During data dependent acquisition (DDA or IDA) or SWATH acquisition, the collision energy can be automatically adjusted according to the mass/charge and charge of the peptide. This dependency has been well characterized on our QTOF systems. By selecting rolling collision energy (Analyst software) or dynamic collision energy (SCIEX OS software) this function is invoked during acquisition.
These collision energy curves were developed from 1000s of peptides, by determining the collision energy that provided the most signal intensity in the higher m/z y-ions. They were first developed using SWATH DIA on 3 different TripleTOF 6600 systems and then validated on additional instruments for both DDA and DIA acquisition. More recently these curves have been confirmed for use on the ZenoTOF 7600 system.
These are the defaults settings in SCIEX OS software when you select Dynamic collision energy. If you are using Analyst software, please download this table and enter these values into the IDA CE Parameters Table found under the Scripts menu.