Protein Metrics’ Intact software relies on a parsimonious charge deconvolution algorithm. This algorithm makes no assumptions about peak shapes and requires separate evidence for each mass peak, thereby reducing “harmonic” and “off-by-one” artifacts, which result from assigning a number of charges to the m/z peak.
Charge range is best set to a wide range, in which case the charge range will be implied by the mass and m/z ranges. The default range of 5–200 covers most applications, but 5 will need to be reduced for deconvolutions with mass range starting below 10 kDa, and 200 increased for targets that may have charges above 200.
To give an example, if the m/z range is 2200–4000 and M range 146,000–150,000, the charge range spans 36 to 68 (146,000/4000 and 150,000/2200).
The charge range parameters can be found in the Byos workflow:
These can also be changed after project creation using the orange Compute button.
A common cause of deconvolution artifacts is not using the correct M range or charge ranges. If the deconvolution is restricted, the software will try to make the best assignments it can within the constraints, which may mean presenting half/double-mass species to account for the m/z ions within the given range.