I hope I'm not too late to comment on some recent interesting questions:
1. Over-alkylation of proteins with iodoacetic acid will give some
S-carboxymethyl-Met, which gives a poor sequencing yield for Met,
usually 10-20%, consistent with Barbara Root's observation. Amino acid
analysis will give homoSer and homoSer lactone, presumably by hydrolysis
liberating CH3-S-CH2-COOH. But in our hands, ESI-MS and MALDI-TOF/MS
gives a +59 Da mass, not dehyro-aminobutyrate (-48 Da).
2. The +161 Da observed by Mary Adomaitis may be Gal(alpha)1-3 linked to
the Gal of a lactosamine group (should give +162 Da). Thus,
Gal(alpha)1-3Gal(beta)1-4(GlcNAc)- at
the non-reducing terminus of the biantennary structure.
3. The +28 Da series described by Mark Liveley is consistent with what
we alway get with CNBr digests using formic acid as the solvent.
Multiple
Lys residues are probably getting formylated.
-- Reed Harris Genentech, Inc. (650) 225-4187 Phone (650) 225-3554 FAX reed@gene.com E-Mail