PNNL-13501 - Pacific Northwest National Laboratory

Development of a New High-Throughput Technology and Data Analysis Capabilities
for Proteomics (a)
Richard D. Smith, Gordon A. Anderson, Tim D. Veenstra, Mary S. Lipton, Ljiljana Pasa-Tolic
Study Control Number: PN99068/1396
Proteomic analysis provides the key to understanding how cellular processes function in concert. The development of
high throughput methods for proteomic studies will allow the effects of a variety of agents, including low-dose radiation
exposure on organisms to be discerned in a rapid and global manner.
Project Description
This project is developing powerful new tools for broad
evaluation and quantitation of protein expression. We
will develop and demonstrate new approaches for
proteome surveys that include the simultaneous
capabilities for global 1) protein identification, and
2) precise determination of relative expression levels
simultaneously for many proteins as a result of an
environmental perturbation. The approach will be orders
of magnitude more sensitive, faster, and informative than
existing methodologies, including unmatched quantitative
expression data. This project is also aimed at the
development of new capabilities for data analysis that will
“mine” these proteomic data and enable improved
understanding of complex cellular signaling networks and
pathways involving large numbers of proteins expressed
by an organism. These capabilities will provide a basis
for studying and understanding the subtle differences in
the expressed proteome of an organism as the result of an
environmental perturbation, such as in response to a
chemical or radiation exposure, or differences arising
from disease state(s), position in the cell cycle, or
between different cell or tissue types. This new approach
will enable systems-level views of differential protein
expression so as to enable a global understanding of gene
function and provide an enhanced view of systems-level
cellular operations.
Introduction
As biological research moves increasingly toward the
study of complex systems (consisting of networks of
networks), the so-called “post genomics era,” there is a
clearer recognition of the complexity of cellular systems,
and the growing optimism that the complexity of these
(a) Project started as a task under project, “Simultaneous Virtual Gel and Differential Display” in FY 1999. Subsequent tasks were added
to this project in FY 2000.
60 FY 2000 Laboratory Directed Research and Development Annual Report
systems is not intractable to understanding. In this new
paradigm, whole cellular systems will be studied and
modeled, and new understandings gained regarding their
systems-level behavior and emergent properties arising
from their complex nature.
Understanding complex cellular systems challenges the
capabilities of all present approaches and research
technologies, particularly since (to be most useful)
understanding must be gained at a level of detail that
provides insights into the various roles of the dominant
chemically active class of cellular components—proteins.
Proteins are, by far, the most important class of
biochemically active molecules in cells, and they are also
the most common target for drug development and
manipulation. Thus, systems-level studies are most
effective when they provide insights into the functional
roles of individual proteins in the context of the complete
system. A key desired goal is the ability to predict
cellular and organism-level responses to environmental
perturbations, which would then provide a basis for
predicting low dose responses to chemical or radiation
exposures and developing much more effective drugs that
can also be tailored to an individual.
While the availability of complete genome sequences
opens the door to important biological advances, much of
the real understanding in cellular systems and the roles of
its constituents will be based upon proteomics (which we
define here as the study of how the proteome responds to
its environment). The proteome may be defined as the
entire complement of proteins expressed by a particular
cell, organism, or tissue at a given time or under a specific
set of environmental conditions. Surveys at the mRNA
level do not provide exact information regarding the
levels of proteins actually expressed or their subsequent