Biomarkers for early detection and other stages (PNNL Scope # 46308, RD Smith's Hutch 1 project)
EMSL Project ID
17798
Abstract
Development and identification of early detection polypeptide biomarkers from tryptic peptides using a random approach may also include application of PNNL very high pressure capillary LC-FTICR instrumentation to provide wide dynamic range and more comprehensive identification of proteins that display distinctive signatures by any selected sample preparation approaches. ASSUMPTIONS: NCI expects us to conduct fundamental research to further our knowledge in areas of importance to their mission, and to disseminate this knowledge through publications in peer-reviewed journals and presentations of research at scientific meetings. PRODUCTS/DELIVERABLES: PNNL will look specifically at size fractionation to isolate a low MW fraction of the plasma, while simultaneously eliminating most all of the (intact) high abundance species found in the sample. Early in year one, aliquots of fractions from 10 independent repeats of the size fractionation scheme on the reference plasma sample will be sent to FHCRC for analysis. Apply protein A/G depletion to mouse plasma for removal of the immunoglobulin fraction from samples, using commercially available protein A/G chromatography. Early in year one, aliquotes of fractions from 10 independent repeats of the Protein A/G fractionation scheme on the reference plasma sample will be sent to FHCRC for analysis. Develop high throughput cysteine-peptide enrichment technology 10,17 (QCET). Aliquots of fractions from 10 independent repeats of this fractionation scheme on the reference plasma sample will be sent to FHCRC for analysis on the common LC-MS platforms being used across all fractionation methods. Incorporate a standard protein mixture into each sample. For the plasma fractionation methods that are most effective we will perform 18O/16O stable isotope labeling on normal and diseased samples to identify potential candidate biomarkers. A monthly progress report is required as a deliverable for this project.
Project Details
Project type
Exploratory Research
Start Date
2006-02-02
End Date
2007-01-15
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Whiteaker JR, H Zhang, JK Eng, R Fang, BD Piening, L Feng, TD lorentzen, RM Schoenherr, JF Keane, T Holzman, M Fitzgibbon, C Lin, K Cooke, T Liu, DG Camp, LN Anderson, J Watts, RD Smith, M McIntosh, and AG Paulovich. 2007. "Head-to-Head Comparison of Serum Fractionation Techniques." Journal of Proteome Research 6(2):828-836.