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.
2. • 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.
6. • TimsTof_HeLa_curve_PASER_DiaNN.sky.zip (3.6 GB)
   • • TimsTOF_curve_rep6_d.zip (9.1 GB - optional)
   • Exploris_HeLa_curve_DiaNN.sky.zip (4.3 GB)
   • Exploris_HeLa_curve_EncycDIA.sky.zip (2.1 GB)
     
   • • Exploris_curve_rep4_mzml.zip (4.9 GB - optional)
       
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.