<div> <div> <div> <p>The exploratory profiling and quantitative bioassays of lipids, small metabolites, and peptides have always been challenging tasks. The most popular instrument platform deployed to solve these problems is chromatography coupled with mass spectrometry. However, it requires large amounts of instrument time, intensive labor, and frequent maintenance, and usually produces results with bias. Thus, the pace of exploratory research is one of poor efficacy and low throughput. The work in this dissertation provides two practical tactics to address these problems. The first solution is multiple reaction monitoring profiling (MRM-profiling), a new concept intended to shift the exploratory research from current identification-centered metabolomics and lipidomics to functional group screening by taking advantage of precursor ion scan and product ion scan. It is also demonstrated that MRM-profiling is capable of quantifying the relative amount of lipids within the same subclass. Besides, an application of the whole workflow to investigate the strain-level differences of bacteria is described. The results have zeroed in on several potential lipid biomarkers and corresponding MRM transitions. The second strategy is aimed to increase the throughput of targeted bioassays by conducting induced nanoelectrospray ionization (nESI) in batch mode. A novel prototype instrument named "Dip-and-Go" system is presented. Characterization of its ability to carry out reaction screening and bioassays exhibits the versatility of the system. The distinct electrophoretic cleaning mechanism contributes to the removal of salt during ionization, which assures the accuracy of measurement.</p></div></div></div>