mystery sequences from pepsin digests

Derek_Ellison@MGDSpeke.CCMAIL.compuserve.com
Wed, 28 Apr 1999 07:00:30 -0400

Dear ABRF,
After carrying out a pepsin digest of our study protein we found the
following peptides (by ES-MS-CAD-MS):

MESDD (partial confirmed sequence) mz 1306.9
AFTVY mz 600.4
VYAQF mz 627.8

These sequences are not in our protein, which we believe is pure, nor
in pepsin A (porcine) which we used from Sigma, cat P-6887. We've done
a database search (OWL) and got about 20 proteins for each peptide.
The only plausible match is pepsinogen C which contains VYAQF. The
other digests we did (same samples) with trypsin didn't throw up any
unexpected sequences. Therefore i'm hoping they're just fragments of
contaminants from the pepsin, although we didn't see them in the
pepsin blank.

Has anyone seen these fragments before from pepsin digests? or can
anyone shed any further light on this? Info would be much appreciated
- thanks in advance

Derek Ellison
Medeva Development
Speke
Liverpool L24 9GR
UK

44 151 486 1866 phone
44 151 486 3138 fax
derek_ellison@mgdspeke.ccmail.compuserve.com