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This meeting took place in 2020



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Proteomics in Cell Biology and Disease (EK2)


Organizer(s) Jennie R. Lill, Forest M. White and Kathryn S. Lilley
September 21—23, 2020
Virtual at your computer • , CO USA
Abstract Deadline: Sep 3, 2020
Scholarship Deadline: Aug 24, 2020
Discounted Registration Deadline:

Part of the Keystone Symposia Global Health Series, supported by the Bill & Melinda Gates Foundation

Summary of Meeting:
Proteomics provides critical biological information about the activation state of enzymes, pathways, and signaling networks that drive all biological processes. However, the power of this approach is currently limited by the capabilities of proteomics technologies and methods. Although single dimensional proteomics analysis is now routine on abundant samples, challenges remain in analyzing limited samples collected from in vivo studies and in examining dynamic cellular processes. This meeting aims to address these challenges, focusing on the latest advances and innovations in sample preparation, instrumentation, and bioinformatic/computational analysis, to push the boundaries of proteomics to enable more powerful analytics for translational research. Specifically, the program will cover: (1) cutting edge sample preparation methods that enable increased sensitivity and functional analysis of proteins; (2) approaches to tackle single cell proteomics analysis, in parallel with genomics and transcriptomics advances; (3) advancing multiplex capabilities beyond 2-10 plex experimentation to for more meaningful clinical analysis; and (4) integration of various “omics” data sets with proteomics to provide a more global view of the dynamic cellular environment. A critical focus of this meeting will be on new technologies needed to further improve the feasibility of looking at multicellular dimensions & multiplexed analyses in proteomics. The program features diverse content on current biological applications and needs, highlighting the application of high sensitivity proteomics to real-world translational questions. Attendees will learn what instrumentation, data acquisition methods, and informatic pipelines allow researchers to answer critical yet challenging questions, while also learning what is not yet feasible. By bringing together a multidisciplinary team of experts across a broad range of fields, this meeting aims to stimulate a collaborative environment and cross-pollination of ideas to drive the next wave of innovation in proteomics approaches and technologies. We will also discuss how we can better work together as a community to disseminate these methods and analytical tools, similar to recent movements in the open source computational programming world. Ultimately our goal is to help build a proteomics community that is ready to tackle even the most complex biological problems.

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No registration fees are used to fund entertainment or alcohol at this conference

Conference Program    Print  |   View meeting in 12 hr (am/pm) time


The meeting will begin on Monday, September 21 with . Conference events conclude on Wednesday, September 23 with a closing plenary session from 14:00 to , followed by . We recommend return travel on Thursday, September 24 in order to fully experience the meeting.

MONDAY, SEPTEMBER 21

08:00—08:10
Welcoming Remarks (8am Denver/Mountain Time Start)

08:10—08:40
Keynote Address (8:10am Denver/Mountain Time Start)

* Jennie R. Lill, Genentech, Inc., USA
Session Chair

Alice Y. Ting, Stanford University, USA
Proximity Labeling for Mapping Spatial Proteomes and Transcriptomes in Living Cells

08:40—10:35
Studying the Cell Surfaceome (8:40am Denver/Mountain Time Start)

* Nadia Martinez-Martin, Regeneron, USA
Mapping the Human Immunoglobulin Superfamily Receptome to Identify Novel Cancer-Relevant Pathways

Bernd Wollscheid, ETH Zürich, Switzerland
Light-Mediated Discovery of Surfaceome Nanoscale Organization and Inter-Cellular Receptor Interaction Networks

Coffee Break

* Gavin J. Wright, University of York, UK
Large-Scale Systematic Approaches to Identify Novel Receptor-Ligand Pairs that Initiate Intercellular Signaling

Sofia Massaro Tieze, Yale University, USA
Short Talk: Identification of Palmitoyl Protein Thioesterase Substrates Defines Roles for Synaptic Depalmitoylation

Monika Vishnoi, Houston Methodist Research Institute, USA
Short Talk: Matrisome Signatures in GBM Heterogeneity

10:35—11:00
Lightning Talks (10:35am Denver/Mountain Time Start)

