For a Thermo-Finnigan LTQ-FT running Xcalibur 2.0.1 how can you automate 10 MS3 experiments where only the activation time is changed?
The instrument is not connected to an autosampler as it has been modified to inject a neutral reagent into the ion trap where varying the activation time allows the study of ion-molecule reaction kinetics. I would like to create an automated processing method that can mass select the product ion of an MS2 experiment and use this in an MS3 experiment where the mass-selected ion is trapped via a specified isolation window and ONLY the activation time is changed over 10 or so data sets.