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The 2019 program has not yet been established. Below is last year's (2018) program.

Monday, July 23, 2018

8:00 am Registration and Light Breakfast
8:45 am Welcome - Rob Moritz (ISB)
8:50 am Chris Overall (UBC) Positional Proteomics by TAILS deciphers a rare human immunodeficiency leading to development of a molecular corrector for personalised medicine

Session 1: Systems Biology - Chair: Chris Barnes (Novo Nordisk)
9:35 Mark Gillespie (ISB) A systems approach to quantifying transcriptional regulation of erythropoiesis
10:00 Rachel Drake (OHSU) Epicardial Adipose Depot Proteome and Secretome Reveal Distinct Biology and Nutrient Utilization
10:25 LT: Abdul Basit (UW) Quantitative proteomic and metabolic characterization of primary human enterocytes
10:30 LT: Seoyeon Hong (UW) Collision Induced Unfolding and Dissociation Reveal the Location of Ni (II) Binding Site in the Alpha Crystallin Domain of HSPB5
10:35 LT: Samuel Entwisle (UW) Acetyl-proteomic and Metabolomic Analysis of Mouse Brown Fat Reveals New Features of Thermogenesis

10:40 Break

Session 2: DIA & Targeted Technologies - Chair: Rich Rogers (Just Therapeutics)
11:10 Brian Searle (UW) XCorDIA: a new database search engine to detect genetic variants from DIA data
11:35 Deanna Plubell (UW) Using data independent acquisition to develop triple quadrupole assays in cerebrospinal fluid
12:00 David Shteynberg (ISB) DISCO: Software to Enable Data-Driven DIA Analysis
12:25 LT: Lindsay Pino (UW) A Novel Workflow for Developing and Validating Quantitative Protein Assays using DIA-MS
12:30 LT: Danielle Faivre (UW) Analysis of peptide acetylation by new acquisition methods combining DIA and DDA
12:35 LT: Bhagwat Prasad (UW) Quality-by-design (QbD) approach to address rigor and reproducibility in DMET quantitative proteomics

12:40 Lunch

Session 3: Disease Proteomics - Chair: Chris Overall (UBC)
13:50 Arti Navare (CIDR) A quantitative analysis of host-pathogen protein-protein interactions of influenza nonstructural pro
14:15 Xuefei Zhong (UW) Comparative interactome analysis of multidrug-resistant and sensitive strains of A.baumannii
14:40 Jaipalreddy Panga (ISB) Proteogenomic resource of Borrelia burgdorferi isolates to develop novel markers for Lyme disease
15:05 LT: Lian Yi (PNNL) Cytokine-induced phosphorylation dynamics reveals molecular mechanisms underlying beta-cell stress
15:10 LT: Hsueh-Fen Juan (NTU) Proteomics reveals the trafficking pathway of mitochondrial ATP synthase to cancer cell surface

15:15 Break

Session 4: Computational Proteomics - Chair: Eric Deutsch (ISB)
15:40 Damon May (UW) Jointly Analyzing Millions of Mass Spectra with Repository-Wide Embedding
16:05 Wout Bittremieux (UW) Fast open modification spectral library searching through approximate nearest neighbor indexing
16:30 Luis Mendoza (ISB) Fast and Efficient Mapping of Peptide Sequences and their Variants to Proteome Databases
16:55 Richard Johnson (UW) Assessing protein sequence database suitability using de novo sequencing
17:20 LT: William Noble (UW) An averaging strategy to reduce variance in target-decoy estimates of false discovery rate
17:25 LT: Eric Deutsch (ISB) The PSI Universal Spectrum Identifier (USI)
17:30 LT: Wenruo Bai (UW) Submodular generalized matching for peptide identification in tandem mass spectrometry
17:35 LT: Ryan Luce (Labkey) Quantification reporting using targeted mass spec assays with Panorama and Skyline
17:40 LT: Xinyu Zhang (UW) A New Set of Metrics for Evaluating LC-MS Global Metabolite Profiling Data Quality

17:45 Wine and Tapas Reception with Posters



Tuesday July 24, 2018


8:30 am Light Breakfast

Session 5: Protein Structure & Interactions - Chair: Bhagwat Prasad (UW)
9:00 Nicholas Brodie (UVic) Structural study of alpha-synuclein misfolding using crosslinking, HDX, and affinity labelling
9:25 Juan Chavez (UW) Protein Conformational and Interaction Dynamics During Cell Cycle Targeted Therapy
9:50 Abhigya Mookherjee (UW) Investigating structural rearrangements in fucosylated glycans by ion mobility
10:15 LT: Rachel Eaton (UW) Studying the Structural Stability of Protein Complexes Using Tandem Ion Mobility
10:20 LT: Sanjit (Sunny) Uppal (UW) Internal Exchange Standards Enable Cross-Platform Reproducibility in Measuring Gas-Phase HDX MS
10:25 LT: Kyle Hess (UW) Quantifying proteoform stability and turnover using peptide-level readouts

