<p>Mass spectrometry-based techniques have been widely used in reaction monitoring due to their high sensitivity and ability to offer structure information by tandem mass spectrometry. We applied nanoelectrospray mass spectrometry (nanoESI-MS) to simultaneously monitor pre-catalysts, catalytic intermediates, reagents, and products of palladium catalyzed Suzuki-Miyaura cross-coupling reactions. A set of Pd cluster ions related to the monoligated Pd (0) active catalyst is detected, and its deconvoluted isotopic distribution reveals contributions from two neutral molecules. One is assigned to the generally accepted Pd (0) active catalyst, seen in MS as the protonated molecule, while the other is suggested to correspond to a deactivated form of Pd catalyst. Oxidative stress testing of the synthetic model catalyst XPhos Pd cyclo-octadiene, performed using oxygen and Fe(III), supported this assignment. Thus, the make-up of the monoligated set of Pd (0) ions appears to indicate the oxidation state of the system. The formation and removal of the oxidative addition intermediate during the catalytic cycle was monitored to provide information on the progress of the transmetalation step. </p> <p> </p> <p><a>Recently, microdroplets created by ambient ionization source have been used as reaction vessels to accelerate organic reactions. Field desorption mass spectrometry under ambient conditions is applied to study solution-phase organic reactions in micro-volumes. Compared to nanoelectrospray, it is noteworthy that radical cations and formation of radical cation products are observed. Three reactions, the hydrazone formation by phenyl hydrazine and indoline-2,3-dione, the Katritzky reaction between a pyrylium salt and anisidine, and the Hantzsch synthesis of 1,4-dihydropyridine, were investigated by this system and reaction acceleration was observed to different extents. The increase in rate relative to that for the corresponding bulk reactions is attributed to solvent evaporation which increases concentration, and to the increase of surface-to-volume ratio with enhanced interfacial reaction rate constants. Later work in this thesis describes explicit solvent calculations to study the energies and structures of the hydrazone formation reaction from phenylhydrazine and indoline-2,3-dione in acidic methanol with density functional tight binding (DFTB) methods. Additionally, the thesis covers MS based methods for determination of isoaspartate and aspartate in peptide by gas-phase chemistry and detection of S-nitrosoglutathione in exhaled breath condensate sample.</a></p>