• Mass Spectrometry in the Health and Life Sciences:
    Molecular and Cellular Proteomics

    August 18–22, 2019, San Francisco


View abstracts for each session in the symposium's supplement to Molecular and Cellular Proteomics.

Saturday, Aug. 17

4 p.m.

Sunday, Aug. 18

7:30 a.m.

Minisymposium on Data-independent Analysis

Organizers: Robert Chalkley and Hannes Röst

Plenary Session  

8:30 a.m.
Improving the robustness, throughput and comprehensiveness of quantitative proteomics
Mike MacCoss, University of Washington

Morning Session — Chair: Robert Chalkley

9:30 a.m.
Complex-centric proteome profiling by SEC-SWATH-MS
Isabell Bludau, ETH Zurich
10:10 a.m.
10:50 a.m.
Aligning label-based discovery and global DIA validation proteomics to explore bacterial virulence phenotypes
Stuart Cordwell, University of Sydney
11:30 a.m.
Advanced algorithms to assess and improve quantitative suitability in large DIA datasets
Sebastian Vaca Jacome, Broad Institute of MIT and Harvard
12:10 p.m.

Afternoon Session — Chair: Mike MacCoss

1:40 p.m.
Parallel accumulation — serial fragmentation combined with data-independent acquisition (diaPASEF)
Florian Meier, Max Planck Institute of Biochemistry, Germany
2:20 p.m.
Mobi-DIK (Ion Mobility DIA Analysis Kit): Targeted analysis software for diaPASEF data improves proteome coverage
Hannes Röst, University of Toronto
3 p.m.
Applications of DIA for PTM research and specific DIA workflows
Birgit Schilling, Buck Institute for Research on Aging
3:40 p.m.
Peptide MS/MS prediction for DDA and DIA
Mathias Wilhelm, Technical University of Munich
6 p.m.
Opening Reception

Monday, Aug. 19

7:30 a.m.
8:15 a.m.
A.L. Burlingame, Steven Carr and Bernhard Kuster  

Plenary Session — Chair: A.L. Burlingame  

8:30 a.m.
The End of the End: High throughput discovery and analysis of degrons
Stephen Elledge, Harvard Medical School

Morning Session — Chair: Bernhard Kuster

9:30 a.m.
Drug effects on protein stability and proteostasis
Marcus Bantscheff, GlaxoSmithKline
10:10 a.m.
10:30 a.m.
Development, use, application of novel TIMS-Tof system
Matthias Mann, Max Planck Institute of Biochemistry, Germany
11:10 a.m.
Lysine-targeted covalent inhibitors and chemoproteomic probes
Jack Taunton, University of California, San Francisco
11:50 a.m.
Mapping proteolysis at the surface of living cells
Amy Weeks, University of California, San Francisco
12:30 p.m.
12:45–1:45 p.m.
Thermo Fisher logo

Sponsored session by Thermo Fisher Scientific
(Registration limited to 35 people, email mineko.horie@thermofisher.com to RSVP)

Introducing a new paradigm for targeted protein quantitation and single cell proteomics
Aaron Gajadhar and Daniel Lopez-Ferrer, Thermo Fisher Scientific

Afternoon Session — Chair: Anne-Claude Gingras

2 p.m.
Characterization and turnover of RNA-binding proteins: Novel insights into ribosome maintenance
Jeroen Krijgsveld, German Cancer Research Center, Heidelberg
2:40 p.m.
Deciphering gene expression regulation in health and disease using integrative omics approaches
Michiel Vermeulen, Radboud Institute for Molecular Life Sciences, Netherlands
3:20 p.m.
Protein interaction networks controlling gene expression programs and beyond
Jeffrey A. Ranish, Institute for Systems Biology
4 p.m.
Poster Session A — Chairs: Robert Chalkley, Jason Maynard

Tuesday, Aug. 20

8:30 a.m.
Flash Talks — Chair: Angus Lamond
Poster presenters will be invited to give 1 min. flash talks on their work.

10:10 a.m.


