Skyline Course Schedule Buck Institute 2/27-3/3 2017

 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.