We're doing some small molecule studies where the high flow chromatography is pretty reproducible, and we want to maintain the same integration boundaries even for blanks and low level samples. Importing the peak boundaries is a good option for this case. I saw that there's at least a few people that really wanted this in the past years (links below), but at that time it seemed things were not working. I found a workaround that lets us do what we want, but you could improve the experience. If one goes to the Peak Boundaries in Document Grid, you can't modify this report to include the Molecule field, it has the Peptide Modified Sequence column by default in the small molecule mode, and it's blank. What you can do is go to the Molecules report, and modify this: remove everything except the Molecule column, then add Min Start Time, Max Start Time, and File Name, and export this to a .csv. Then change the Molecule column header to Peptide Modified Sequence. Then you can change any values in the .csv file and reimport it and the peak boundaries will change.
So the changes that could improve this experience would be that the report in the Document Grid for Peak Boundaries would by default include the Molecule column instead of Peptide Modified Sequence, and that the Peak Boundaries importer would allow Molecule to be the column header instead of Peptide Modified Sequence.