Michael MacCoss (University of Washington)
Jennifer Van Eyk (Cedars Sinai Medical Center)
Catamaran Resort Hotel, San Diego, CA
The goal of this workshop is to instruct and discuss with scientists / researchers who are currently applying data-independent acquisition-mass spectrometry (DIA-MS), data acquisition and data analysis workflows that maximize the reproducible quantification of the proteome in a variety of samples.
The program will use a combination of lectures, hand-on tutorials and focused discussion panels to maximize interactions between workshop participants and to drill down into what is required to obtain reproductible DIA-MS data sets. For the hands-on tutorial workshop participants will compare current peptide- and spectrum-centric analysis packages using a model DIA-MS data sets. These model data sets will allow participants to dig into the robustness of the data using either Peptide- and Spectrum-central data analysis approaches. Furthermore, we will concentrate on the logistics required for generate reproducible data in large cohorts/studies as and emerging approaches in DIA-MS, specifically its use for quantification of protein post-translational modifications. Finally, the group will discuss the next steps in application of DIA-MS and what will be required to push this method to new frontiers.
https://panoramaweb.org/2022-asms-workshop.url
In preparation:
| Attached Files | ||
asms-panorama.bat rename4.bat7:30 – 9:00 Enhanced Continental Breakfast & Badge pick-up, Kon Tiki Ballroom
9:00 - 9:05 Welcome, Michael MacCoss, University of Washington
and Jennifer Van Eyk, Cedars-Sinai Medical Center
DIA-MS INTRODUCTION
9:05 – 9:35 01 Introduction to DIA Concepts, Drive for Reproducible Large Scale Datasets and Comparison of Different Data Acquisition Methods for Q-Orbitrap, Q-TOF, IMS-TOF, etc.
Brian Searle, Ohio State University
9:35 – 10:05 02 Peptide-Centric Approaches for Data Analysis (e.g. Open-SWATH, Skyline, EncyclopeDIA, Spectronaut)
Lilian Heil, University of Washington
10:05 – 10:30 Coffee Break
10:30 - 11:00 03 Spectrum-Centric Approaches for Data Analysis (e.g. Pular-X, DIA-Umpire)
Alexey Nesvizhskii, University of Michigan
11:00 - 11:30 04 Skyline Tools and Applications Including Quantification
Brendan MacLean, University of Washington
11:30 – 12:00 05 Small Group Discussion: Current Challenges and Issues in DIA-MS, Specifically around Robustness and Scalability
Michael MacCoss, University of Washington, Hannes Röst, University of Toronto and Niveda Sundararaman, Cedars-Sinai Medical Center
12:00 - 1:00 Group Photo & Lunch hosted by ASMS, Beach North (outside)
DIGGING INTO THE NITTY GRITTY OF SOFTWARE AND ANALYTICS AROUND DIA-MS
1:00 – 1:30 06 Hands-On Skyline Tutorial
Brendan MacLean, University of Washington
Hands-On Tutorials Using Thermo Fisher Orbitrap and Bruker timsTOF Instruments on the Same Real Data
1:30 – 2:15 07 Part 1: Effect of Missingness and Linearity on Quantitation: Orbitrap MS (Exploris 480) Data Analysis by DIA-NN and EncyclopeDIA
Michael MacCoss, Deanna Plubell and Aaron Maurais, University of Washington
2:15 – 3:00 08 Part 2: Effect on Library Size on Protein Identification and Quantification timsTOF (TimsTOF Pro) by TIMS-DIA-NN
Qin Fu and Niveda Sundararaman, Cedars-Sinai Medical Center
3:00 – 3:30 Coffee Break
NEW AND EMERGING APPROACHES
In this session, each new approach will outline the novelty and the pros and cons compared to peptide- and spectrum- centric approaches based on showing the data generated on the same model data set as above.
3:30 – 3:50 09 New Approach: DeepSearch and Orbitrap Data
Gautam Saxena, DeepDIA
3:50 – 4:10 10 New Approach: AI and TimsTOF Data
Robin Park, Bruker
4:10 – 4:30 11 Update on New Approaches with a Focus on Unmet Needs of DIA-MS
Hannes Röst, University of Toronto
4:30 – 5:00 12 Panel Discussion: Current Challenges in Data Acquisition and Data Handling.
The focus is on establishing the issues around misinterpreting spectra and establishing what should be the gold standard.
Brian Searle, Michael MacCoss, Niveda Sundararaman
7:30 – 9:00 Enhanced Continental Breakfast & Badge pick-up, Kon Tiki Ballroom
ESTABLISHING REPRODUCIBLE DIA-MS RESEARCH
The goal of this session is to provide real-life examples focusing on quality control, reproducibility of data and highlighting lessons learned sets.
9:00 – 9:20 13 Sample Preparation and Automation
Qin Fu, Cedars-Sinai Medical Center
9:20 – 9:40 14 Setting Up Systems Suitability, Process Control and QC for Sample Preparation
Deanna Plubell, University of Washington
9:40 – 10:00 15 Full System Automation with Tracking and Automated Data Reports
Sarah Parker, Cedars-Sinai Medical Center
10:00 – 10:30 16 What Is Wrong with This Data?
Michael MacCoss, University of Washington
10:30 – 10:50 Coffee Break
10:50 – 11:30 Small Group Discussion
Discuss the challenges and potential solutions based on a series of targeted questions. Questions will include:
11:30 – 12:00 20 Full Group Discussion and Brainstorming
Alek Binek, Cedars-Sinai Medical Center and Michael MacCoss, University of Washington
12:00 – 1:00 LUNCH, Beach North (outside)
PUSHING DIA-MS INTO LARGE SCALE REPRODUCIBLE SCIENCE
The goal of this session is to provide real-life examples of the lectures, focusing on real questions and reproducibility of data and highlight the lessons learned.
1:00 – 1:05 21 Introduction of Case Studies
Jennifer Van Eyk, Cedars-Sinai Medical Center
1:05 – 1:45 22 Case Study 1: 350 CSF Samples from Different Disease Categories. Challenge: Sample Numbers and Individual Variation
Michael MacCoss, University of Washington
1:45 – 2:25 23 Case Study 2: 1,000 IPSC Derived Motor Neurons for Answer ALS. Challenge to overcome are samples arriving over time. DIA-MS carried out on 6600 triple tof
Jennifer Van Eyk and Niveda Sundararaman, Cedars-Sinai Medical Center
2:25 – 2:50 Coffee Break
2:50 – 3:30 24 Case Study 3: Single Cell (Aorta). Challenge: Scaling down the input and scaling up data acquisition and analysis
Sarah Parker, Cedars-Sinai Medical Center
3:30 – 4:30 25 Panel Discussion
Will summarize needs and next steps in DIA-MS applications.
Moderated by Qin Fu, Cedars-Sinai Medical Center
and Lilian Heil, University of Washington
4:30 – 5:00 Summary and Conclusion
Michael MacCoss, University of Washington
Jennifer Van Eyk, Cedars-Sinai Medical Center