Analysis of DIA/SWATH Data


Get hands-on experience working with a data independent acquisition (DIA) data, from either a Q Exactive or a TripleTOF 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 Q Exactive] [data Q Exactive]
[pdf TripleTOF] [data TripleTOF]

* - 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.

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.

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.

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