[Biojava-dev] Calculation error in MassCalc.getMass()

[Jerry Thomas]

I believe the masses returned by MassCalc.getMass() to be incorrect.

The internal residue masses used for amino acids are correct, but the 
terminii are calculated incorrectly.  Instead of adding H for the 
N-terminus and OH for the C-terminus, the masses of two OHs are added. 
For M+H, instead of adding an extra H, the mass of a third hydroxyl is 
added!

For example, MassCalc gives a monoisotopic M+H mass for angiotensin 
(DRVYIHPFHL) of 1328.6751, whereas the correct value is 1296.6853.  The 
difference is due to the two extra oxygens (2 * 15.9949 = 31.9898).

If there are no objections, I will correct the code, and add a test app 
to demos.

cheers,

Jerry