A recent assessment of the capabilities of current proteomics technologies states that """"""""the top proteomics labs can identify and quantify more than 6,000 distinct proteins from individual cells and tissues at a time"""""""" and this number is probably close to the maximum number of proteins known in plasma. Strikingly however, it has been estimated that human plasma contains 550,000 """"""""protein forms"""""""" (excluding immunoglobulins), leaving over 500,000 distinct species to discover. Although there are discussions underway about a Human Proteome Project to """"""""survey the landscape of human proteins"""""""", such an effort, which is thought to potentially cost hundreds of millions to billions of dollars and take decades to complete, does not seem to be immediately viable in the current funding environment. Therefore at present there is apparently no general, scalable, and cost- and time- effective proposal for discovering the approximately 98% of the remaining plasma proteome. One of the major hurdles for detecting novel plasma proteins has been the approximately 10 orders of magnitude relative abundance difference between serum albumin (35-50 x 109 pg/ml) and low abundance proteins such as Interleukin-6 (0-5 pg/ml). This application evaluates both peptide and antibody phage display libraries, using either native or reduced and alkylated proteins for sample preparation, to determine which library type and protein epitope composition will detect the greatest number of novel proteins. It then seeks to test an innovative approach to fractionate plasma, on the basis of relative protein abundance to allow detection of the lower abundance species. These studies will demonstrate proof-of-principle data to support the large- scale generation of novel protein/affinity capture sets for biomarker discovery and validation by the Bioscience Research &Development community.
Specific Aim 1 : To determine whether a pool of random peptide phage libraries or an scFv antibody phage library, for either the native proteins or the reduced and alkylated proteins, will yield the most comprehensive plasma proteome coverage.
Specific Aim 2 : To test the performance of a plasma protein fractionator procedure in revealing novel protein species not previously detected with current proteomics technologies.

Public Health Relevance

At present only about 2% of the human plasma proteome is known, and there is no general, scalable, and cost- and time- effective method available for discovering the approximately 98% of the remaining plasma proteome. This project will investigate a new cost- and time- effective approach to the large-scale generation of novel protein/affinity capture sets for biomarker discovery and validation by the Bioscience Research &Development community.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Small Business Innovation Research Grants (SBIR) - Phase I (R43)
Project #
1R43RR026182-01
Application #
7748629
Study Section
Special Emphasis Panel (ZRG1-BCMB-M (10))
Program Officer
Sheeley, Douglas
Project Start
2009-09-15
Project End
2011-06-30
Budget Start
2009-09-15
Budget End
2010-06-30
Support Year
1
Fiscal Year
2009
Total Cost
$278,586
Indirect Cost
Name
Differential Proteomics, Inc.
Department
Type
DUNS #
087269069
City
Natick
State
MA
Country
United States
Zip Code
01760