Table of Contents

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2024-12-30
2022 ASMS Fall Workshop Intro
Agenda

2022 ASMS Fall Workshop Intro


Data Independent Acquisition (DIA) and Getting to More Biology

November 7 - 8, 2022

Organizers:

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:

  1. Bring a fast laptop (i5 or i7 with 8-16 GB of RAM) running Windows 10 or 11, with at least 50 GB of free disk space.
    • If all you have is a Mac, you will need a Windows VM or dual boot to be able to follow along during tutorials.
  3. Install Skyline 22.2 on it.
  4. Tutorial data (24 GB total) will be provided on flash drives with USB 3.0 and USB C connectors.
  5. If your IT security does not allow flash drive connection to your laptop, you should download the 3 .sky.zip files in the TimsTOF and Exploris folders below.
  7. You can download and double-click the attached asms-panorama.bat to set-up a computer with all of the necessary files.
  8. For downloads before 11/8 or from the workshop flash drives: To fix spectrum display for TimsTOF data download the rename4.bat file attached here and run it.


Agenda


Monday, November 7

7:30 – 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

5:00 – 6:00      RECEPTION

 

 

Tuesday, November 8

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:

  • 17 What are criteria for quantification if based on a single peptide, and then extract those criteria to if you have to quantify 20,000 peptides?
  • 18 Is identification equal to quantification? Is quantification equal to precision on different instruments?
  • 19 What is the strategy for using DIA-MS on PTMs that can be isolated in different DIA-windows (e.g., mono-, di- versus tri-methylation)? What is the strategy for using DIA-MS on PTMs that cannot be isolated in different DIA-MS windows (e.g., citrullination, deamidation, etc.)?

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