2008 Poster Sessions : Quantitative methods for Biomarker Discovery Using High-throughput Mass Spectrometry Proteomics

Student Name : Amit Kaushal
Advisor : Russ B. Altman
Research Areas: Artificial Intelligence
A platform that can rapidly, reliably, and reproducibly discover clinically relevant protein biomarkers from human body fluid samples would have a significant impact on human health, as it would allow for earlier diagnosis, targeted intervention, and better understanding of disease pathology in many fields of medicine. While mass spectrometry-based methods have shown promise for as a high-throughput proteomics platform, there are data analysis challenges with the current approach that must be overcome to make it a reliable platform for biomarker discovery. Specifically, data is gathered at the peptide level, but must be integrated to make protein-level quantitative estimates of abundance or differential expression.

We have collaborated with the laboratory of Richard Smith (Pacific Northwest National Laboratories), where the lab has developed a proteomics platform that utilizes liquid chromatography separation of trypsin-digested proteins followed by mass spectrometry analysis. In collaboration with Dr. Smith's group, we have used this method to carry out large-scale clinical plasma proteomics studies to determine candidate protein markers that correlate with survival outcomes in burn patients.

Amit Kaushal is an MD/PhD student in Biomedical Informatics at Stanford University.