Fall Workshop Homepage

Data Independent Acquistion (DIA) and Getting to More Biology

November 7 - 8, 2022


Michael MacCoss (University of Washington)
Jennifer Van Eyk (Cedars Sinai Medical Center)



Important Deadlines

September 16

Application Deadline for Student and Postdoc Travel Stipends

September 30

Registration Deadline - Limited Availability

October 4

Hotel Reservation Deadline


About the Fall Workshop 2022: Goal and Overview

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. This includes focusing on system suitability, QC, maximizing MS data acquisition parameters and establishing transparent data analysis.

The heart of the workshop is focused on current and upcoming data analysis pipelines. Here we propose a hands-on tutorial that will allow workshop participants to compare current peptide- and spectrum-centric analysis packages using a model DIA-MS data sets generated on the same sample set acquired on 3 different instrument using DIA-MS. These model data sets will allow participants to dig into the robustness of the data using either Peptide- and Spectrum-central data analysis approaches. This session will be followed up by a discussion on data handling of DIA-MS data sets and introduce emerging data analysis packages that are currently being developed.  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.

Attendee Requirements

  • At least two years of DIA experience, this in NOT an introductory workshop for new users.
  • Attendees need to bring a laptop that they can download and install software on.
  • PC laptops are preferred over MACs.

Workshop Focus

  • Main focus: This workshop focus on user-focused learning and discussion on DIA-MS applications in proteomics specifically on the technical requirements for the generation of reproducible and scalable DIA-MS data sets. It will emphasis data acquisition and data analysis including peptide- and spectrum-centric approaches, exploration of the current state-of-the-art DIA-MS application in post-translational modifications and large scale studies.
  • The workshop includes lectures, hands-on tutorial and discussion panels to explore the current challenges of DIA-MS accompanied by discussion on solutions. A highlight is a hands-on session centered on data analysis using a choice of a model DIA-MS data sets from the same samples run on 3 different vendor instruments that the participants can analyze using peptide- and spectrum-centric data analysis package. The model DIA-MS data set will be already generated and analyzed by experts prior to meeting to allow the participates to compare and contrast their data analysis workflows. Comparison to several emergying data anlasyis approaches will be presented.
  • The workshop participants should be DIA-MS scientists beit bioinformatics, biologists, clinician and/or mass spectrometrists.

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