Preliminary Program: Fall Workshop on DIA and Getting More Biology

Subject to change.

Monday, November 7

9:00 am - 12:00 pm, DIA-MS introduction

The goal of this session is to introduce the workshop participate to differences in DIA-MS data acquisition and data analysis while setting up comparison of peptide- verses spectrum-centric data analysis of DIA-MS generated data. 30-45  mins lectures with 1 hr discussion.

 Introduction to DIA concepts and drive for reproducible large scale datasets. Comparison of different data acquisition methods for Q-Orbitrap, Q-TOF, IMS-TOF, etc. 45 min. (Brian Searle, The Ohio State University)

  • Peptide-Centric approaches for data analysis (e.g. Open-SWATH, Skyline, EncyclopeDIA, Spectronaut). 30 min. (Lilian Heil, University of Washington)
  • Spectrum-Centric Approaches for data analysis (e.g. Pular-X, DIA-Umpire). 30 min. (Alexey Nesvizhskii, University of Michigan)
  • Small group discussion around current challenges and issues in DIA-MS specifically around robustness and scalability. 1 hr

1:00 - 5:00 pm, Digging into the nitty gritty of software and analytics around DIA-MS

The goal of this session is for workshop participates to examine DIA-MS data sets using the two primary approaches and to understand the underlying assumptions and limitations of peptide- and spectrum-centric data analysis approaches and how new emerging methods may address some of these challenges. This session is comprised of two parts: The first part is a 3 hrs. hands on tutorial using pregeneated data sets followed by 60 min small group discussion. The second part is on new and emergying approaches and includes 30 min talks on their appaoach and results from analyzing the same data set used in the tutorals followed by a 1 hr panel discussion.

  •  Hands-on tutorial looking at Peptide-Centric data in Skyline. 60 min. (Brendan MacLean, University of Washington)
  • Hands-on tutorial looking at Spectrum-Centric data. 60 min. (Niveda Sundaraaman, CSMC)
    • Both tutorials will use a pre-generated model DIA-MS data sets from ThermoFisher Orbitrap, Sciex 6500 Triple TOF and or Bruker TimsTOF instrument will be provide to the participants. Prior to the workshop, this data set will be generated on the same samples by organizers and analyzed so existing data set can be compared. Each participate can choice to run data set via peptide- or spectrum-centric data analysis using different existing tools.
  • Small group discussion around results from the different data analysis approaches with report to the general group. 1 hr.
  •  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.

      • New Approach: DeepSearch 45 mins (Gautam Saxena, DeepDIA)
      • New Approach: AI 45 mins (Robin Park, Scripps)
  •  Panel discussion on current challenges in data acquisition and data handling (30 mins). The focus is on establishing the issues around misinterpreting spectra and establishing what should be the gold standard. 30 mins (lead by Hannes Rost, University of Toronto)



Tuesday, November 8

9:00 am - 12:00 pm, Establishing Reproducible DIA-MS Research

The goal of this session is for workshop participates to explore the study design and infrastructure that can assist in generating reproducible (large scale) DIA-MS data sets. 3 diadictal lectures (20 mins. each) 

  • Sample Preparation and automation. 20 min. (Rena Robinson, Vanderbilt University)
  • Setting up systems suitability, process control and QC for sample preparation. 20 mins. (Deanna Plubell, University of Washington)
  • The hope for a full system automation, sample tracking, data analysis  and batch correction. 20 mins. (Sarah Parker, CSMC)
  • Small group discussion (1 hr) around where there are challenges and potential solutions based on series of targeted questions. Questions will include:
    • What are criterial for quantification if based on a single peptide and then extract those criteria to if you have to quantify 20,000 peptides.
    • What are the criteria for comparing DIA-DA data sets obtained using different acquisitions or MS instruments (e.g. boxcar/overlap vs traditional acquisition on Thermo. E.g. Triple TOF vs Thermo vs Tims TOF instruments).
    • What is the strategy for using DIA-MS on PTMs that can be isolated in different DIA-windows. (e.g. mono-, di- verse tri-methylation).
    • What is the strategy for using DIA-MS on PTMs that cannot be isolated in different DIA-MS windows (e.g. citrullination).
  • Discussion and brain storming by full group (1 hr) (Jenny Van Eyk, CSMC)

1:00 - 5:00 pm, Pushing DIA-MS into Large Scale Reproducible Science 

The goals of this session is to provide real life examples with the lectures focusing on the real Q  and reproducibility data and highlight the lessons learnt. There will be a directed  and moderated directed Q and A on what would you change now that you have done this large scale study (moderator. Lisa Jones (30 mins lecture with 10 min Q and A for each PI)

  • 100s mouse models of neurological disease. 30 mins. (Mike MacCoss, UW)
  • ISPC answer in solving ALS or large scale plasma projects. 30 mins (Jenny Van Eyk or one of her Trainees, CSMC)
  • Plasma and AD biomarkers. 30 mins. (Rena Robinson, Vanderbilt)
  • Panel discussion (all instructors and participants involved) will summary needs and next steps in DIA-MS application. 1 hr. (Sarah Parker, CSMC)

 At the end of the course, the participants should have a good understanding of:

  • Challenges and unmet need in the application of DIA-MS for protein quantification
  • Existing and emerging data analysis pipeline and their pros and cons.
  • New emerging areas of DIA-MS application including post-translational modifications
  • Key concepts and innovations in area of large scale applications of DIA-MS including setting up automation, systems suitability and QC.