To ensure proper operation of the Orbitrap and linear ion trap mass analyzers, the MS regulates ion populations at a defined target level. This process is known as automatic gain control (AGC). The MS regulates the ion population by performing a fast ion-trap full scan called a prescan. The system does not display or record the prescan in the raw data file.
Prescans apply to full-scan, data-dependent, and targeted experiments. In data-dependent experiments, the prescan regulates ion population for both the master scan and the dependent scans.
The prescan measures the ion flux and determines the ion injection time required to maintain the optimum quantity of ions for each scan.
- Data-dependent experiments: In data-dependent experiments, the prescan executes immediately before the master scan and uses the master scan settings. The MS uses the total ion current (TIC) from the prescan to set the injection time for the master scan. The MS extracts the precursor ion identities (m/z and charge) for the dependent scans from the previous master scan. However, it calculates the injection times for the dependent scans from the prescan intensities.
- Targeted experiments: In targeted experiments, the prescan analyzes the mass range that spans the smallest target to the largest target. The MS calculates the injection time for each target from the prescan intensities.
Analyte intensities vary considerably as each compound elutes from the column. Therefore, the time between the prescan and the subsequent scans is an important factor. When the list of targeted scans is large, the time between the prescan and the later targeted scans can increase and reduce the accuracy of ion population regulation.
When you set the Loop Control parameter to Time, the prescan executes at intervals that are less than or equal to the specified time period. This setting maintains close timing between the prescan and the targeted scans. Using the Time option improves the accuracy of the calculated injection times and the quality of the acquired data.