2026 Frontiers in Proteomics: Advanced Skyline Applications
Monday:
- Meet at Foege S. (between Foege South and North) at 9am
- Welcome and lecture: What do we mean when we say quantitative proteomics?
- DIA Review and Primer
- Skyline for Chromatogram based proteomics data review and analysis
- Hands:On: Practical DIA Acquisition and Basic Data Analysis with Skyline
- Tutorial: DIA analysis with libraries in Skyline
Tuesday:
- Practical DIA measurements
- How do you know your data is ok? Intro to system suitability, quantitative QC, and process controls.
- What is wrong with this data?
- Viewing the output of other DIA tools in Skyline
Wednesday:
- Experiment design, minimizing confounders, block design and randomization. When experiments go wrong.
- Case Studies: How would you design this experiment?
- Octopus Block Randomizer and tutorial
- Using AI generated Peptide Property Libraries in the analysis of mass spectrometry data
- Tutorial: Generating fine-tuned libraries
Thursday:
- Plasma Proteomics - Review. Challenges and Progress in the field.
- Case Study in CSF proteomics
- Analysis of multibatch complex experimental data.
- Peak Imputation
- Tutorial: Advanced workflows involving Skyline
Friday:
- Low input, spatial, and single cell proteomics
- Highly Multiplexed Targeted Proteomics
- DIA > PRM workflow tutorials
- Quantitative assay validation
- Conclusion: The future of targeted proteomics
The course also includes popular morning “Sky-Jam” sessions led by Brendan MacLean with hands-on Skyline processing.
Note: As instructors update their content for this course, this agenda may change.