Get hands-on experience working with a data independent acquisition (DIA) dataset, from either a Q Exactive instrument, using a 3-organism mix data set created for instruction, based on the Navarro, Nature Biotech 2016 benchmarking paper. Use the Import Peptide Search wizard for DIA to build a spectral library from DDA data with automatic iRT calibration for retention time calibration and an mProphet learned model for peptide peak detection. Assess the data quality using a rich collection of Skyline summary plots including Retention Times, Peak Areas, Mass Accuracy, and CVs. Finally, perform a group comparison and make your own assessment of how well the data capture the expected ratios for each organism. (32 pages)

[pdf] [html] [data]

* - written on v20.1, updated for v21.1 and v22.2

On April 7th, 2020, the Skyline Team produced Webinar #18: DIA/SWATH Data Analysis in Skyline Revisited, a live presentation of this new material.
[webinar]

On January 25, 2017 the Skyline Team produced Webinar #14: Large Scale DIA with Skyline, which highlighted the additional research and workflows developed in the 28 months since our first DIA webinar.
[webinar]

On April 4, 2017 the Skyline Team produced Webinar #15: Optimizing Large Scale DIA with Skyline, which added new insights from working with a new dataset and a new instrument type.
[webinar]