In response to the EBís side of the PARG fiasco. Please bear in mind I was
on the Protein sequencing research committee for 3 years and worked very
closely with Sheenah Mische (our labís director at the time) who was on the
committee the previous 3 years. I was also involved in the first internal
sequencing committee studies (about 2 years) when that committee was a
sub-committee of the Protein sequencing committee.
1) I have not received an electronic copy of the EB statement. I am
going by the copy that the director of this facility received. Was every
member of the ABRF sent a copy of this or is it sent only to the
directors? Maybe mine got lost in the mail. Also the copy I am reading
(which seems to be the same as Paulís) ends ìÖopinions,î. Is this what
everyone else received?
2) I agree 100% with Paulís comments about the publication
issues. EB, you are plain wrong with this in my opinion. Members of the
ABRF appear satisfied with the way results are represented and it serves
our interests. The only thing I would add is I disagree with the EBís tone
that no suitable conclusions/data could be drawn from the study. Seems to
me a very simple spread sheet could be made: how many of the 15 proteins
each lab attempted to identify, how many did it get right, how many
identified the 2 abundant proteins (most should have), number and types of
methods used (Edman, MALDI-TOF, MS-MS etc..), which method had the greatest
incidence if correct or incorrect identification, how many got it right who
used multiple tools (which I have always favored). Very simple without the
details.
3) In my opinion the EB has put the PARG in a no win situation. Three
committees were dissolved ( again I disagree this was ever necessary) at
the end of the ABRF 2000 meeting and combined them into PARG. Now this
group (of 6 members and one EB liason) is pretty much forced to do a study
covering three areas and make everyone happy. To their credit they came up
with a decent study, although I agree with the EB that the timing was
almost impossible for the ABRF 2001. On top of this the EB starts
pressuring committees with a deadline, and in the newly formed PARG an
unfair one. This new committee has only 2-3 monthes to get a
proposal?? Then the EB has the nerve to consider disbanding the PARG (I am
unsure if this is quite admitted or denied in the EB letter) because they
did not meet a deadline. At the least the EB should have suggested what
Jay Gambee (who was a protein sequencing committee member AND Chair
himself) has, a simple premade peptide to analyze. The more detailed study
(proposed as the 2001 sample) could have been held until the following
year. With the difficulties of the new PARG, this would have been
understood and probably accepted by the ABRF community.
4) SO as the EB says, where do we go from here? Here are my
suggestions for the immediate future. A) DO NOT DISBAND THE PARG without
an suitable protein committee(s) in place. This will cause tremendous
ill-will and will definitely result in lost members (you can start with me
if that happens). B) Listen to Jay Gambeeís suggestion about sending a
peptide that has already been characterized. I have 2 such peptides, one
characterized for 3 years in our lab, the other chraracterized for 7 years
by ourselves and other labs. Our center would be willing to dry this down
into tubes and send them to the PARG for distribution.
5) The long term future. There is too much protein work for PARG,
remember they are volunteers and have other responsibilities. It should
never have been burdened with such a responsibility. I suggest you form 2
new committees from it. The first would be essentially the old Protein
Sequence Research Group and would deal with protein primary structure
analysis. This would include Edman, MS-MS, and any other ingenious
technology to read a protein/peptide sequence. I can think up 3-4 yearís
studies I would like to see off the top of my head. The second committee
would be a protein identification technique, but not limited to that name
(I canít get the right name in my head). Proteins islolated by SDS-PAGE
would be identified by any technique (MALDI-TOF, ESI-MS, Q-tof, MS-MS,
Edman, etc.). Labs could move onto things like post-translational
modifications. One study I would like to see is identifying the
phorphorylation site(s) in a protein, only my personal preference. Then
when you have these committees, leave them alone!! Stop restructuring
things and let the committees grow as need be with the EBís guidance but
not interference. I remember the Ad-Hoc (EB Liason) member on the
committee I was on. This person offered advice, kept us moving in a timely
fashion (without a dictated time schedule), and left the committee alone to
decide things. The two committees could feasibly alternate studies every
year so members are not swamped around the holidays. By the way, the time
issue has always been a problem since the results are presented at the
winter ABRF meeting rather than the old summer protein society meeting
(when the ABRF was a satellite meeting).
6) Finally I agree with Paul about staying committed to the original
ABRF mission statement. I think that sums up my concern about the ABRF in
my previous post. The ABRF and meeting is becoming a showcase for emerging
technologies and instrumentation, not to help/inform the labs that use
those instruments/techniques. The ABRF, I think, may be losing its
way. For example, the statement by the EB ìÖ we should consider a separate
group devoted to `self-evaluation` samples: this may avoid conflicts over
whether the research is progressive or notî. PLEASE!, this is extremely
insulting. If I need to explain why it is then the EB and the ABRF has
truly lost itís way. Come on, multi-level approaches??? Can you do the
work in your lab or not, period!
7) The damage done by this conflict between the PARG and the EB is
severe (more than I think the EB realizes) but repairable. We have/will
hear from both sides and hear excuses, but the bottom line for us ABRF
members is we do not have a single protein sample to study for this
upcoming ABRF meeting. That is absolutely unacceptable.
Joe
PS: Paul, I was born and raised in New York City and donít mind some
fisticuffs myself. To quote Bily Joel from Keepiní the Faith ìÖthe good
old days werenít always so good and tomorrowís not as bad as it
seems. Learned stickball as a formal education. Lost a lot of fights but
it taught me how to lose OK.î
Joseph Fernandez
Associate Director
Protein/DNA Technology Center
The Rockefeller University
1230 York Ave.
NY,NY 10021
Phone: 212-327-8869
FAX: 212-327-8620
Email: fernaj@rockefeller.edu
website: pdtc.rockefeller.edu
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