Garner Lab

Research

Informatics

Instrumentation

Genomics/Proteomics

Project: A Software Analysis Pipeline for Mass Spectrometry Data

Champion: Wayne Fisher

Blood serum, plasma, and other readily available body fluids bathe the tissues of the body and thus contain a wealth of information about the state of health of an individual. This information can be extracted from these fluids by mass spectrometry, thus providing the means for both the discovery of new biomarkers and the measurement of these biomarkers to determine the condition of a patient. We have developed a suite of software tools to compare the mass spectra of samples from patients with and without a disease or condition and to find differences between them in the intensities of peaks. The biochemical species responsible for these peaks, alone or in combination with each other, are potential biomarkers for the presence or absence of disease, and identification of these species provides new candidate biomarkers for the disease. Further, analysis of spectra from individual samples allows classification of the patient into the disease or non-disease groups. A major challenge overcome by this software is the simultaneous analysis of the very large data sets produced when replicate spectra are obtained from hundreds of individual samples.

Algorithm for analysis of mass spectrometer data. The training phase (left) identifies differences between groups of spectra. The testing phase classifies unknowns into one of the two groups.

Spectra from two different patient samples (blue and green spectra) produce different signal intensities when the concentration of the underlying biochemical species differs between the conditions.

Related Publications

W.G. Fisher, K.P. Rosenblatt, D.A. Fishman, G.R. Whiteley, A. Mikulskis, S.A. Kuzdzal, M.F. Lopez, and H.R. Garner. A Robust Biomarker Discovery Pipeline for High Performance Mass Spectrometry Data. Journal of Bioinformatics and Computational Biology 5(5), 1023-45 (2007).

D.C. German, P. Gurnani, A. Nandi, H.R. Garner, W. Fisher, R. Diaz-Arrastia, P. O’Suilleabhain, and K.P. Rosenblatt. Serum Biomarkers for Alzheimer’s Disease: Proteomic Discovery. Biomedicine and Pharmacotherapy 61(7), 383-9 (2007).