The Capstone Project will focus on data-independent acquisition (DIA), and will knit together many of the skills learned throughout the rest of the May Institute. The program will introduce DIA workflows, and their role in large-scale biological investigations. Hands-on exercises will use experimental datasets from a controlled mixture, to allow the participants to gain experience working with design and analysis of DIA experiments in Skyline. Next, the participants will perform the downstream statistical analysis and visualization in R, and evaluate the impact of various choices made at the data processing stage on the downstream conclusions.

Target audience

    Target audience are experimental and computational scientists with experience in proteomic experiments. Scientists without prior exposure to these data, but interested in expanding their expertise, are also welcome. Prerequisites are ‘Targeted proteomics with Skyline’, ‘Beginner’s statistics with R’ and ‘Statistics for quantitative mass spectrometry’ (or an equivalent prior expertise). Prior exposure to DIA is useful but not required.


    Ruedi Aebersold, Meena Choi, Ben Collins, Mike MacCoss, Brendan MacLean