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Introduction to targeted quantitative proteomics and Skyline
- Meet at Buck Institute at 9 am
- Welcome and intro to quantitative analysis
- Basics of mass spectrometry for targeted MS
- Intro to Skyline
- High throughput SRM assays
- Tutorial: SRM method development and refinement
Posttranslational modifications, MS1 and targeting DDA data
- Posttranslational modifications – specific challenges
- PRM assays
- MS1 Filtering
- Tutorial: SRM libraries and iRT
- Small molecules
Computational methods, statistics for quantitative experiments and Panorama
- Statistical considerations in study design
- Statistical analysis of proteomics experiments
- Data reports
- System suitability and quality control
- Tutorial: Sharing and publishing Skyline processed data in Panorama
DIA, methods and integrated data analysis
- Introduction data independent acquisition (DIA)
- Skyline peak picking algorithms, FDR rates, high throughput pipeline
- Tutorial: Analysis of DIA data in Skyline
- DIA FDR rates, automatic interference filter
- DIA high throughput and comprehensive quantification for biological datasets
Additional DIA and industry applications, targeted experiments and the future
- Keynote Lecture by Buck Institute Faculty – Aging Research and Mass Spectrometry
- DIA applications and discussions
- Combining different scan-types and workflows (MS1 Filtering, SRM, PRM, DIA)
- Tutorial: Processing grouped study data in Skyline
- Review and test
- Skyline and Industry applications
- Conclusion: The future of targeted proteomics
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