Fall Workshop on DIA and Getting More Biology
Remember to Bring!
All participants must show a negative Covid test result AND proof of vaccination. Masking required except when eating or drinking. Be prepared, read more on Health & Safety page.
All participants must bring a laptop with them for use during the workshop. We recommend you bring a PC laptop and have credentials to load software (some company laptops have security protocols preventing this).
Registration and Breaks
Monday, November 7
7:30 - 9:00 am Registration, Kon Tiki Ballroom
- Badge pickup
- Have your proof of vaccination AND proof of negative COVID test result easily accessible and available to show.
- Enhanced continental breakfast with breakfast sandwiches will be served, so arrive early!
9:00 am Fall Workshop begins, Kon Tiki Ballroom
10:00 - 10:30 am Coffee Break
12:00 - 1:00 pm ASMS hosted lunch provided to attendees, Beachside North
3:00 - 3:30 pm Coffee Break
5:00 pm Fall Workshop instruction ends for the day
5:00 - 6:00 pm Reception, Kon Tiki Ballroom
Tuesday, November 8
7:30 - 9:00 am Enhanced continental breakfast with breakfast sandwiches will be served
9:00 am Fall Workshop instruction begins, Kon Tiki Ballroom
10:00 - 10:30 am Coffee Break
12:00 - 1:00 pm ASMS hosted lunch provided to attendees, Beachside North
3:00 - 3:30 pm Coffee Break
5:00 pm Workshop concludes
Detailed Program of Instruction
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.
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 (The Ohio State University), 30 minutes
Peptide-Centric Approaches for Data Analysis (e.g. Open-SWATH, Skyline, EncyclopeDIA, Spectronaut), Lilian Heil (University of Washington), 30 minutes
Coffee Break
Spectrum-Centric Approaches for Data Analysis (e.g. Pular-X, DIA-Umpire), Alexey Nesvizhskii (University of Michigan), 30 minutes
SKYLINE Tools and Applications Including Quantification, Brendan MacLean (University of Washington), 30 minutes
Small Group Discussion: Current Challenges and Issues in DIA-MS, Specifically around Robustness and Scalability. (Hannes Roste, Michael MacCoss and Niveda Sundararaman will lead discussion), 30 minutes
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 hands-on tutorial using pre-generated data sets followed by small group discussion. The second part is on new and emerging approaches for analyzing the same data set, followed by discussion.
Hands-On SKYLINE Tutorial, Brendan MacLean (University of Washington), 30 minutes
Hands-On Tutorials Using Thermo Fisher Orbitrap and Bruker timsTOF Instruments on the Same Real Data.
- Effect of Missingness and Linearity of Quantitation: Expolresis on Same Data Analyzed by DIA-NN and EncyclopeDIA, Michael MacCoss, Deanna Plubell and Aaron Maurais (University of Washington), 45 minutes
- Effect on Library Size and Type: timsTOF Data Using TIMS-DIA-NN, discussion on different approaches on library and filtering and look at linearity on CV% and timsTOF data, Qin Fu, Niveda Sundararaman and Alek Binek (Cedars-Sinai Medical Center), 45 minutes
Coffee Break, 30 minutes
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, Gautam Saxena (DeepDIA), 20 minutes
New Approach: AI, Robin Park (Scripps), 20 minutes
Update on New Approaches with a Focus on Unmet Needs, Hannes Rost (University of Toronto), 20 minutes
Panel Discussion: Current Challenges in Data Acquisition and Data Handling. The focus is on establishing the issues around misintergpreting specta and establishing what should be the gold standard. Brian Searle, Michael MacCoss, Niveda Sundararaman, 30 minutes
Reception, 1 hour