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, absolute quantification, MS1 and targeting DDA data

• Posttranslational modifications – specific challenges
• Signal calibration and absolute quantification
• PRM assays
• MS1 Filtering
• Tutorial: SRM libraries and iRT

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 thoughput pipeline
• Tutorial: Analysis of DIA data in Skyline
• DIA FDR rates, automatic interference filter
• DIA high throughput and comprehensive quantification for biological datasets

Industry applications, targeted experiments and the future

• nanoLC for proteomics
• 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

The course includes popular morning (8am) “Sky-Jam” sessions led by Brendan with hands-on Skyline processing.