, Germany
4:00Poster Set-up – all authors to mount posters on boards
Carmel and Monterey Rooms, 3rd Floor
4:00 – 6:00 p.m.Exhibits Open
Nikko Ballroom Foyer, 3rd Floor
6:00Opening Reception
Golden Gate Room, 25th Floor
7:30 – 4:00 p.m.Registration open
Nikko Ballroom Foyer, 3rd Floor
8:00 – 1:00 p.m.Exhibits Open
Nikko Ballroom Foyer, 3rd Floor
Nikko Ballroom, 3rd Floor
8:15 a.m.Introduction
A.L. Burlingame, Steven Carr, and Bernhard Kuster
Plenary Session
Chair: A.L. Burlingame, University of California, San Francisco, CA, USA
8:301.1The End of the End: High through-put discovery and analysis of degrons
Stephen Elledge, Harvard Medical School, Cambridge, MA, USA
Morning Session
Chair: Bernhard Kuster, Technical University of Munich, München, Germany
9:301.2Drug effects on protein stability and proteostasis
Marcus Bantscheff, Glaxo Smith Kline, Heidelberg, Germany
10:10Coffee Break in foyer
10:301.3Development, use, application of novel TIMS-Tof system
Matthias Mann, Max Planck Institute of Biochemistry, Martinsried, Germany
11:101.4Lysine-targeted covalent inhibitors and chemoproteomic probes
Jack Taunton, University of California, San Francisco, CA, USA
11:501.5Mapping proteolysis at the surface of living cells
Amy Weeks, University of California, San Francisco, CA, USA
12:30 p.m.Lunch on own
Afternoon Session
Chair: Anne-Claude Gingras, Lunenfeld-Tanenbaum Research Institute, Toronto, Canada
2:001.6Characterization and turnover of RNA-binding proteins: Novel insights into ribosome maintenance
Jeroen Krijgsveld, German Cancer Research Center, Heidelberg, Germany
2:401.7Deciphering gene expression regulation in health and disease using integrative Omics approaches
Michiel Vermeulen, Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands
3:201.8Protein interaction networks controlling gene expression programs and beyond
Jeffrey A. Ranish, Institute for Systems Biology, Seattle, WA, USA
4:00Poster 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, USA
A.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 Meissner
A.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 Ellis
A.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 Ori
A.5Affinity Proteomics Reveals Assembly of PPP-type Phosphatase Holoenzyme by PPM1G-B56δ
Parveen Kumar*, Prajakta Tathe, Subbareddy Maddika
A.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-Molina
A.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 Lee
A.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 Larsen
A.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 Bence
A.10Vascular Cell Surface Proteomics In Vivo
Dirk Walther*, Elizabeth Gordon, Benjamin Smith, Thomas Cameron, Ru Wei, Peter Juhasz
A.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 Urlaub
A.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 Luo
A.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 Lehtiö
A.15Native Mass Spectrometry Study on the Stoichiometry of Proteasome AAA+ ATPase Nucleotide Binding
H. Ewa Witkowska*, Yadong Yu, Haichuan Liu, Zanlin Yu, Yifan Cheng
A.16Towards Elucidation of Muscle-Specific Receptor Tyrosine Kinase (MuSK) Signaling Pathway by Differential Agonists
Hanna Budayeva*, Arundhati Sengupta Ghosh, Lilian Phu, Donald Kirkpatrick
A.17Multiplexed and Quantitative Assessment of the Cellular Reactive Cysteinome in T cell activation
Liang Xue*, Uthpala Seneviratne
A.18Enzyme toolkit for selective enrichment and analysis of mucin-domain glycoproteins
Stacy Malaker*, Judy Shon, Kayvon Pedram, Nicholas Riley, Carolyn Bertozzi
A.19Functional Metabolomics uncovering the role of Trp–KYN–KA Axis in Intestinal Injury and Repair
Di Wang*, Huimin Guo, Zunjian Zhang, Fengguo Xu
A.20Metabolic Control of OGT Interactome in Hepatocytes
Krista Kaasik*, Chin Fen Teo, Robert Chalkey, Alma Burlingame
A.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 Wiita
A.22Characterization of KRAS 4B C-Terminal Hypervariable Region using LC/MS
James Wilkins*, A.L. Burlingame
A.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 Carr
