New Method to Identify Blood Proteins May Spur Novel Disease Marker Discoveries
Using conventional technologies, researchers supported by the National
Cancer Institute (Science Applications International Corporation-Frederick,
Inc. (SAIC)) have developed a new method for identifying proteins
found in trace quantities in the blood.* The method offers hope for
detecting tiny amounts of these blood-borne molecules that signal
the presence of certain diseases, such as cancer, infectious diseases,
behavioral disorders, developmental defects, and neurodegenerative
diseases. These molecules might be useful biomarkers to aid in earlier
detection and treatment of ovarian, breast, and prostate cancer.
The National Cancer Institute (NCI) is part of the National Institutes
of Health (NIH) and is the government's principal agency for cancer
Working at the Laboratory of Proteomics and Analytical Technologies
at NCI-Frederick, Md., the researchers crafted a multi-step procedure
for separating blood proteins derived from serum, which is the clear,
yellowish liquid that separates out from blood after clotting and
does not contain any cells. Together, all of these proteins are
known as the serum proteome. Prior efforts to identify low-abundance
proteins were not as successful mainly because separation steps
to reduce amounts of large, high-abundance proteins caused a simultaneous
loss of the smaller, low-abundance proteins. Separation and fractionation
are needed to produce samples that can be analyzed by mass spectrometry,
a high-throughput technique for identifying individual proteins.
To address this problem, the researchers performed a series of fractionations
on a tiny volume of serum about 0.04 teaspoons. The steps included
several different methods of separation, called isoelectric focusing
and chromatography, that are based on the size, electric charge,
and other chemical properties that differ between proteins. These
samples were then injected onto a mass spectrometer to acquire the
raw sequence data that was subsequently linked to a human proteomic
database to identify the observed molecules.
"Our investigation resulted in the identification of 1,444
proteins in serum," said Thomas Conrads, Ph.D., associate director of the Mass Spectrometry
Center at NCI-Frederick. A wide range of proteins from different
cellular compartments was identified. Another research group using
different methods previously had identified 490 serum proteins.
"The proteins identified by earlier research overlapped only
slightly with those characterized by our group," said Conrads.
"This emphasizes the wide scope and complexity of the human
serum proteome, which has been estimated to contain more than 10,000
Previous studies by other scientists had found evidence of blood-borne
molecules related to disease states. This new method offers refinement,
which may lead to identification of more sensitive disease markers.
"This study shows the extent of the number of proteins that
can be characterized within serum using conventional technologies
commonly available within proteomic laboratories around the world.
The next step will be to apply what has been learned and developed
in this study to identify disease-specific biomarkers with greater
positive predictive value than those presently being used for diagnostic
purposes," added Conrads.
The researchers created a publicly available database of the newly
identified human blood proteins. Located online at http://bpp.nci.nih.gov,
the database will serve as a resource for other investigators studying
For more information about cancer, please go to http://cancer.gov.
*The official report of the new method appears in the June 2004 issue of Clinical Proteomics (Volume 1, Issue 2; Humana Press).