10:30 Break

Session 6: Cross-linking - Chair: Judit Villen (UW)
11:00 Karl Makepeace (UVic) Improving crosslink identification with affinity-enrichment, isotopic-coding, and MS-cleavability
11:25 Jared Mohr (UW) Tetra-link: Cross-linking goes multidimensional
11:50 Michael Hoopmann (ISB) Kojak 2.0: New features for the analysis of cross-linked proteins
12:15 LT: Martin Mathay (UW) Antibiotic-induced bacterial ribosome conformational changes by cross-linking mass spectrometry
12:20 LT: Ian Smith (UW) A novel method to identify functional phosphorylation sites across the proteome

12:25 Lunch

Session 7: Metaproteomics - Chair: Martin Sadilek (UW)
13:40 Brook Nunn (UW) Taking protein inference out of the pipeline. Can we use peptides to link microbial taxa with their functional role in ocean ecosystems?
14:05 Megan Duffy (UW) De-novo assisted protein sequencing reveals degradation patterns in marine organic matter
14:30 Rachel Lundeen (UW) Production and secretion of polycyclic peptide secondary metabolites in marine cyanobacteria
14:55 LT: Miklos Guttman (UW) Combining gas-phase hydrogen/deuterium exchange with ion mobility for glycan structural analysis
15:00 LT: Yuko Ogata (Just) High Throughput Multi-Attribute Method (MAM) Analysis of Fc-Fusion Biotherapeutics

15:05 Break

Session 8: New Technologies and Resources - Chair: Dan Raftery (UW)
15:30 Meagan Gadzuk-Shea (UW) Memory of the Condensed-Phase in the Gas-Phase: Effects of Solution, Charge, and Energy on Structure
15:55 Ying Zhu (PNNL) Single Cell Proteome Mapping of Tissue Heterogeneity using nanoPOTS and Ultrasensitive LC-MS
16:20 Maowei Dou (PNNL) Nanowell-Mediated 2D LC Enables Deep Proteome Profiling of <1000 Mammalian Cells
16:45 Phillip Wilmarth (OHSU) Reproducible quantitative proteomics analyses using Jupyter notebooks, the R language, and Github
17:10 LT: Yiran Liang (PNNL) Nanoliter Sample Preparation Enables Spatially Resolved Proteome Profiling of <200 Plant Cells
17:15 LT: Randy Bolger (Agilent) Automated, reproducible phosphopeptide enrichment using AssayMAP platform and Fe(III)-NTA cartridges

17:20 Closing

17:40 Wine and Tapas Reception with Posters



Posters:


1 Yiran Liang (PNNL)    Nanoliter Sample Preparation Enables Spatially Resolved Proteome Profiling of <200 Plant Cells
2 Abdul Basit (UW)    Quantitative proteomic and metabolic characterization of primary human enterocytes
3 Lindsay Pino (UW)    A Novel Workflow for Developing and Validating Quantitative Protein Assays using DIA-MS
4 Lian Yi (PNNL)    Cytokine-induced phosphorylation dynamics reveals molecular mechanisms underlying beta-cell stress
5 William Noble (UW)    An averaging strategy to reduce variance in target-decoy estimates of false discovery rate
6 Rachel Eaton (UW)    Studying the Structural Stability of Protein Complexes Using Tandem Ion Mobility
7 Seoyeon Hong (UW)    Collision Induced Unfolding and Dissociation Reveal the Location of Ni (II) Binding Site in the Alpha Crystallin Domain of HSPB5
8 Danielle Faivre (UW)    Analysis of peptide acetylation by new acquisition methods combining DIA and DDA
9 Hsueh-Fen Juan (NTU)    Proteomics reveals the trafficking pathway of mitochondrial ATP synthase to cancer cell surface
10 Wenruo Bai (UW)    Submodular generalized matching for peptide identification in tandem mass spectrometry
11 Martin Mathay (UW)    Antibiotic-induced bacterial ribosome conformational changes by cross-linking mass spectrometry
12 Eric Deutsch (ISB)    The PSI Universal Spectrum Identifier (USI)
13 Samuel Entwisle (UW)    Acetyl-proteomic and Metabolomic Analysis of Mouse Brown Fat Reveals New Features of Thermogenesis
14 Bhagwat Prasad (UW)    Quality-by-design (QbD) approach to address rigor and reproducibility in DMET quantitative proteomics
15 Miklos Guttman (UW)    Combining gas-phase hydrogen/deuterium exchange with ion mobility for glycan structural analysis
16 Kyle Hess (UW)    Quantifying proteoform stability and turnover using peptide-level readouts
17 Ryan Luce (Labkey)    Quantification reporting using targeted mass spec assays with Panorama and Skyline
18 Ian Smith (UW)    A novel method to identify functional phosphorylation sites across the proteome
19 Yuko Ogata (Just)    High Throughput Multi-Attribute Method (MAM) Analysis of Fc-Fusion Biotherapeutics
20 Randy Bolger (Agilent)    Automated, reproducible phosphopeptide enrichment using AssayMAP platform and Fe(III)-NTA cartridges
21 Sanjit (Sunny) Uppal (UW)    Internal Exchange Standards Enable Cross-Platform Reproducibility in Measuring Gas-Phase HDX MS
22 Xinyu Zhang (UW)    A New Set of Metrics for Evaluating LC-MS Global Metabolite Profiling Data Quality
23 Jiyang Dong (UW)    Significant Metabolic Pathway Identification Based on Multi-Block Partial Least Squares Analysis
24 Austin Keller (UW)    A Platform for High-Throughput Data Independent Acquisition Analysis on the Cloud