* Kathryn S. Lilley, University of Cambridge, UK
Session Chair

Emma Borgeson, University of Gothenburg, Sweden
Advanced Multiplex Protein Analysis of Obesity-Related Cardiometabolic Biomarkers in Human Plasma and Serum

Dustin T. King, Simon Fraser University, Canada
Ultraviolet Photodissociation Mass Spectrometry Enables Precise Mapping of O-GlcNAc Sites in Proteins

Josie Amber Christopher, University of Cambridge, UK
Spatial Dynamics of the DNA Damage Proteome

Daniel Hornburg, Seer, USA
Proteograph™, a Multi-Nanoparticle Platform, Enables Plasma Proteomics Profiling at Scale and Speed, Significantly Improving Coverage and Scalability versus Traditional Deep fractionation methods

Justin McKetney, University of Wisconsin-Madison, USA
Proteomic Analysis of Cerebrospinal Fluid in Alzheimer's Disease

Nicolas Hartel, University of Southern California, USA
Deep Protein Arginine Methylation Profiling by LC-MS Proteomics

Samuel B. Pollock, Genentech, Inc., USA
Semi-Automated MHC-I Enrichment and TOMAHAQ Mass Spectrometry for the Sensitive and Quantitative Detection of Neoepitopes

12:00—14:00
Poster Session (12pm Denver/Mountain Time Start)

14:00—17:00
Dissection of Complex Data Sets: Informatic and Statistical Tools of the Trade (2pm Denver/Mountain Time Start)

Jyoti Choudhary, Institute of Cancer Research, UK
Integrative Proteogenomics Deconvoluting the Landscape of Lung Adenocarcinoma in Never-Smokers

* Lennart Martens, Ghent University, Belgium
Machine Learning Powered Next-Generation Proteomics

* Olga Vitek, Northeastern University, USA
Challenges in Large-Scale Computational Mass Spectrometry and Multiomics

Coffee Break

Mikhail Savitski, European Molecular Biology Laboratory, Germany
Phenotyping Cellular States with Functional Proteomics

Kevin Drew, University of Illinois at Chicago, USA
Short Talk: Hu.MAP2.0: Integration of over 15,000 Proteomic Experiments Builds a Global Compendium of Human Multiprotein Assemblies

Nader Morshed, Massachusetts Institute of Technology, USA
Short Talk: Quantitative Phosphoproteomics Uncovers Dysregulated Kinase Networks in Alzheimer's Disease

Devin K. Schweppe, University of Washington, USA
Short Talk: Millisecond Informatics: Real-Time Analytics for Quantitative Proteomics

Nicholas M. Riley, Stanford University, USA
Short Talk: Designing Methods and Software to Suit the needs of O-glycopeptide Characterization


TUESDAY, SEPTEMBER 22

08:00—11:00
Working Towards Single Cell Proteomics (8am Denver/Mountain Time Start)

* Jennie R. Lill, Genentech, Inc., USA
Session Chair

* Matthew S. Bogyo, Stanford University School of Medicine, USA
Chemical Proteomic Tools for Identification and Imaging of Enzymes Involved in Cancer and Infectious Disease

Edward M. Marcotte, University of Texas at Austin, USA
Single Molecule Protein Sequencing

Ryan Kelly, Brigham Young University, USA
One Cell at a Time: Nanodroplet Sample Preparation Enables In-Depth Single Cell Proteomics

Coffee Break

Joseph Gogain, SomaLogic, Inc, USA
Discovery and Validation of a Blood-Based Protein Signatures for Assessing Human Health

Laura Muehlbauer, University of Wisconsin-Madison, USA
Short Talk: Global Phosphoproteome Analysis using FAIMS on a Hybrid Orbitrap Mass Spectrometer

Mahmoud-reza Rafiee, Francis Crick Institute, UK
Short Talk: SPACE Exploration of RNA-Binding Proteins Reveals Diminished Chromatin-Binding of Mutant VCP in a Human Stem Cell Model of Neurodegeneration

12:00—14:00
Poster Session (12pm Denver/Mountain Time Start)

14:00—17:00
Integrative Multidimensional Omics (2pm Denver/Mountain Time Start)

