This should be fun, Ken. I'll start with my own point of view (accurate or
not). Genomics has really begun to affect all aspects of experimental (&
theoretical) science and is resulting in new experimental paradigms and even
scientic disciplines, which leads to new terms. The new words can be confusing
at times even to the people who use them (or define them) in part because their
definitions (& the science) are in flux.
Proteomics, literally defined, is the study of the proteome.
The proteome was originally defined as all the proteins coded by the genome of
an organism (a list, in other words). I would prefer another definition (or
term), but I'm not above using the existing one (see job postings to follow
soon). As worded, it defines a static set of components in the same sense that
a genome is static. As a side note, I suspect that there is no such thing as a
protein with only a single chemical form, which confuses me further about what a
proteome is by the original definition. Are all the 20+ forms of apolipoprotein
D part of the proteome? What about transient phosphorylation states of
proteins? Transition state complexes? Alternate splice products or even simple
conformers? Whatever.
We all deal with the real world where function also has some value. We've begun
to use the term "functional proteome" meaning all the proteins produced by a
specific cell in a single time slice (ie, a dynamic situation- which I am much
more comfortable with). We also use the term "protein expression profiles".
So, function brings us back to proteomics. Most investigators are assuming or
implying some degree of function, not just structure when they use the term
"proteomics". There are plenty of related terms including "functional genomics"
and "integrative molecular biology". Perhaps others can add to this list.
"Proteomics" implies to me an effort to link structure to function by whatever
means are appropriate. I expect my personal definition to change with time as
the field and my view of it evolves.
Sorry Ken, I'm on a tear tonight. Another night you'd have gotten a straight
answer.
I'll leave informatics (bio & otherwise), information technology, computational
biology to someone else tonight.
Coming soon: The Physiome.
Phil Andrews
University of Michigan Med. School
Ann Arbor, MI 48109 http://www.brcf.med.umich.edu
I think it is... sad that you can no longer destroy an entire area of science by
a single, simple experiment. Frederic Richards, speech at the Protein Society
(Baltimore, 1991).