A.24Characterization of a hybrid insulin peptide as an autoantigen in human type 1 diabetes
Timothy Wiles*, Rocky Baker, Maki Nakayama, Thomas Delong
A.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 Carr
A.26Proteome-wide analysis of protein stability in E. coli using pulse proteolysis
Roman Körner*, Liang Zhao, Giulia Vecchi, Michele Vendruscolo, Manajit Hayer-Hartl, Ulrich Hartl
A.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 Mann
A.28Characterization of the Sin3 HDAC complex interaction network
Mark Adams*, Charles Banks, Janet Thornton, Cassandra Kempf, Sayem Miah, Laurence Florens, Michael Washburn
A.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 Macek
A.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 MacLean
A.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 Chi
A.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-Alvarado
A.33Elucidating Changes in O-GlcNAcylation in Pancreatic Cancer
Talieh Zomorrodinia*, Jason Maynard, Krista Kaasik, Alma Burlingame
A.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 Babalola
A.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 Burlingame
A.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 Krogan
A.37Tuning residence time with lysine-targeted, reversible covalent probes
Tangpo Yang*, Adolfo Cuesta, Xiaobo Wan, Jack Taunton
A.38Characterizing and Targeting the Hypoxic T Cell Surfaceome to Promote Immune Function in Cancer
James Byrnes*, Lisa Kirkemo, Amy Weeks, James Wells
A.39Twins Labeling Derivatization-based LC-MS/MS Strategy for absolute quantification of modified metabolites
Wei Li*, Zunjian Zhang, Fengguo Xu
A.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 Meier
A.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 Alzari
A.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 Bock
A.43Discovery of a common target of natural products through combination of chemical genomics and proteomics
Haijun Guo, Yang Yang, Jieren Deng, Mankin Wong, Qian Zhao
A.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. Anslyn
8:00 – 1:00 p.m.Exhibits Open
Nikko Ballroom Foyer, 3rd Floor
Nikko Ballroom, 3rd Floor
8:30 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, Scotland
10:10 a.m.Coffee Break in foyer
Morning Session
Chair: Don Kirkpatrick, Genentech, Inc.
10:302.1The growing molecular complexity of ribosome biology
Maria Barna, Stanford University, Stanford, CA, USA
11:102.2Deciphering cellular organization using protein thermal stability and solubility
Mikhail M. Savitski, European Molecular Biology Laboratory, Heidelberg, Germany
11:502.3A proteomics view of mTOR signaling in humans
Anne-Claude Gingras, Lunenfeld–Tanenbaum Research Institute, Toronto, Canada
12:30 p.m.Lunch on own
Afternoon Session
Chair: Bernhard Kuster, Technical University of Münich, München, Germany
2:302.4New Ub profiling approaches and applications
Namrata Udeshi, Broad Institute of MIT and Harvard, Cambridge, MA, USA
3:102.5Proteomic exploration of lysine acetylation signaling
Chuna Choudhary, University of Copenhagen, Copenhagen, Denmark
3:502.6Characterization of complexes and organelles
Kathryn Lilley, University of Cambridge, United Kingdom
4:30Poster Session B
Carmel and Monterey Rooms, 3rd Floor
Chairs: Michael Trnka, University of California, San Francisco, CA, USA and Nancy Phillips, University of California, San Francisco, CA, USA
B.1Identification and Quantification Method for UCN2 by LC/MS/MS from Plasma/Serum from Mouse Disease Models
Shakey Quazi*, Wei Zheng, Olivier Bezy
B.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 Hopkins
B.3High-Throughput PEAKS Workflow for Large Scale Quantitative Proteomics using PEAKS Online X
Jonathan Krieger*, Julia Hopkins, Lei Xin, Baozhen Shan
B.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 Carr
B.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, Marie-Soleil Gauthier
B.6Comprehensive Comparative Immunopeptidome Analysis of I-Ab-bound peptides from Thymus, Splenic B cells and Dendritic cells in C57BL/6 mice
