I think this issue must have popped up previously for you all. I saw this one is similar, but was fixed some time ago.
Anyways, the problem is, I've got a targeted MS2 method, with a large number of targets. There are several peptides for which no data are imported, although the majority do have data.
I chose one of the problem peptides,
There's a target in the method for m/z 591.294. I set the Method Match Tolerance m/z to various values, including 0.01, which should be plenty for the method target to pass the filter. I see in the raw file the filter and scans for this target starting at 20.91 minutes.
I've attached the File|Share|Everything zipped folder here. Could you have a look and see what's going on?