The 2019 Program

Monday, July 8

Tuesday, July 9

Posters

8⁰⁰

Registration & Continental Breakfast

8⁴⁵

Welcome
Chair: Rob Moritz (ISB)

8⁵⁰

Keynote
Alexey Nesvizhskii (U Michigan)
Applications of Ultrafast Database Searching in Proteomics and Proteogenomics

9³⁵

Session 1: Systems Biology
Chair: Chris Barnes (Novo Nordisk)

9³⁵

Mark Gillespie (ISB)
A systems approach to quantifying transcriptional regulation in atherosclerosis

10⁰⁰

Marli Vlok (UBC)
Positional proteomic analysis reveals novel cleavage products that promote enterovirus infection.

10²⁵

Lightning Talk: Juan Chavez (UW)
Systems structural biology of the heart: Impact of acetylation on protein conformations/interactions

10³⁰

Lightning Talk: Clint Vorauer (UW)
Biophysical Properties of Refractile Bodies

10³⁵

Break

11⁰⁵

Session 2: Degradomics and PTMs
Chair: Alexey Nesvizhskii (U Michigan)

11⁰⁵

Daniele Canzani (UW)
Degronomics: Integrative Mass Spectrometry for Identifying Cellular E3 Ligase interactions

11³⁰

Nestor Solis (UBC)
TAILS terminomics, shotgun proteomics and transcriptomics analysis of macrophage differentiation

11⁵⁵

Abhigya Mookherjee (UW)
Hybrid mass spectrometric-based methods for distinguishing isomeric oligosaccharides

12²⁰

Lightning Talk: Anthony Valente (UW)
Towards targeted phosphoproteomics by machine learning

12²⁵

Lightning Talk: Christopher Adams (Bruker)
Identification and Quantitation of Phosphopeptide Positional Isomers using TIMS and PASEF

12³⁰

Lightning Talk: Drake Russell (UW)
An Exploration of the Post Translational Structure of a Novel S-Methyltransferase

12³⁵

Lightning Talk: Alex Zelter (UW)
Elucidating protein-xenobiotic interactions by mass spectrometry

12⁴⁰

Lunch

13⁵⁰

Session 3: Disease Proteomics
Chair: Wei-Jun Qian (PNNL)

13⁵⁰

Phillipp Lange (UBC)
The first 50 cases in BRAvE: Using genomics and proteomics to advance pediatric precision oncology

14¹⁵

Jaipalreddy Panga (ISB)
Characterizing clinically relevant "Borrelia Burgdorferi" isolates in the era of proteogenomics

14⁴⁰

Deanna Plubell (UW)
Detecting peptide level changes in cerebrospinal fluid proteome of neurodegenerative disease by DIA

15⁰⁵

Adam Swensen (PNNL)
Nanoproteomic Characterization of Functional Dysregulation in Islets of Pre-Type 1 Diabetic Patients

15³⁰

Lightning Talk: John Cha (Providence)
Highly sensitive detection of immune checkpoint drugs in blood via nSMOL LC-MS assay

15³⁵

Break

16⁰⁰

Session 4: Computational Proteomics
Chair: Eric Deutsch (ISB)

16⁰⁰

William Noble (UW)
A learned embedding for efficient joint analysis of millions of mass spectra

16²⁵

David Shteynberg (ISB)
Computing Information Content of PTM Localization with PTMProphet

16⁵⁰

Yang Lu (UW)
DIASibling: Learning to detect sibling peptide pairs in DIA mass spectrometry data

17¹⁵

Brian Searle (ISB)
Building DIA MS libraries for non-model organisms with empirically corrected peptide predictions

17⁴⁰

Lightning Talk: Andy Lin (UW)
Targeted database search strategies: Searching only for relevant peptides

17⁴⁵

Lightning Talk: Luis Mendoza (ISB)
Integration of Known Variants and Modifications from PEFF into the Trans-Proteomic Pipeline

17⁵⁰

Lightning Talk: Seth Just (Proteome Software)
Influence of Library Selection for Proteomics Experiments on the Accuracy of Error Rate Estimation

17⁵⁵

Lightning Talk: Richard Johnson (UW)
Assessing protein sequence database suitability using de novo sequencing

18⁰⁰

Wine and Tapas Reception with Posters

8³⁰

Continental Breakfast

9⁰⁰

Session 5: Proteomes and Metabolomes
Chair: Kristin Burnum-Johnson (PNNL)

9⁰⁰

Gilbert Omenn (U Michigan/ISB)
Progress on Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project

9²⁵

Kyle Hess (UW)
Proteome-wide mistranslation identifies proline residues important for protein stability

9⁵⁰

Lightning Talk: Samuel Smukowski (UW)
Analyzing Proteome-Wide Stability Changes Across Organismal Lifespan

