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Monday, July 17, 2017

8:00 am Registration and Continental Breakfast
8:45 am Welcome - Rob Moritz (ISB)
8:50 am Gil Omenn (U Michigan,ISB) Perspectives from HUPO - The HPP
9:00 am Dick Smith (PNNL) SLIM SUPER high resolution IM-MS and its applications to proteomics

Session 1 Systems Biology - Chair: Chris Barnes (Novo Nordisk)
9:45 am Miguel Martin-Perez (UW) Large-scale characterization of drugs 'mode-of-action' by protein turnover profiling
10:10 am Wei-Jun Qian (PNNL) Thiol-based Redox Proteomics and Stoichiometric Quantification of Redox PTMs
10:35 am LT: Samuel Entwisle (UW) Cold adaptation remodels the mitochondrial proteome and acetyl-proteome in mouse brown fat
10:40 am LT: Lindsay Pino (UW) Lessons learned in high-dimensional analysis of quantitative DIA-MS proteome profiling

10:45 am Break

Session 2 Biomarker Discovery and Validation - Chair: Brook Nunn (UW)
11:15 am Han-Yin Yang (UW) Evaluation of different data acquisition methods and analysis strategies for amyloidosis typing
11:40 am Komal Kedia (PNNL) Application of IM-MS for Identification of Protein Signatures of Treatment of Tuberculosis
12:05 pm Junyan Shi (UBC) Quantification of C-Reactive Protein in Plasma by HPLC-MS/MS
12:30 pm LT: Mukul Midha (ISB) Industrialization of quantitative proteomics measurements by SWATH-MS
12:35 pm LT: Brian Searle (UW) Quantifying phosphopeptide positional isomers in DIA experiments

12:40 pm Lunch


Session 3 Disease Proteomics - Chair: Dick Smith (PNNL)
1:55 pm Sandra Spencer (UW) Monitoring the Activity of Kinase Pathways using Phosphoproteomics of Effector Transcription Factors
2:20 pm Xuefei Zhong (UW) Comparative interactome analysis of multidrug-resistant and sensitive A.baumannii bacteria strains
2:45 pm Isabel Pablos Ocampo (UBC) Proteomic profiling of feverfew pollen, a relevant allergen source
3:10 pm LT: John Wilson (CSHL) Clinical applications of universal S-Trap sample processing
3:15 pm LT: Hsueh-Fen Juan (IMCB) Integrative phosphoproteome and proteome reveal key protein phosphorylation by MCM2 in lung cancer

3:20 pm Break

Session 4 Computational Proteomics - Chair: Eric Deutsch (ISB)
3:45 pm Aivett Bilbao (PNNL) Enhancing Computational Tools for Ion Mobility-Mass Spectrometry-Based Untargeted Workflows
4:10 pm David Shteynberg (ISB) Exploring the Universe of Known and Unknown Post-Translational Modifications with PTMProphet
4:35 pm Andy Lin (UW) A new well-calibrated shotgun proteomics score function for high-resolution MS/MS data
5:00 pm Deanna Plubell (OHSU) Quantitative proteomics comparison of individual vs pooled biological replicates
5:25 pm LT: Richard Johnson (UW) de novo DIA analysis (dDa)
5:30 pm LT: Damon May (UW) Param-Medic Breathes New Life into MS/MS Database Search by Optimizing Parameter Settings
5:35 pm LT: Joon-Yong Lee (PNNL) Blazing Signature Filter and Its LINCS applications
5:40 pm LT: Eric Deutsch (ISB) The PSI Extended FASTA Format (PEFF) and its implementation in Comet

5:45 pm Poster Reception with wine and tapas



Tuesday July 18, 2017


8:30 am Continental Breakfast

Session 5 Protein Interactions - Chair: Jim Bruce (UW)
9:00 am Meagan Gadzuk-Shea (UW) Folding and Unfolding of Protein Ions in the Gas Phase
9:25 am Martin Mathay (UW) Investigation of interactome differences with phase of bacterial growth
9:50 am Jared Mohr (UW) Mango: A general search tool for CID-cleavable cross-linked peptide identification
10:15 am LT: Austin Keller (UW) Data Independent Acquisition with a Fast Scanning, Low Resolution Hybrid Quadrupole-Linear Ion Trap
10:20 am LT: Daniele Canzani (UW) Glycan Standards for Ion Mobility Mass Spectrometry