Morning Session — Chair: Don Kirkpatrick

10:30 a.m.
The growing molecular complexity of ribosome biology
Maria Barna, Stanford University
11:10 a.m.
Deciphering cellular organization using protein thermal stability and solubility
Mikhail M. Savitski, European Molecular Biology Laboratory, Heidelberg, Germany
11:50 a.m.
A proteomics view of mTOR signaling in humans
Anne-Claude Gingras, Lunenfeld–Tanenbaum Research Institute, Toronto
12:30 p.m.
12:45–2 p.m.
Bruker logo

Sponsored session by Bruker
( Separate registration required)

Mobi-DIK enables deconvolution of multiplexed diaPASEF data for high protein coverage
Hannes Rӧst, University of Toronto

Moving proteomics to the clinic with the PASEF tims-TOF
Matthias Mann, Max Planck Institute of Biochemistry




 Afternoon Session — Chair: Bernhard Kuster

2:30 p.m.
New Ub profiling approaches and applications
Namrata Udeshi, Broad Institute of MIT and Harvard


3:10 p.m.
Proteomic exploration of lysine acetylation signaling
Chuna Choudhary, University of Copenhagen, Denmark
3:50 p.m.
Characterization of complexes and organelles
Kathryn Lilley, University of Cambridge
4:30 p.m.
Poster Session B — Chairs: Michael Trnka, Nancy Phillips

Wednesday, Aug. 21

Plenary Session — Chair: Steven Carr  

8:30 a.m.
Proteogenomics-based diagnostics for cancer
Matthew Ellis, Baylor College of Medicine

Morning Session — Chair: Bernhard Kuster

9:30 a.m.
Proteins to pathways: Functional insights from comprehensive proteomics and phosphoproteomics
Karin Rodland, Pacific Northwest National Laboratory
10:10 a.m.
10:30 a.m.
Non MS-based techniques for proteomic profiling of large human cohorts: Trust ... but verify
Robert Gerszten, Beth Israel Deaconess Medical Center

Plenary Session  

11:10 a.m.
Proteogenomic analyses of lung adenocarcinoma
Michael Gillette, Broad Institute of MIT and Harvard
12:10 p.m.

 Afternoon Session — Chair: Nicholas Hertz

1:20 p.m.
The human iPS cell proteome in health and disease
Angus Lamond, University of Dundee, U.K.
2:00 p.m.
Modulating nerve growth through RNA-protein interactions
Jeff Twiss, University of South Carolina
2:40 p.m.
Mapping axon initial segment structure and function by multiplexed proximity biotinylation
Brian Lim, Baylor College of Medicine
6 p.m.
Reception and Dinner
Fort Mason Center for Arts & Culture
General's Residence
Fort Mason, San Francisco
* Advance ticket purchase required (includes transportation)

Thursday, Aug. 22

Morning Session — Chair: Steven Carr

8:30 a.m.
Cancer proteomics — connecting genotype with molecular phenotype
Janne Lehtiö, Karolinska Institute, Sweden
9:10 a.m.
A link between gut infection, autoimmunity and Parkinson's disease
Michel Desjardins, University of Montreal
9:50 p.m.
Identification of mechanisms of activity and resistance to thalidomide analogs with a targeted quantitative immuno-mass spectrometry assay
Adam Sperling, Dana–Farber Cancer Institute
10:30 a.m.
11 a.m.
Crosslinking 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
11:40 a.m.

Afternoon Session — Chair: Pierre Thibault

1:40 p.m.
Systematic profiling of HLA class I immunopeptidome improves neoantigen binding prediction
Susan Klaeger, Broad Institute of MIT and Harvard
2:20 p.m.
Ribo-seq predicted novel unannotated open reading frames contribute peptides to the MHC class I immunopeptidome
Tamara Ouspenskaia, Broad Institute of MIT and Harvard
3 p.m.
The genomic dark matter is a major source of targetable tumor-specific antigens
Pierre Thibault, University of Montreal

Plenary Session — Chair: Pierre Thibault  

3:40 p.m.
Proteogenomics and immunopeptidomics for the development of personalized cancer immunotherapy
Michal Bassani-Sternberg, Ludwig Cancer Center, Switzerland
Molecular and Cellular Proteomics Lecturer  
4:40 p.m.
Closing Remarks
5 p.m.