* Nathalie Agar, Brigham and Womens Hospital, USA
Mass Spectrometry Imaging Methodologies, to Study Neuro-Oncology in Brain Cancer

Jonathan S. Weissman, Whitehead Institute, HHMI, and MIT, USA
Multidimensional Omics - Harnessing Ribosomal Profiling and Proteomics to Investigate Non Canonical Translation Events in Disease

Claudia Andrea Escher, Biognosys AG, Switzerland
Proteomics for Precision Medicine: A High-Throughput Platform for Proteome and Phospho-Proteome

Coffee Break

Aditya Murthy, Gilead Sciences, USA
Short Talk: Multiplexed Proteomics in Macrophages Uncovers Novel Roles of Autophagy in Anti-Microbial Immunity

Roberta Migale, Francis Crick Institute, UK
Short Talk: Dynamics of FOXL2 Gene Regulation in the Mouse Ovary

Liang Zhang, City University of Hong Kong, Hong Kong
Short Talk: Dissect RNA-Protein Interactome in Living Cells Using CRISPR-Assisted Proximity Labeling

Carlos Cruchaga, Washington University School of Medicine, USA
Short Talk: Genomic and Multi-Tissue Proteomic Integration for Understanding the Biology of Disease and other Complex Traits

* Christine Vogel, New York University, USA
Short Talk: Integrative Systems Profiling Identifies New Signatures of Neurodegeneration – and Novel Roles of the Core Proteasome


WEDNESDAY, SEPTEMBER 23

08:00—11:00
Spatial Proteomics (8am Denver/Mountain Time Start)

* Kathryn S. Lilley, University of Cambridge, UK
Spatial Organization of the Transcriptome and Proteome

Anne-Claude Gingras, Lunenfeld-Tanenbaum Research Institute, Canada
Tracking Spatiotemporal Proteomics in Complex Systems using Proximity Tagging

* Matthias Trost, Newcastle University, UK
Proteome Analysis Identifies Novel Roles for Ubiquitylation in the Innate Immune Response from the Phagosome

Coffee Break

Cecilia Lindskog, Uppsala University, Sweden
The Human Protein Atlas – Integrated Omics for Single Cell Analysis

Xinying Zong, St. Jude Children's Research Hospital, USA
Short Talk: Dynamic cis-Proteomics Comprehensively Reveals Signal-Dependent Regulators

Ashley Frankenfield, George Washington University, USA
Short Talk: A Specific and Sensitive Proximity-labeling Proteomics Approach for Studying Protein-Protein Interactions of the Lysosome Membrane

12:30—13:30
Career Roundtable (12:30pm Denver/Mountain Time Start)

Anne-Claude Gingras, Lunenfeld-Tanenbaum Research Institute, Canada

Marcus Bantscheff, GlaxoSmithKline, Germany

Nathalie Agar, Brigham and Womens Hospital, USA

14:00—16:45
Elucidation of in vivo Signaling Networks (2pm Denver/Mountain Time Start)

* Forest M. White, Massachusetts Institute of Technology, USA
Phosphoproteomics for Characterization of Therapeutic Resistance Pathways

Jennie R. Lill, Genentech, Inc., USA
Hippo Pathway Deregulation in Cancer

David E. James, University of Sydney, Australia
Personalised Phosphoproteomics – Studying the Exercise Response in Individuals

Coffee Break

* Marcus Bantscheff, GlaxoSmithKline, Germany
Chemoproteomics for the Elucidation of Signaling Networks

Xiaoyu Zhang, The Scripps Research Institute, USA
Short Talk: Electrophilic PROTACs that Degrade Nuclear Proteins by Engaging DCAF16

Nida Haider, Joslin Diabetes Center/ Harvard Medical School, USA
Short Talk: Distinct Male and Female Phosphoproteomic Signatures Underlie Human Insulin Resistance

Brendan Floyd, University of Texas at Austin, USA
Short Talk: Systematic Identification of Protein Phosphorylation-Mediated Interactions

16:45—17:00
Closing Remarks (4:45pm Denver/Mountain Time Start)


*Session Chair †Invited, not yet responded.



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ReSyn Biosciences

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