SELECT SERIES Cyclic IMS DDA setup
Introduction
In Data Dependent Acquisition (DDA) mode, the system performs a full scan with low energy, and then runs quadrupole isolated MS/MS scans on components meeting a user defined set of criteria.
Global Settings tab:
MS Settings tab:
DDA Settings tab:
Minimum Intensity:
The minimum intensity is set with the centroid spectrum (Process, Center). To calculate the value, determine the background response in the LC analysis.
In the following example, a minimum intensity of approximately 25,000 is required to prevent switching on background ions. This is important when the analyte and background are expected to have the same charge state i.e for small molecule applications.
Note: The minimum intensity value also depends on where on the LC peak the switching is desired, as a more intense precursor peak usually gives a better quality MS/MS spectrum. For this reason, the threshold can be set to a higher value to enable MS/MS on more intense peaks.
Stop MSMS Acquisition:
* For example, if a scan time of 0.1 s is set and you want to include 5 components, then the "Timeout (sec)" must be set to 0.6 s.
Notes
- In the "Select a Threshold (counts per second)" field:
| Selection | Value |
|---|---|
| Cumulative TIC Threshold | All summed centroid peaks in the MS/MS spectrum must be above the "Threshold Value". |
| TIC Falls Below | MS/MS analysis aborted on a component if the sum of all ions falls below the "Threshold Value" |
| Cumulative BPI Threshold | The summed Base Peak ion in the MS/MS spectrum must be above the "Threshold Value" |
| BPI Falls Below | MS/MS analysis aborted on a component if the Base Peak Ion intensity falls below the "Threshold Value" |
- Initially Waters recommends a combination of "Number of Directed Scans" and "Cumulative TIC Threshold" as the system will perform a maximum number of e.g. two scans per MS/MS component unless the TIC Threshold is not achieved in the first MS/MS scan. In this case, the system will only perform one scan on that particular component.
Exclude tab:
Notes:
| Exclusion Time | Useful to set the exclusion time to coincide with the width at half height of the chromatographic peak of interest to capture the top of the peak and enhance MS/MS data quality. |
| Dynamic Exclude List | If selected, a .csv file is created containing the m/z and retention times for all components switched at the end of the acquisition. |
| Table Settings | Mass Tolerance in mDa or ppm. |
Include tab:
- Selecting "Preferentially" will include other components but gives priority to those specified in the list.
- Selecting "Only" will include only those listed.
Collision Energy tab:
