Why are scan windows longer than detection windows in a scheduled MRM method in Analyst® software?

For research use only. Not for use in diagnostic procedures.

Answer

When setting up a scheduled MRM (sMRM) method in Analyst® software, users must add the time for the detection window (in seconds). Occasionally, the resulting scan window for some of the analytes is larger than that set in the method. There are two reasons for this:

1) For the software to scan a continuous total ion chromatogram (TIC), at least one transition must be scanned at any given time. If there is no analyte to be scanned at the start of the experiment, the software will use the analyte with the smallest retention time (RT) and start the scanning with this first transition. As a result, the analyte with the smallest RT will have a longer scan window starting at 0 min. For the same reason, after the last analyte is scanned, the software will use the first analyte in the acquisition method’s MRM table to continue scanning for it until the method's end to ensure that data is available to complete the TIC. Similarly, the first analyte will be scanned in the middle of the experiment if there is a long gap in detection mid-experiment.

This scenario is demonstrated below, where the real scan time is longer than the designated window (30 s) in the acquisition method. In this instance, the transition for cotinine 1 has the earliest RT and a longer scan window to cover the start of the experiment where no other analytes are being acquired. Note: The second panel below shows a magnification of cotinine's extracted ion chromatogram (XIC) from 0-2 min to show the extended baseline clearly. The 0-0.3 min time range is also scanned; however, intensity is almost equal to zero due to flow being diverted to waste by diverter valve.

The figure below shows the experiment’s end from 6.5-7 min. The software uses the 6-MAM-1 transition (the first analyte in the method’s MRM table) to scan the end stages of the experiment when no other analyte transitions are being monitored.

2) If the Advanced feature was activated in the Scheduled MRM (sMRM) window, the Analyst software may extend the scan window to two half windows, a possibility for any of the analytes (optional in Analyst® 1.7.x). The Scheduled MRM Pro™ Algorithm automatically extends the detection window until the intensity drops below the extension threshold. This happens for half of the MRM detection window and, after two occurrences, will stop. In other words, after the extension, the duration of the method-specified detection window can double. The link below shows how to disable this extension if it is not desired.

Also see: Turning off the Dynamic Window Extension when using the Scheduled MRM™ algorithm in Analyst® software