Hello,
we are in the process of using your paper Multiplexed Peptide Analysis using Data Independent Acquisition and Skyline on our Thermo Q Exactive Plus with Easy-nLC 1200. This paper references version 2.6
At this time the current version is Skyline 4.1. When following your paper I got stuck on Step 18 in Thermo Xcalibur Instrument setup as it asks me to import Targeted MS2, and the closest option is Targeted-SIM / dd-MS2. we are unsure if this is the appropriate option and if so should the SIM values match the dd-MS2 values or be left at factory settings.
Do you have an update reference paper, updated manual, or any suggestions otherwise.
Please see attached screen shot for step 18 hang up on Targeted MS2 option.
Thank you for your help.