1) Sensitivity: The Procise HS is obviously the most sensitive because of
the cLC HPLC (10-50 femtomoles above background). The Procise HT (250
femtomol above background) is more sensitive than the HP (1-2 pmol above
background) although I have been told the 1100 on the HP is more sensitive
than the 1090 I currently use.
2) Repetitive yield: The HP sequencer clearly produces higher repetitive
yields than either ABI instrument, with 98% repetitive yields not uncommon.
This refers to peptides as well as proteins. The Procise HT does OK but
the Procise HS appears to have more washout than either of the other two.
3) Initial Yields: My observation is that the more sensitive the
sequencer, the higher the percent initial yield, meaning Procise HS>Procise
HT>HP.
4) Proteins: Proteins in salt solutions can be loaded onto the HP with no
prior cleanup steps, while it is not really possible on the Procises.
PVDF-bound proteins run best on the HP providing you use Dave Reim and Dave
Speicher's modifications. The Procise HT runs OK, but definitely not like
the HP (or like our old retired 470 did). We have never tried PVDF on the
Procise HS and would be interested to hear from those who have.
5) Peptides: Based on equal amounts loaded per instrument, the Procise HT
will more often than not produce the complete sequence (using MALDI-TOF as
support of corse). The Procise HS tends to wash out fairly fast, and the
HP runs into problems with sensitivity at peptide levels less than 5 pmol
(even when we see a sequence, there may always be a degree of uncertainty
if not high level). Our Procise HT we consider the workhorse as more than
50% of our samples are internal peptide fragment at the 1-5 pmol range.
6) Problem amino acids: HP has problems with a) ILE being observed as both
ILE and PHE (PHE does show up as only F though), b) SER shows up as both
SER and ALA, c) unmodified CYS and phospho-SER show up as a low yield ALA.
HP appears particularly good at identifying TRP, HIS and ARG. Procise HT
has problems with low yields of GLU and TRP plus occasionally resolution
of GLU from CAMC. Procise HS has problems with low yields of GLY, TRP, LYS
as well as aniline coelutes with ASN on this system.
7) Operation time: Both the HP and Procise HT are fairly easy and reliable
to operate. The procise HS is a handful and only experienced protein
sequencers should probably use this. It also requires alot more
maintenance time and TLC.
8) Service and Reagent quality: Both company's have had their share of
reagent problems although if you look back on it over a long time period
neither have been as bad as they could have been. HP appears faster at
responding and addressing reagent problems (at least in our experience)
than ABI has. Service for HP has always been slow (typically 1 week or
more to get in) although competant. To be fair to HP, we have not had a
service contract for about 2 years so they may have solved this problem
(don't think so but I would like to hear everyone elses opions). We also
have very few mechanical problems with the HP except for intermittant HPLC
air injections due to conversion flask problems and an inexact injection
system. ABI has been fairly good with the Procise HT ( although parts
appear to get back ordered) but they did not have a good plan for our
Procise HS when we had pumps problems (they finally gave us a loaner HPLC
pump 10 monthes ago after the instrument was malfunctioning for a month, we
still have the loaner although it has been working well).
There you go Dalmia! Probably made an apparent easy decision more
complex. One other thing to consider is that new HP systems come with the
option of running C-terminal chemistry and you may want to investigate this
possibilty if there is a need.
Joseph Fernandez
Associate Director
The Rockefeller university
Protein/DNA Technology Center
1230 York Ave. New York, NY 10021
Phone: (212)-327-8869
FAX : (212)-327-8620
email: fernaj@rockvax.rockefeller.edu
Lab Web Page: http:\\pdtc.rockefeller.edu