<p>Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) has been established as a powerful tool for qualitative and quantitative analysis of biomolecules. However, mass spectrometric analysis of biomolecules is often limited by poor ionization efficiency of analyte for sensitive detection and limited fragmentation for structural characterization. Over the years, various solution phase as well as gas-phase derivatization techniques, have been coupled with MS to increase the ionization efficiency and facilitate the formation of structural informative fragment ions. The research presented in this dissertation falls into two major parts; focusing on method development and application of radical chemistry for enhanced biomolecule analysis on an ESI-MS/MS platform. In the first part, a method of rapid charge tagging of neutral lipids (e.g. sterols, glycerides) with a thiol radical-based charge tag is developed, followed by comprehensive analysis via ESI-MS/MS without the use of a chromatographic separation (shotgun lipidomics). This charge tagging is performed in an easily constructible fused silica capillary-based microflow photo-reactor which is relatively low in cost and requires no instrument modifications. This method significantly enhances the ionization efficiency of the neutral lipids for sensitive MS detection (pM range). This method can be applied to the small volume of biological complex samples (e.g. 1 µL plasma) and doesn’t require extensive sample pretreatment procedure (analysis time of 2 min vs. traditional >60 min on GC-MS and HPLC-MS systems). Furthermore, the derivatized neutral lipids can also be fragmented via soft collision-induced dissociation to obtain fatty acyl chain composition of the neutral lipids (sterol esters, diacylglycerols, triacylglycerols, etc.) for structural characterization. This can especially be useful for determination for fatty acyl compositional isomers in neutral lipids for analysis related to biomarker detection. The characteristic fragmentation pattern of tagged neutral lipids has also been utilized for quantitation of lipids from biological mixture samples. Initial application of this method has shown alteration in the concentration of diacylglycerol lipid species in clinical samples of Type 2 Diabetes Mellitus patients, suggesting the potential of understanding the biological roles of such lipids in insulin resistance. </p> <p>In the second part, a unique approach of radical-induced disulfide bond cleavage in peptides and proteins is demonstrated. Using 254 nm UV emission, acetone was used as a photoinitiator to initiate secondary radical formation i.e. hydroxyalkyl radical, from alcohol co-solvents used for electrospray. These radicals can then be used to efficiently cleave the disulfide bonds (R-S-S-R) in peptide/proteins to give reduced reaction products (RSH) at the cleavage site. Upon soft collision-induced dissociation, the reduced product gave abundant <i>b-</i> and <i>y-</i> type fragment ions for complete or enhanced sequence coverage as compared to intact disulfide-linked peptides and proteins. With the use of a simple microflow photo-reactor, this radical based approach can also be coupled with infusion ESI-MS/MS for a rapid online-based peptide and protein analysis. The yield for disulfide bond reduction was almost 100% within less than 5 s of UV irradiation. Furthermore, by adjusting the UV irradiance time, different degrees of partial reduction could be achieved, which greatly facilitated the disulfide linkage mapping in peptides and proteins with multiple disulfide bonds. This method has been incorporated with both bottom-up and top-down approach for protein analysis for unraveling the molecular complexity, quantifying and deep sequencing of disulfide-linked proteins.</p>