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LC-MS Proteomics Workshop Program
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Workshop Program

Thursday, September 27, 2018

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Program as of June 4, 2018 - Subject to Change

Sunrise Session

7:00 AM - 7:30 AM - Registration for Attendees of the Sunrise Session

7:30 AM - 8:30 AM - Pre-Workshop Sunrise Session: Ins and Outs of Quantitative Proteomics: Beginners’ Guide to Concepts, Tools, Requirements, Applications and Challenges!

Introduction to the Session: Amin Rostami (University Manchester)

Speaker: Bhagwat Prasad (University of Washington)

This sunrise lecture will introduce the audience to the basics of quantitative proteomics (QPr) including terminology, current methods, and applications. This will enable attendees not experienced with QPr to follow the in-depth discussion in the main workshop.


8:00 AM - 8:45 AM - Registration for Attendees of the Workshop 

8:45 AM – 8:55 AM - Introduction to the Workshop 

Jash Unadkat (University of Washington)

Session 1: Choice of LC-MS/MS Proteomic Techniques: Horses for Courses!

Chairs and Moderators: Bhagwat Prasad (University of Washington) and Marcel Hop (Genetech)


9:00 AM – 9:30 AM: Philip Smith (University of North Carolina): Targeted SIL-peptide based proteomics

9:30 AM – 10:00 AM: Jill Barber (University of Manchester): QconCAT method for targeted proteomics

10:00 AM – 10:30 AM: Jacek Wisniewski (Max Planck Institute): Global proteomics of ADME proteins and relevant tissues and cell lines

10:30 AM – 11:00 AM - Coffee Break & Poster Viewing

11:00 AM-12:10 PM - Viewpoints on Various Proteomic Methods (10 minutes each): 

  • Anna Vildhede (AstraZeneca): Tandem mass tags and global proteomics

  • Michael Wang (University of Kansas): Targeted proteomics of enzymes using MRM

  • Haojie Zhu (University of Michigan): PRM vs. MRM Quantification 

  • John Fallon (University of North Carolina): MRM quantification of transporters

  • Fatemeh Akhlaghi (University of Rhode Island): SWATH MS for targeted proteomics

  • Brahim Achour (University of Manchester): Head-to-head comparison of proteomics methods

12.10 PM – 1:00 PMSession 1 Discussion

1:00 PM – 2:00 PM - Lunch Break


Session 2:  Sample Preparation and Data Analysis Matter! The Concept of ‘Fit for Purpose’

Chair and Moderator: Brahim Achour (University of Manchester) and Yurong Lai (Gilead)


2:00 PM – 2:30 PM: Per Artursson (Uppsala University): Whole cell lysate sample preparation for global and targeted proteomics

2:30 PM – 3:00 PM: Yasuo Uchida (Tohoku University): Membrane enrichment and sample preparation for targeted proteomics

3:00 PM – 3:30 PM: Dan Spellman (Merck): Skyline/Panorama and SWATH analysis approaches

3:30 PM – 4:00 PM - Beverage Break

4:00 PM – 5:00 PM - Viewpoints on Sample Preparation and Data Analysis

  • Oliver Poetz (University of Tubingen): Peptide-group specific immuno-enrichment from whole cell lysate digests for targeted protein analysis

  • Buyun Chen (Genentech): Selecting Surrogate Peptide for Transporter Quantitation by using Authentic Protein Standards

  • Evita van de Steeg (TNO): Plasma membrane enrichment for targeted proteomics

  • Ryota Kikuchi (Abbvie): Use of plasma membrane markers in targeted plasma membrane protein quantification

  • Martyn Howard (University of Manchester): New approaches in sample preparation and data analysis

  • Vineet Kumar (University of Washington): A method to quantify plasma membrane abundance of transporters

  • Stefan Oswald (University of Greifswald): Whole cell lysate vs. enriched membrane proteomics

5.00 PM – 6.00 PM - Session 2 Discussion 

Session 3:  PBPK, QSP, QST: Academic, Industrial and Regulatory Applications in Modern Drug Development - SPONSORED BY CERTARA

Chair and Moderator: Jash Unadkat (University of Washington) and Michael Zientek (Takeda)


8:00 AM – 8:30 AM: Jash Unadkat (University of Washington): Applications of proteomics in PBPK, QSP and QST  – An academic view

8:30 AM – 9:00 AM: Yurong Lai (Gilead): Applications of proteomics in IVIVE, PBPK, QSP and QST – An industry view

9:00 AM – 9:30 AM: A SPEAKER from EMA/FDA: Applications of proteomics in PBPK, QSP and QST – A regulatory view

9:30 AM – 10:00 AM: Amin Rostami (University of Manchester): Applications of proteomics in PBPK, QSP and QST – Summary and outlook

10:00 AM – 10:30 AM - Beverage Break

10:30 AM -11:30 AM - Viewpoints on applications of quantitative proteomics

  • Frans Russell or Rick Greopick: Application of Proteomics in PK/PD and Toxicity Prediction in Paediatrics

  • Mathena Varma (Pfizer): Transporter Protein Driven REF vs. RAF Approach to Predict Transporter-mediated Drug Clearance 

  • Matthew Harwood (Certara): The use of Proteomics Data in the Prediction of Drug Absorption and DDIs

  • Abdul Basit (University of Washington): MRM vs. SWATH for Inter-species Profiling of DMEs and Transporters

  • Sumio Ohtsuki (Kumamoto University): Membrane Enrichment for Targeted Proteomics of Enzymes and Transporters in Different Tissues and Cell Lines

  • Katsuaki Ito (Teijin Pharma): Proteomics for Predicting DDIs using Sandwich-cultured Human Hepatocytes

11.30 AM – 12.30 PM - Session 3 Discussion

12:30 PM - 1:30 PM - Lunch Break

1:30 PM – 4:00 PM - Session 4:  Break-out Parallel Round Table Discussions

Moderators and topics for discussion will be selected from the organizers, chairs and speakers in the above sessions.

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