Padma Nanaware*, J. Mauricio Calvo-Calle, Liying Lu, Mollie Jurewicz, Laura Santambrogio, Lawrence Stern
B.7Diversity of the MHC-II immunopeptidome is modulated by the non-classical MHC proteins HLA-DM and HLA-DO and controls thymic selection of CD4+ and regulatory T cells
Lawrence Stern*, Padma Nanaware, Mollie Jurewicz, John Leszyk, Scott Shaffer
B.8Size exclusion chromatography-based proteomics to identify novel components of the HSP90-dependent proteome following pharmacologic inhibition in colon cancer cells
Rahul Samant*, Silvia Aires-Batista, Bugra Ozer, Mark Larance, Craig McAndrew, Alexia Hervieu-Vilches, Bissan Al-Lazikani, Paul Clarke, Angus Lamond, Paul Workman
B.9Disruption-Compensation (DisCo) analysis of RNA polymerase II Protein Interactome
Katlyn Burriss*, Guihong Qi, Whitney Smith-Kinnaman, Amber Mosley
B.10Plasma proteome profiling to detect and avoid sample-related biases in biomarker studies
Philipp Geyer*, Matthias Mann, Lesca Holdt
B.11Production and Generation of Proteogenomics Databases using PyPGATK
Husen Umer*, Yafeng Zhu, Enrique Audain, Janne Lehtiö, Rui Branca, Yasset Perez-Riverol
B.12Multi-omic profiling reveals differential kinase activity in neuronal differentiation
Dmitry Kuchenov*, Fima Zaltsman, Jeremy Willsey, Ruth Huttenhain, Nevan Krogan
B.13A novel HLA-peptide profiling workflow called MAPTACTM (Mono-Allelic-Purification-with-Tagged-Allele-Constructs) leverages mass spectrometry to improve neoantigen prediction
Lia Serrano*, Dominik Barthelme, Rob Oslund, Amanda Creech, Tyler Colson, Scott Goulding, Daniel Rothenberg, Chris McGann, Ying Ting, Yusuf Nasrullah, Janani Sridar, Dewi Harjanto, Matt Malloy, Christina Kuksin, Joel Greshock, Terri Addona, Michael Rooney, Jennifer Abelin
B.14Selective capture and release of nascent proteins for translatome profiling
Nancy Phillips*, Craig Forester, Bala Vinaithirthan, Juan Oses-Prieto, Robert Chalkley, Alma Burlingame
B.15Targeting a subset of the membrane proteome - the proteolipids that extract into chloroform, the proteolipidome
Julian Whitelegge*
B.16Allosteric HSP70 inhibitors overcome proteasome inhibitor resistance by perturbing mitochondrial proteostasis
Arun Wiita*, Ian Ferguson, Christine Lam, Sami Toumivaara, Margarette Mariano, Paul Phojanakong, Donghui Wang, Hao Shao, Byron Hann, Jason Gestwicki
B.17Comparative Proteomic in Multiple Brain Regions of the Naked Mole-Rats and Mice
Thu Nguyen*, Emily Vice, Melissa Pergande, Vince Amoroso, Thomas Park, Stephanie Cologna
B.18Development and Application of a Targeted immuno-MRM-MS Assay to Identify the Mechanism of Activity and Resistance to Thalidomide Analogs
Michael Burgess*, Adam Sperling, Hasmik Keshishian, Eric Kuhn, Steven Carr, Benjamin Ebert
B.19ITRAQ Proteomic Profiling of Tissue Interstitial Fluid from Paired High Grade Serous Ovarian Cancer and Fallopian Tube Samples Reveals Novel Biomarker Candidates
Shayan Avanessian*, Eric Kuhn, Karsten Krug, Yi Feng, Alexandra Cocco, Sho Sato, Yiling Liu, Paul Ippoliti, Marilyn Mitchell, Lauren Schwartz, Daniele Moreira, Kai Doberstein, Michael Birrer, DR Mani, Steven Skates, Steven Carr, Ronny Drapkin, Michael Gillette
B.20Application of Quantitative Phosphoproteomics in the Study of Plant Mechanosignaling
Zhu Yang*, Ning Li
B.21Deep Label-Free Quant: Deciphering the MS1 Hieroglyph with IT and AI
David Chiang*, Patrick Chu, Brian Chiang
B.22Quantitative proteomics of MPK4 phosphorylation dynamics and interacting proteins
Sixue Chen*, Tong Zhang, Chuwei Lin, Jacqueline Schneider, Tianyi Ma, Sisi Geng, Sheldon Lawrence, Craig Dufresne, Alice Harmon
B.23Composition of the myddosome during the innate immune response
Joseph Gillen*, Aleksandra Nita-Lazar
B.24Thermal profiling as a novel tool to analyze the impacts of missense mutants on the proteome
Sarah Peck Justice*, Quihong Qi, H.R. Sagara Wijeratne, Jose Victorino, Aruna Wijeratne, Amber Mosley
B.25Quantitative Proteomic Analysis to Identify Developmentally Regulated Proteins in Leishmania Major Isolate
