MS and peptide MW's
lsiconolfi-baez@netmail.hscbklyn.edu
Mon, 27 Apr 98 15:17:23 -0500
The discussion of oligo programs and mass calculations prompted me to
ask you about a related issue. In trying to get theoretical mass
calculations of peptides for an MS ananysis, I get different numbers
from different programs. There are additional particular problems when
I input a CNBr peptide.
The project involves identifying methylations on myosin peptides
prepared from digestions (Currently the last two stages are CNBr
peptide separation followed by trypsin digestion of the CNBr peptides.
Let me state two observation and ask for your input.
1. In Protein Prospectors MS-Digest, the Protein MW of an intact CNBr
peptide that is trypsin digested does not agree with the mass of that
peptide as generated from the CNBR digest of the entact myosin.
I have seen residue mass tables with homoserine lactone (Hsl) listed
as 83.09 (avg). This seems to be an error generated from removing
water from the lactone weight which already has water removed and no
longer has a free carboxyl. I've calculated the Hsl weight as 101.1,
so expect that the residue weight is 100.1 (minus the amine hydrogen).
2. In PCGene and other programs, the masses listed seem to be the sum
of the residue weights without the water added back. Is this a common?
3. If mass calculations are generally performed using unionized
species, and if one is looking at electrospray data in TFA, shouldn't
there be NH3+'s adding proton masses to the total mass? How do you
handle that for proteins and large peptides?
I'd better stop here before I go on and this becomes a babble
Linda