Monday: Introduction to targeted quantitative proteomics and Skyline

• Meet at Buck Institute 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, posttranslational modifications, system suitability and targeting DDA data

• Plasma proteomics, high throughput SRM assays
• Posttranslational modifications
• MS1 Filtering and PRM assays
• System suitability and quality control
• Tutorial: SRM libraries and iRT

Wednesday: computational methods, statistics for quantitative experiments and Panorama

• Statistical considerations in study design
• Statistical analysis of proteomics experiments
• Computational  methods in R and Skyline
• Signal calibration and absolute quantification
• Tutorial: Sharing and publishing Skyline processed data in Panorama

Thursday: DIA, methods and integrated data analysis

• Introduction data independent acquisition (DIA)
• Skyline peak picking algorithms, FDR rates, high though put pipeline
• Tutorial: Analysis of DIA data in Skyline

Friday: nanoLC, targeted experiments and the future

• nanoLC for proteomics
• Tutorial: Processing grouped study data in Skyline
• Review and test
• Skyline and Industry applications
• Conclusion:  The future of targeted proteomics

The course also includes popular morning “Sky-Jam” sessions led by Brendan MacLean with hands-on Skyline processing.