Regarding peptide MW (or mass, I use the two terms interchangeably)
calculations here are some thoughts as to what the issues are:
1. Computer programs that perform such calculations should use the IUPAC
values [Pure Appl. Chem. 63(7), 975-990, 1991] for the various elements to
compute amino acid and peptide MWs. If you are not sure whether the
program you are using has the correct values "built in", my suggestion is
to carry out these calculations by hand using an amino acid such as Met
that contains CHNOS, "construct" a poly-Met peptide and then try out your
computer program and see what you get. Computer rounding errors may also
contribute to slihtly different values calculated for the same sequence by
different programs.
Homoserine is isomeric with Threonine, therefore the monoisotopic
(12-C) residue mass is 101.0477 and the average mass 101.11 (greater
uncretainty in average mass calculations). To form the homoserine lactone,
just subtract the mass of water from the above to get 83.0371 and 83.09,
for average and monoisotopic values, respectively. By doing this you
should still add, at the end, the mass of water to form a neutral peptide
molecule (assuming that the peptide N-terminus is not modified; the
C-terminus is, of course, the lactone). This is all a numerical construct,
and it is equivalent to caluclating the mass of the full peptide using the
homoserine residue mass (101) first, adding a water molecule mass to form a
neutral peptide molecule, and finally "forming" the lactone by subtracting
the mass of water. In terms of calculations, there is no difference how
its done.
2. I am not familiar with the programs you mention, but, in general, the
amino acid masses which are listed in various tables that mass
spectrometrists (and protein chemists) use to calculate peptide MWs are the
residue masses. The mass of one water molecule (or, if the N- or
C-terminus of the peptide is modified, the mass of the appropriate
modifying group) is added to the sum of the amino acid residue masses to
obtain the peptide MW. If a program gives the peptide MW as the sum of its
amino acid residue masses only, then this calculation is in error.
3. How many hydrogens you add to the mass of the neutral peptide or
protein molecule depends on your method of analysis (e.g. MALDI vs. ESI).
Since computer programs do not know a priori what the user's prefernce will
be they should calculate the mass of the non-ionized molecule, unless told
to do otherwise. By definition, a MW is the mass of a neutral molecule, so
if a program calculates a MW this is what it should be.
I hope this helps.
Ioannis Papayannopoulos
CytoMed, Inc.
Cambridge, MA