Both Mascot and X!Tandem offer a parameter for "monoisotopic vs average" (X!Tandem calls it "spectrum, fragment mass type"). Even after reading the documentation, I'm unclear on the meaning of this parameter - perhaps someone can clarify?
In general, I understand the difference between MS1 and MS2 scans, and I understand the existence of isotope envelopes at both MS1 and MS2 levels. I'm also clear on the point that the first peak (all-12C) of an isotope envelope is the monoisotopic peak, which may or may not be the most intense peak.
My best guess regarding the parameter (although I'm not at all confident): both engines assume that you have de-isotoped your MS2 spectra before submission, and that this parameter is asking the user to clarify whether the deisotoping procedure retained the monoisotopic peak or the most intense peak.
Thanks for your time.
UPDATE: I have cross-posted this to the spctools-discuss mailing list since those folks are more focused on proteomics.