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Data Independent Acquisition Using Skyline and the Thermo Q-Exactive

Reputable Mentor II
Reputable Mentor II
Egertson J.
This brief tutorial describes how to generate a DIA method using the Skyline Targeted Proteomics Enivronment suitable for running on the Q-Exactive. Skyline generates an optimized list of isolation windows to cover a m/z range of interest which is then entered into the Q-Exactive method editor. Here, we create a method covering 500-900 m/z with 20 m/z wide isolation windows. At the end of the tutorial, there is a note on how to generate a multiplexed method as in This tutorial was written for use with Skyline 2.1 and Q-Exactive software version 2.2 SP1. Please post any questions, comments, or suggestions on the Skyline support board at

University of Washington
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Last update:
‎10-15-2021 11:56 AM
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