Pre-HUPO Workshop on Targeted Proteomics

Pre-HUPO Workshop on Targeted Proteomics

16-17th September 2017, Dublin

Ben Collins – ETH Zurich
Brendan MacLean – University of Washington
Christina Ludwig – TU Munich

The goal of the course will be to introduce theoretical and practical concepts in targeted proteomics. The first day will cover targeted acquisition focusing on selected reaction monitoring (SRM). The second day will extend the concepts of targeted proteomics to cover data independent acquisition (DIA) mass spectrometry with a focus on SWATH-MS. We will introduce the targeted proteomic software environment Skyline and provide hands-on tutorials that demonstrate its functionality for the analysis of SRM and SWATH-MS data. Participants will be required to bring their own laptop with Skyline installed (requires Windows, or a Windows virtual machine for Mac/Linux users). Some basic knowledge of mass spectrometry-based proteomics is assumed.

Day 1 – Targeted Proteomics via selected reaction monitoring (SRM)

9.00 – 9.15 Opening remarks (Ben Collins)

9.15 – 10.30 Lecture: The ABC of Selected Reaction Monitoring (Christina Ludwig)

10.30 – 10.50 Coffee

10.50 – 11.30 Lecture: Introduction to Skyline (Brendan MacLean)

11.30 – 12.30 Tutorial: Setting up in Skyline

12.30 – 13.30 Lunch

13.30 – 14.30 Lecture: SRM in practice – assay design and quantitative considerations (Christina Ludwig)

14.30 – 15.30 Tutorial: Manual SRM data analysis in Skyline

15.30 – 15.50 Coffee

15.50 – 16.50 Tutorial: Manual SRM data analysis with Skyline (continued)

16.50 – 17.30 Lecture: Spectral library generation and publically available library resources (Ben Collins)

17.30-18.30 SkyJam: tips and tricks in Skyline (Brendan MacLean)

Day 2 – Towards large-scale analysis using DIA/SWATH

09.00 – 10.00 Lecture: Introduction to DIA/SWATH acquisition and data analysis concepts (Ben Collins)

10.00 – 10.15 Coffee

10.15 – 11.00 Lecture: Statistical considerations for experimental design and data analysis (Brendan MacLean)

11.00 -12.00 Lecture: Automated peak picking and false discovery rate estimation in targeted proteomics (Ben Collins)

12.00 – 13.15 Lunch

13.15 – 14.00 Tutorial: SWATH data analysis in Skyline

15.00 – 15.20 Coffee

15.20 – 16.00 Tutorial: SWATH data analysis in Skyline (continued)

16.00 – 16.30 Wrap up/ Feedback/ Closing

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