Chuck
If it's like a lot of the IgG's I've looked at, you could have a pyro-Glu at
the N-terminus. As I recall, this was on the heavy chain of IgG's I was
analyzing. This would change the mass of the normal Gln residue by -17 Da.
As you suggested, if SEQUEST does not know the mass of the modification, it
will not find it. If you set up your SEQUEST search to look for
modifications of -17 on Gln residues, that should help. You can also setup
SEQUEST so that the modification is considered only on terminal residues of
the protein or peptide fragments. The most comprehensive list of mass
modifications that I know of is deltamass at
http://www.abrf.org/ABRF/ResearchCommittees/deltamass/deltamass.html. Hope
that helps.
Regards,
Mark Hail
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-----Original Message-----
From: Association of Biomolecular Resource Facilities
[mailto:abrf-request@aecom.yu.edu]On Behalf Of Chuck Hannum
Sent: Wednesday, May 02, 2001 5:05 PM
To: Recipients of ABRF List
Subject: ProtSeq/MS/Comp
Dear ABRF folks,
I would like to determine the N-terminal sequence of an immunoglobulin chain
that is apparently chemically blocked (as indicated by failed Edman
degradation). I am now approaching the problem by LC/MS/MS on a tryptic
digest and find that I am in a bit over my head in trying to use Sequest to
interpret the data. I can find internal sequences that tell me which V gene
is involved, but I cannot find the N-terminal peptide, presumably because
its parent ion mass is significantly altered by its chemical blockage. Can
anyone give me a little guidance on how to approach this problem or possibly
direct me to a pertinent publication that might help? I would also very much
like to find a comprehensive list of possible N-terminal modifications with
their resultant masses.
Thanks very much for any help you can give.
Chuck Hannum
DNAX Research Institute
Palo Alto, CA
hannum@dnax.org
This archive was generated by hypermail 2b29 : Wed Nov 21 2001 - 14:16:28 EST