Hi Rick,
The process for this is currently:
- Try to align peaks in order to narrow the time range that is considered (if unsuccessful, all peaks are considered)
- Score each peak against the one being applied. The score is a weighted combination of ion dot product, retention time, and peak area
- Choose the highest scoring peak, unless it does not meet a minimum threshold in which case a manual selection is made
Also note that if the applied peak's boundaries have been changed, each selected peak will have its boundaries changed proportionally.

So there is some guessing involved and it doesn't always work well. In the future we hope to improve this feature to be more accurate and possibly allow for more user control over how peaks are picked.

Thanks,
Kaipo