Bottom-up proteomics has been significantly advanced in last decade, enabling the detection of thousands peptides in a single analysis. However, various protein processing events such as post-translational modifications (PTMs) frequently are untraceable using these approaches. The alternative approach is “top-down” proteomics, where the intact protein samples are analyzed directly by MS, can more accurately reflect protein biological significances and properties of actual biological systems. Our research aims to develop next generation top-down proteomics approaches that combine biochemistry, separation science, mass spectrometer (MS) instrumentation, and bioinformatics to understand protein dynamics in different biological systems (bacteria, fungi, and mammalian cells). Specifically, we are focused on the following directions:
Fungal secretome analysis: Functional characterization of fungi secretome is essential for the understanding of the biochemical regulation and mechanisms involved in the secondary metabolite biosynthesis. Almost all of fungal extracellular enzymes are post-translational modified (e.g., glycosylated). The major objective of our research is to develop a multiplexed PTM analysis platform for characterizing and quantifying the functional proteins constituting the fungal secretome.
Histone code deciphering: Core histones are modified heavily by multiple PTMs (e.g., methylation, acetylation, phosphorylation, SUMOylation, and ADP-ribosylation), generating a "histone code" that is implicated in most chromatin-related cellular processes. Our research objective is to develop an intact histone profiling platform using top-down proteomics that has proven to be advantageous for the characterization of multiple PTMs dispersed along the primary protein sequence.