Nasrin Amiri-Dashatan*, Nayebali Ahmadi
B.26SC-514 Loaded PLGA Particle Formed by Single Emulsion Method
Toluleke Famuyiwa*
B.27Purification and Proteomic Analysis of the Golgi Outpost – an Organelle that Nucleates Microtubules in Oligodendrocytes
Meng-meng Fu*, Thomas MacAlear, Juan Oses-Prieto, Huy Nguyen, Alex Valenzuela, Rebecca Shi, Ting-Ting Wang, Alma Burlingame, Susanne Bechstedt, Ben Barres
B.28Autoimmune regulator dependent alterations in proteome profiles in spermatogonial cells
Pradeep Kumar*, Karthika Radhakrishnan, Kongattu Bhagya, Anil TR Kumar, Anandavally Devi, Sengottiyan Jeeva
B.29Molecular bases of ferroptosis induction by endoperoxides
Juan Oses-Prieto*, Ying-Chu Chen, Al Burlingame, Adam Renslo
B.30Systematic identification of fat-derived secreted factors acting on the brain
Pierre Jean-Beltran*, Lucy Liu, Tess Branon, Alice Ting, Norbert Perrimon, Steven Carr
B.31Improved HLA peptide sequencing accuracy and sensitivity via optimized scoring of database search results and de novo interpretations
Karl Clauser*, Susan Klaeger, Tamara Ouspenskaia, Travis Law, Derin Keskin, Siranush Sarkizova, Nir Hacohen, Catherine Wu, Steven Carr
B.32Plasma proteome profiling discovers potential biomarkers of non-alcoholic fatty liver disease
Rajat Gupta*, Lili Niu, Philipp Geyer, Nicolai J Albrechtsen, Lise Gluud, Alberto Santos, Sophia Doll, Jens Holst, Filip Knop, Tina Vilsbøll, Anders Junker, Stephan Sachs, Kerstin Stemmer, Timo Müller, Matthias Tschöp, Susanna Hofmann, Matthias Mann
B.33Discovery of Mitochondrial Protease ClpP as a Target for the Anticancer Compounds ONC201 and Related Analogs
Lee Graves*, Paul Graves, Lucas Aponte-Collazo, Emily Fennell, Adam Graves, Andrew Hale, Nedyalka Dicheva, Laura Herring, Thomas Gilbert, Michael East, Ian McDonald, Matthew Lockett, Hani Ashamalla, Nathaniel Moorman, Donald Karanewsky, Edwin Iwanowicz, Ekhson Holmuhamedov
B.34Functional Versatility of Mycobacterium marinum Type III Polyketide Synthases
Priti Saxena*, Amreesh Parvez, Samir Giri, Gorkha Giri, Monika Kumari, Renu Bisht
B.35Characterizing and Targeting the Cell Surface Proteome of Hypoxic Pancreatic Cancer
Lisa Kirkemo*, James Wells
B.36Automated Quality Assessment of Chromatographic Peaks in Targeted Proteomics Data using Machine Learning
Shadi Eshghi*, Erick Velasquez, W. Rodney Mathews
B.37Application of TurboID-mediated proximity labeling for mapping a GSK3 kinase signaling network in Arabidopsis
Chuan-Chih Hsu*, Chan Ho Park, Tae-Wuk Kim, Jia-Ying Zhu, Yu-Chun Hsiao, Tess Branon, Alice Ting, Shou-Ling Xu, Zhi-Yong Wang
B.38MHC-TreASUre_Hunt: a computational pipeline for the identification of MHC-I peptides from mass spectrometry
Eric Wilson*, Melissa Wilson, Karen Anderson
B.39Identification of spatiotemporally resolved GPCR protein interaction networks regulating receptor function
Ruth Huttenhain*, Braden Lobingier, Jiewei Xu, Brian Shoichet, Mark Von Zastrow, Nevan Krogan
B.40Accelerating DIA Studies to Extend Workflow Utility, Using Fast Microflow LC Gradients
Loren Olson*, Christie Hunter, Nick Morrice
B.41eIF4E selective control for metabolic fitness and healthspan
Haojun Yang*, Crystal Conn, Kenji Ikeda, Juan Oses-Prieto, Supna Nair, Matt Parker, Patrick Ventura, Saul Villeda, Shingo Kajimura, Alma Burlingame, Davide Ruggero
B.42Profiling of phosphorylation sites of Arabidopsis microsomes with PolyMAC-Ti nanoparticle bead enrichment and mass spectrometry
Ing-Feng Chang*, Tsung-Ju Hsieh, Man-Hsuan Lee, Pei-Yuan Chen
B.43Characterizing the role of ribosomal protein phosphorylation in control of gene regulation and cell fate
Victoria Hung*, Juan A. Oses-Prieto, Steven M. Moss, Jack Stevenson, Kevan M. Shokat, Alma L. Burlingame, Maria Barna
B.44HYPERsol: flash-frozen results from archival FFPE samples for clinical proteomics
Dylan M. Marchione, Ilyana Ilieva, Benjamin A. Garcia, Darryl J. Pappin, John B. Wojcik, John P. Wilson*
B.45Tag-free rapid enrichment of ribosome-associated proteins across cell types, tissues, and species.
