Ken Mitchelhill
Ken,
I think you have misinterpreted Ken's comments. When he says he has
identified 65% of his proteins, that doesn't mean there is a 35%
uncertainty in the identification. It means that 65% of the proteins have
been unequivocally identified based on a mass map. Having spoken at length
to Ken about this, they have never been wrong on one of these calls when
challenged by an investigator. The other 35% are either "no calls"
"proceed at your own risk calls" (which I doubt he advocates) or had to be
done some other way.
Our own experience is very similar to this, though because we are not a
service facility, we don't have these kinds of numbers. When I tell
someone the identity of a protein based on a mass map, I am certain of it.
When challenged to go forward and prove it, we have also never been wrong.
The amazing thing is that even when I wasn't confident of the answer, and
went ahead myself with painfully generating some sequence information, the
mass map result was proven to be correct.
The real discussion is not on how good high mass accuracy mass mapping
is, (because it's very good) but rather how do you do it to achieve results
like those Ken spoke of. It's all in the quality of the data, and how it is
used to do the search. In inexperienced hands it is very easy to come up
with the wrong answer.
There are some rather interesting results from this years Internal Study,
but I won't let the cat out of the bag.
I'm sure you will hear from Ken Williams, and perhaps from Carl Klauser as
well.
Roland Annan
SmithKline Beecham