Jim,
Before you head out and buy another piece of equipment, I want to make it
clear that what I meant to say was that WE had used everything we had on
the problem AS WE FACED IT. In no way did I mean to imply that other labs
might not have been more successful or that our approach was the correct or
only one. These were two proteins, both were N-terminally blocked,
submitted on PVDF.
It is well known that different peptides show up in MALDI with different
matrices and are subject to suppression effects. Large vs small, acidic vs
basic often dictates the matrix of choice. In ESI small peptides can be
lost on sample cleanup or in the flow through during LC/MS making 100%
coverage difficult or impossible. That's what I wanted to say.
In our particular case, accurate mass analysis on the starting sample
was'nt performed, an obvious first step, because the samples were on PVDF,
and because digestion was specified. We had already tried Edman on both
(twice), they were N-blocked. In spite of that, I wholeheartedly agree with
those who take the position that both techniques are complementary, and I
have no plans to shutdown my chemical sequencer anytime soon.
Like many core labs, we often find ourselves in the situation of "advise
and consent" and are not always able to carry out the approach we think
appropriate or even in the order we wish.
keep on truckin!
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Gary M. Hathaway, Director
PPMAL - Protein/Peptide Micro Analytical Laboratory
California Institute of Technology
139-74, Division of Biology
Pasadena, CA 91125
http://www.cco.caltech.edu/~ppmal
email Gary: hathaway@caltech.edu
email facility: ppmal@caltech.edu
phone: lab (818) 395-6388 or office (818) 395-2769
FAX (818) 449-3414
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