Teodorus Theo Susanto*, Victoria Hung, Kotaro Fujii, Maria Barna
6:00Poster Dismantle – all authors to remove posters from boards
Carmel and Monterey Rooms, 3rd Floor
8:00 – 1:00 p.m.Exhibits Open
Nikko Ballroom Foyer, 3rd Floor
Nikko Ballroom, 3rd Floor
Plenary Session
Chair: Steven Carr, Broad Institute of MIT and Harvard, Cambridge, MA, USA
8:303.1Proteogenomics-based diagnostics for cancer
Matthew Ellis, Baylor College of Medicine, Houston, TX, USA
Morning Session
Chair: Bernhard Kuster, Technical University of Munich, München, Germany
9:303.2Proteins to pathways: Functional insights from comprehensive proteomics and phosphoproteomics
Karin Rodland, Pacific Northwest National Laboratory, Richland, WA, USA
10:10Coffee Break in foyer
10:303.3Non MS-based techniques for proteomic profiling of large human cohorts: Trust … but verify
Robert Gerszten, Beth Israel Deaconess Medical Center, Boston, MA, USA
Plenary Session
11:103.4Proteogenomic analyses of lung adenocarcinoma
Michael Gillette, Broad Institute of MIT and Harvard, Cambridge, MA, USA
12:10Lunch on own
Afternoon Session
Chair: Nicholas Hertz, Mitokinin
1:203.5The human iPS cell proteome in health and disease
Angus Lamond, University of Dundee, United Kingdom
2:003.6Modulating nerve growth through RNA-protein interactions
Jeff Twiss, University of South Carolina, Columbia, SC, USA
2:403.7Mapping axon initial segment structure and function by multiplexed proximity biotinylation
Brian Lim, Baylor College of Medicine, Houston, TX, USA
6:00 p.m.Reception & Dinner at the General's House at Fort Mason Center for Arts & Culture Advance ticket purchase required
Nikko Ballroom, 3rd Floor
Morning Session
Chair: Steven Carr, Broad Institute of MIT and Harvard, Cambridge, MA, USA
8:304.1Cancer proteomics—connecting genotype with molecular phenotype
Janne Lehtiö, Karolinska Institute, Stockholm, Sweden
9:104.2A link between gut infection, autoimmunity and Parkinson's disease
Michel Desjardins, University of Montreal, Quebec, Canada
9:504.3Identification of mechanisms of activity and resistance to thalidomide analogs with a targeted quantitative immuno-mass spectrometry assay
Adam Sperling, Dana–Farber Cancer Institute, Boston, MA, USA
10:30Coffee Break in foyer
11:004.4Crosslinking mass spectrometry and single particle cryoEM describe the structure of a novel translocon in complex with the ribosome
Michael Trnka, University of California, San Francisco, CA, USA
11:40Lunch on own
Afternoon Session
Chair: Pierre Thibault, University of Montreal, Quebec, Canada
1:404.5Systematic profiling of HLA class I immunopeptidome improves neoantigen binding prediction
Susan Klaeger, Broad Institute of MIT and Harvard, Boston, MA, USA
2:204.6Ribo-seq predicted novel unannotated open reading frames contribute peptides to the MHC class I immunopeptidome
Tamara Ouspenskaia, Broad Institute of MIT and Harvard, Boston, MA, USA
3:004.7The genomic dark matter is a major source of targetable tumor-specific antigens
Pierre Thibault, University of Montreal, Quebec, Canada
Plenary Session
Chair: Pierre Thibault, University of Montreal, Quebec, Canada
3:404.8Proteogenomics and immunopeptidomics for the development of personalized cancer immunotherapy
Michal Bassani-Sternberg, Ludwig Cancer Center, Lausanne, Switzerland
Molecular and Cellular Proteomics Lecturer
4:40Closing Remarks