10:25 am Break

Session 6 Cross-Linking - Chair: Judit Villén (UW)
10:55 am Juan Chavez (UW) Cross-linking and mass spectrometry: taking systems structural biology to heart
11:20 am Michael Hoopmann (ISB) Kojak: pipeline developments and new features for the analysis of chemically cross-linked proteins
11:45 pm Michael Riffle (UW) Analyze, visualize, and share your cross-linking proteomics data with proxl
12:10 am LT: Kevin Felt (UW) Molecular crowding and its effect on protein conformations and interactions
12:15 pm LT: Andrew Keller (UW) Computational Tools for Systems Structural Biology

12:20 pm Lunch

Session 7 Metaproteomics and Metabolomics - Chair: Martin Sadilek (UW)
1:35 pm Jason Gilmore (UW) Characterizing the metaproteome of glacial meltwater and its implications for climate change
2:00 pm Muaaz Gul Awan(PNNL) Enabling massive peptide library search with GPU-FLASH
2:25 pm Rich Rogers (Just) Leveraging the MAM to Reveal New CQAs for our Biotherapeutics
2:50 pm LT: Haiwei Gu(UW) Metabolism is Widely Altered in C. elegans Under Hypoxic Preconditioning
2:55 pm LT: G. A. Nagana Gowda(UW) Human Whole Blood Metabolomics: Measuring Redox and Energy Coenzymes and Antioxidants
3:00 pm LT: Xinyu Zhang(UW) Evaluation of Data Quality in Global Metabolic Profiling

3:05 pm Break

Session 8 New Technologies and Resources - Chair: Jim Kapron (Bruker)
3:30 pm Rachel Eaton (UW) Stability of Trapped Native-like Protein Ions using Structures for Lossless Ion Manipulation
3:55 pm Abhigya Mookherjee (UW) Mapping Gas-Phase Fragmentation Pathways of Isomeric Protonated Carbohydrates using IM-MS and HDX
4:20 pm Ian Smith (UW) A Pulsed-SILAC Approach for Global Identification of Functional Phosphorylation Sites
4:45 pm Tujin Shi (PNNL) A carrier-assisted targeted mass spectrometry approach for proteomics analysis of single cells
5:10 pm LT: Miklos Guttman (UW) Gas-phase hydrogen/deuterium exchange as a new tool for structural glycoproteomics
5:15 pm LT: Sanjit (Sunny) Uppal (UW) Development of an Internal Exchange Standard for Gas-phase HDX Mass-Spectrometry
5:20 pm LT: Luis Mendoza (ISB) New functionality for the Trans-Proteomic Pipeline: tools for the analysis of proteomics data

5:25 pm Awards and prize presentation

5:45 pm Poster Reception with wine and tapas



Posters:


1 Samuel Entwisle (UW) Cold adaptation remodels the mitochondrial proteome and acetyl-proteome in mouse brown fat
2 Richard Johnson (UW) de novo DIA analysis (dDa)
3 Lindsay Pino (UW) Lessons learned in high-dimensional analysis of quantitative DIA-MS proteome profiling
4 Hsueh-Fen Juan (IMCB, TW) Integrative phosphoproteome and proteome reveal key protein phosphorylation by MCM2 in lung cancer
5 Damon May (UW) Param-Medic Breathes New Life into MS/MS Database Search by Optimizing Parameter Settings
6 Haiwei Gu (UW) Metabolism is Widely Altered in C. elegans Under Hypoxic Preconditioning
7 Brian Searle (UW) Quantifying phosphopeptide positional isomers in DIA experiments
8 Eric Deutsch (ISB) The PSI Extended FASTA Format (PEFF) and its implementation in Comet
9 Kevin Felt (UW) Molecular crowding and its effect on protein conformations and interactions
10 G. A. Nagana Gowda (UW) Human Whole Blood Metabolomics: Measuring Redox and Energy Coenzymes and Antioxidants
11 Xinyu Zhang (UW) Evaluation of Data Quality in Global Metabolic Profiling
12 Austin Keller (UW) Data Independent Acquisition with a Fast Scanning, Low Resolution Hybrid Quadrupole-Linear Ion Trap
13 Miklos Guttman (UW) Gas-phase hydrogen/deuterium exchange as a new tool for structural glycoproteomics
14 Sanjit (Sunny) Uppal (UW) Development of an Internal Exchange Standard for Gas-phase HDX Mass-Spectrometry
15 John Wilson (CSHL) Clinical applications of universal S-Trap sample processing
16 Andrew Keller (UW) Computational Tools for Systems Structural Biology
17 Luis Mendoza (ISB) New functionality for the Trans-Proteomic Pipeline: tools for the analysis of proteomics data
18 Daniele Canzani (UW) Glycan Standards for Ion Mobility Mass Spectrometry
19 Mukul Midha (ISB) Industrialization of quantitative proteomics measurements by SWATH-MS