Dr. Margaret Baker serves as the University of Hawaii, John A. Burns School of Medicine Proteomics Core Co-Director. She maintains three mass spectrometers, provides consultation for the medical community and other departments, and conducts proteomics experiments.

During her predoctoral work, she explored the role of N-glycosylation in a stable peroxidase from palm tree leaves. Plant peroxidases are extensively used in bioresearch and bioanalysis. These enzymes are also capable of synthesizing conductive, biodegradable plastics, and remediation of contaminated industrial wastewater. Plant peroxidases rely on N-glycosylation for full enzyme activity and stability, however, the mechanism is poorly understood. She developed a sensitive technique for mass spectrometry-based amino acid sequencing, published in Analytical Chemistry. Next, she used a mass spectrometry-guided approach to clone the gene and verify the amino acid sequence. They found that windmill palm tree peroxidase is a heterogeneous glycoprotein with 13 sites for N-glycosylation. Next, she studied the site-specific glycosylation of windmill palm tree peroxidase, which was published in Journal of Proteome Research. In this work, she overcame the lack of tools for interpreting plant glycopeptide mass spectrometry data by developing a workflow and bioinformatics tools. The analysis gave an in-depth view of the glycosylation of windmill palm tree peroxidase.

Her current research examines the contribution of native glycosylation to windmill palm tree peroxidase function by comparing the native enzyme to those expressed in Nicotiana benthamiana and Pichia pastoris. Differences in glycosylation are hypothesized to affect enzyme stability and activity. Her workflow and tools for analysis of plant glycopeptide mass spectrometry data will be instrumental for interpretation of the results.