The code in Skyline looks like:
_massDiffZ = _massDiffY - _massCalc.CalculateMassFromFormula("NH2");
But this page on wikipedia:
Sure makes it look like the code should be changed to:
_massDiffZ = _massDiffY - _massCalc.CalculateMassFromFormula("NH");
Which would result in a 1 Da mass difference. Does this seem right to you?
On the N-terminal side, the mass deltas look like:
_massDiffA = -_massCalc.CalculateMassFromFormula("CO");
_massDiffB = 0.0;
_massDiffC = _massCalc.CalculateMassFromFormula("NH3");
This also seems wrong. Shouldn't the c ion delta also be NH? or:
_massDiffC = _massDiffB + _massCalc.CalculateMassFromFormula("NH");
(where _massDiffB is 0).