Dick,
Many protein sequences in databases are conceptual tranlations of
corresponding genes, i.e, DNA sequence. Many database entries do comment on
posttranslational modifications, if known. Walsh's Rule (see Note #1) states
that there are no eukaryotic proteins that are simply linear translations of
their encoding genes, that is to say ALL eukaryotic proteins are
posttranscriptionally modified. The modification may be as simple as removal
of the N-terminal Met, N-terminal acylation, or other. I use this concept
dogmatically to rationalize any "proteomics" inquiry. Based on this concept,
I find searching databases by molecular weight interesting in that one may
find oneself in the correct ballpark, but of modest utility otherwise. If
indeed all eukaryotic proteins are posttranslationally modified, this type
of database search should NEVER work.
NOTEs TO ALL:
1. "Walsh's Rule" was named by me based on ideas stated by Ken Walsh, whose
opinion I admire greatly. If you disagree, please direct all hate mail to me
not Ken. All kidding aside, I would be interested in hearing about
exceptions of this "Rule".
2. Please be aware that there are many bacterial proteins that are linear
translations of their encoding genes. Obviously, if one expresses a
eukaryotic gene in bacteria, it may not be properly modified.
3. The case of peptides, prepeptides, propeptides, and prepropeptides may
necessitate a corollary, we'll see.
Regards,
Jeff Kowalak
Jeffrey A Kowalak, Ph.D.
Mass Spectrometry Facility Manager
Laboratory of Neurotoxicology
National Institute of Mental Health
Building 10 Room 3D40
Bethesda, MD 20892-1262
telephone: 301-496-4242
facsimile: 301-480-0198
jkowalak@codon.nih.gov
-----Original Message-----
From: Association of Biomolecular Resource Facilities
[mailto:abrf-request@aecom.yu.edu]On Behalf Of NobleRN@pebio.com
Sent: Thursday, March 23, 2000 12:50 AM
To: Recipients of ABRF List
Subject: RE. Searchable Mass Database
I found the site (http://sx102a.niddk.nih.gov/smass.html) that Len Packman
(Thank you very much) passed along to the ABRF Bulletin Board to be very
exciting. I think Dr. Lewis Pannell and his group should be congratulated,
and
supported in their dealings with the NCBI.
I just have a quick comment from my brief experience using the searchable
mass
database this evening for a couple of peptides I have recently synthesized.
When I searched for the mass for Neuropeptide Y, 4271.7, the result was for
Neropeptide Y, # P09640, having a mass of 4272.7 while noting that the 36th
position (the C-terminus) was amidated. Also, when I searched for the mass
of
the chemokine MIP-1alpha, 7783.7, the result was for MIP-1alpha, #
AAC03539.1,
having a mass of 7787.7. Both differences seem to stem from the one-letter
code
sequence for the protein generating the mass value and not taking into
account
things like C-terminal amidation or disulfide bridges (2 in the case of
MIP-1alpha). I know the above issues are trivial, but should be
recognized.
Personally, I would love to see a searchable mass software application that
allows the synthetic peptide chemist to enter the side-chain protecting
groups
used in the synthesis, in order to more easily identify side products.
Yeah, I
know it would be challenging, but wishful thinking is nice too.
Again, I encourage others to use the searchable mass database and support
Dr.
Pannell in his dealings with the NCBI and the National Librarty of Medicine.
Cheers,
Dick
Dr. Richard Noble
PE Biosystems
email: noblern@pebio.com
This archive was generated by hypermail 2b29 : Mon Mar 27 2000 - 11:29:47 EST