In Byos, under the Byonic node, and in stand alone Byonic, you can adjust the monoisotopic assignment by changing the settings under "Precursor isotope off by x":
The Off-by-X setting is a post-search correction of the precursor ion.
During this process, Byonic can move the monoisotopic ion by +/- 1 to assign a better ID for the spectrum. If correction is made, then you will see "off-by-x" column populated in the peptides table in the inspection view.
This option usually gives more IDs in searches. However, it is very data dependent. If you look at your results, and conclude that almost all of the off-by-x correction peptides are false positive, then you can turn this feature off.
The settings available in the Off-by-X are as follows:
- No error Check: Assume correct monoisotope.
- Too high (narrow): (0-1000Da)-> no error check, (1000-2500Da)-> +1 error check, (2500+Da)-> +2 error check.
- Too high (wide): Error check= +floor((mass in Da)/1000).
- Too high or low (narrow): Error check=+/-floor((mass in Da)/4000.
- Too high or low (wide): Error check=+/-floor((mass in Da)/2000.
For example, the +/- floor((mass in Da)/4000) means up to 4000 Da no correction is made, between 4000-8000 monoisotopic ion is allowed to be off-by-1, 8000-12000 off-by-2, so on.