9⁵⁵

Lightning Talk: Fausto Carnevale Neto (UW)
Untargeted Mass Spectrometry Analysis and Molecular Networking in the Context of Metabolomics

10⁰⁰

Lightning Talk: Jacob Lippincott (Proteome Software)
Incorporating In-Source Fragments Improves Identification Accuracy in Untargeted LC-MS Metabolomics

10⁰⁵

Break

10³⁵

Session 6: Protein Structure and Cross-linking
Chair: Rich Rogers (Juno)

10³⁵

Danielle Faivre (UW)
Protein structural accessibility in cerebrospinal fluid by limited proteolysis-mass spectrometry

11⁰⁰

Andrew Keller (UW)
Prediction of an Upper Limit for the Fraction of Inter-Protein Cross-Links in Large-Scale Studies

11²⁵

Jared Mohr (UW)
Multidimensional cross-linking with a tetra-reactive cross-linker

11⁵⁰

Lightning Talk: Michael Hoopmann (ISB)
Kojak 2.0: New features for the analysis of cross-linked proteins

11⁵⁵

Lunch

13¹⁰

Session 7: Single Cell Proteomics
Chair: Matt Bush (UW)

13¹⁰

Wei-Jun Qian (PNNL)
A Boosting Strategy for Comprehensive Quantitative Phosphoproteomics of Small Cell Populations

13³⁵

Bingyun Sun (SFU)
Sensitive Analysis towards Single-Cell Proteomics: from Sample Preparation to MS Parameters

14⁰⁰

Chia-Feng Tsai (PNNL)
Integrated carrier-assisted sample preparation and BASIL strategy toward nanoscale phosphoproteomics

14²⁵

Break

14⁵⁰

Session 8: New Technologies and Resources
Chair: Jim Kapron (Bruker)

14⁵⁰

Kristin Burnum-Johnson (PNNL)
Mass spectrometry imaging of over 2,000 proteins from tissue sections at 100-micron spatial resolution

15¹⁵

Stephanie Zimmerman (UW)
Measuring the functional effect of amino acid substitutions proteome-wide using mistranslation

15⁴⁰

Mario Leutert (UW)
Automated high-throughput proteome and phosphoproteome analysis using paramagnetic bead technology

16⁰⁵

Meagan Gadzuk-Shea (UW)
Determining How Long Solutions Stay "Native" in nESI Experiments Using a Fluorescent Probe

16³⁰

Closing

16⁵⁰

Wine and Tapas Reception with Posters

Andy Lin (UW) LT
Targeted database search strategies: Searching only for relevant peptides

Seth Just (Proteome Software) LT
Influence of Library Selection for Proteomics Experiments on the Accuracy of Error Rate Estimation

Jacob Lippincott (Proteome Software) LT
Incorporating In-Source Fragments Improves Identification Accuracy in Untargeted LC-MS Metabolomics

Juan Chavez (UW) LT
Systems structural biology of the heart: Impact of acetylation on protein conformations/interactions

Clint Vorauer (UW) LT
Biophysical Properties of Refractile Bodies

Drake Russell (UW) LT
An Exploration of the Post Translational Structure of a Novel S-Methyltransferase

Michael Hoopmann (ISB) LT
Kojak 2.0: New features for the analysis of cross-linked proteins

Luis Mendoza (ISB) LT
Integration of Known Variants and Modifications from PEFF into the Trans-Proteomic Pipeline

John Cha (Providence) LT
Highly sensitive detection of immune checkpoint drugs in blood via nSMOL LC-MS assay

Fausto Carnevale Neto (UW) LT
Untargeted Mass Spectrometry Analysis and Molecular Networking in the Context of Metabolomics

Samuel Smukowski (UW) LT
Analyzing Proteome-Wide Stability Changes Across Organismal Lifespan

Richard Johnson (UW) LT
Assessing protein sequence database suitability using de novo sequencing

Anthony Valente (UW) LT
Towards targeted phosphoproteomics by machine learning

Christopher Adams (Bruker) LT
Identification and Quantitation of Phosphopeptide Positional Isomers using TIMS and PASEF

Eric Deutsch (ISB)
Proteomics Standards Initiative Extended FASTA Format (PEFF)

Alex Zelter (UW) LT
Elucidating protein-xenobiotic interactions by mass spectrometry

Jim Kapron (Bruker)
Proteome quality control addressing qualitative & quantitative needs for TIMS & PASEF

Julia Robbins (UW)
A Robust and Reproducible Method for Preparing Brain Tissue for Proteomics Applications

Bianca Ruiz (UW)
Functional selections to investigate the effects of amino acid substitutions across the proteome

Peter Bell (UBC)
Analysis of human bone for the ID of 'missing proteins' and characterisation of the bone N-terminome