Theoretical and Hands-on Program


Day 1 – 05/11 – Introduction into targeted proteomics – SRM
8:30 AM Registration
8:45 AM Welcome
Adriana Franco Paes Leme and Birgit Schilling
9:00 AM Basics of Quantitative Proteomics – from relative to absolute
Tina Ludwig
10:30 AM Coffee break – Poster presentation 1-12
11:00 AM Introduction into targeted mass spectrometry
Tina Ludwig
12:00 PM The biological relevance of targeted proteomics (case study)
Ariel Bensimon
1:00 PM Lunch
2:00 PM Introduction to Skyline
Ariel Bensimon
2:30 PM Tutorial: SRM method development
Tina Ludwig/ Ariel Bensimon
4:00 PM Tutorial: Data analysis
Tina Ludwig/ Ariel Bensimon
6:00 PM Science Slam – Poster presentation 1-12 (30 min)
8:30 PM End of day

Day 2 – 06/11 – Building prior knowledge for targeted proteomics
9:00 AM Building prior knowledge for targeted proteomics
Birgit Schilling
10:00 AM Coffee break – Poster presentation 13-24
10:30 AM Hands-On: Method refinement 
Lindsay Pino / Tina Ludwig
12:00 PM Panorama Introduction and Hands-On: Panorama targeted
knowledge base
Birgit Schilling
1:15 PM Lunch
2:15 PM System suitability and Panorama QC
Lindsay Pino
3:30 PM Coffee break – Poster presentation 13-24
4:00 PM Hands-on retention time prediction with iRT in Skyline
Ariel Bensimon / Lindsay Pino
6:00 PM End of day
6:30 PM Extra time for installation of necessary R scripts and MSstats

Day 3 – 07/11 – Study design and statistical considerations in targeted proteomics
9:00 AM Hands-On: Grouped study data processing with Skyline 
Ariel Bensimon
10:15 AM Coffee break – Poster presentation  25-36
10:45 AM Study design and statistical considerations
Lindsay Pino
12:00 PM MSstats and its integration with Skyline
Lindsay Pino
1:00 PM Lunch 
2:00 PM Tutorial: MSstats for statistical analysis
Lindsay Pino
3:00 PM Targeting proteomics at high throughput (research examples)
Lindsay Pino
4:00 PM Coffee break – Poster presentation 25-36
4:30 PM Waters – The Science of What’s Possible
Alexandre Gomes – Mass spectrometry Specialist
4:45 PM Introduction to Calibration Curves / Absolute Quantification 
Birgit Schilling
5:15 PM Hands-On: Calibration Curves / Absolute Quantification 
Tina Ludwig / Birgit Schilling
6:45 PM End of day

Day 4 – 08/11 – Performing PRM and DIA measurements
9:00 AM Intro to MS1 Filtering (from DDA data) and from DDA to PRM 
Birgit Schilling
9:30 AM Hands-On: MS1 Filtering with Skyline
Birgit Schilling
10:30 AM Coffee break – Poster presentation 37-41
11:00 AM Hands-On: PRM with Skyline
Birgit Schilling
12:30 AM Introduction to Data-Independent Acquisition (DIA) 
Lindsay Pino
1:30 PM Lunch
2:30 PM Hands-On: Analysis of DIA data in Skyline
Lindsay Pino
4:00 PM Coffee break
4:30 PM Future of targeted proteomics
Birgit Schilling an all
5:00 PM Feedback and Course Certificates
5:30 PM Kahoot – final quiz and contest
6:30 PM End of course


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