Monday: Introduction to targeted quantitative proteomics and Skyline
- Meet at Foege S. (between Foege South and North) at 9am
- Welcome and intro to quantitative analysis
- Basics of mass spectrometry for targeted MS
- Intro to Skyline
- Tutorial: SRM method development and refinement
Tuesday: Plasma, immuno-enrichment, system suitability and targeting DDA data
- Plasma proteomics
- Immuno-SRM and SISCAPA
- System suitability and quality control
- Tutorial: Targeting DDA data with MS1 filtering in Skyline
Wednesday: Standards, calibration, statistics for quantitative experiments and Panorama
- Standards for targeted proteomics
- Signal calibration and absolute quantification
- Statistical considerations in study design
- Statistical analysis of proteomics experiments
- Tutorial: Processing grouped study data in Skyline
- Tutorial: Sharing and publishing Skyline processed data in Panorama
Thursday: Sample prep, DIA, methods and data analysis
- Sample prep for targeted proteomics
- Introduction data independent acquisition (DIA)
- Setting up targeted methods at the instrument
- Tutorial: Analysis of DIA data in Skyline
Friday: nanoLC, troubleshooting and the future
- nanoLC for proteomics
- System troubleshooting for best results
- Conclusion: The future of targeted proteomics
- End at 2:30pm