Analytical method validation is the process of establishing that an analytical technique is applicable for a proposed objective. Early in the method development of a new analytical technique an understanding of the instrumental components and procedures is elaborated through scientifically based optimization. The optimization experiments are used to define the operational parameters that yield the maximum performance by the analytical technique for the target analyte before commencing validation studies. This dissertation details method development through experimental investigations instrumental components of LEMS (substrate, laser parameters, and electrospray source conditions). Each instrumental component has a number of induvial parameters which are optimized to yield the maximum laser electrospray mass spectrometry (LEMS) signal intensity for a given analytical problem. LEMS uses a nonresonant, femtosecond (fs) laser to ablate analytes from a surface. Those ablated analytes are then captured by a perpendicular electrospray, ionized, and desolvated to produce ions which travel into the inlet of the mass spectrometer for analysis. Each element of the LEMS experimental setup works in a complementary fashion to generate a mass spectral signal which have specific optimization steps that can dramatically impact the data that can be acquired. The results of the optimization for each instrumental component will then be applied to preliminary method development experiments for the analysis of pharmaceutical compounds from complex formulations biomarker discovery for mice afflicted with a traumatic brain injury.The effect of the laser pulse duration on the ablation mechanism and amount of laser induced conformational changes of aqueous myoglobin was investigated using 55 fs, 56 picosecond (ps), and 10 nanosecond (ns) pulses and laser pulse energies from 0.05 to 1.6 mJ. It was found that the optical properties of the substrates (stainless-steel and quartz) and laser intensity regimes accessible by each pulse duration determined the amount of myoglobin ablated and subsequent mass spectral signal intensity. Laser ablation of myoglobin from both substrates using all laser pulse energies was observed for the 55 fs pulse while the 10 ns pulse required minimum pulse energies of 0.4 and 1.2 mJ for ablation of myoglobin to occur from stainless-steel and quartz, respectively. As the pulse duration increases, thermal processes increase which dictated the relative amount of protein unfolding, number of phosphate adducts, and degree of solvent adduction. Many of the common laser electrospray ionization (ESI) hybrid techniques employ ns pulse durations. However, the amount of ablated myoglobin originating from a ns pulse was observed to be dependent on the amount of energy that was absorbed by the substrate or sample. Experiments to increase the signal intensity while implementing ns laser electrospray mass spectrometry (ns-LEMS) were performed by exploiting the optical properties of nanomaterials as a potential matrix for desorption and detection of myoglobin. To estimate the contribution of the surface plasmon resonance (SPR) to the desorption of myoglobin under the different pulse duration regimes, the addition of an aqueous gold nanostar (GNS) matrix was implemented. GNSs have a SPR maximum of ~750 nm which overlaps strongly with the 780 nm laser wavelength. Gold nanospheres, which have a SPR of ~530 nm, have an absorption overlap 25 times less than that of the nanostars with the 785 nm laser light and therefore were chosen as a control gold nanoparticle matrix. It was observed that protein mixed with solution phase GNSs improved the laser ablation and consequent mass spectral signal intensity of the protein in comparison to both the nanosphere addition and ablation from quartz without nanomaterial addition for the 55 fs, 56 ps, and 10 ns pulses. This dissertation also extends to an investigation of the electrospray source and the roles that the nebulizing gas pressure, electrospray solution flow rate, and needle protrusion from the emitter sheath effects the electrospray analyte signal and stability. Interactions between the electrospray droplets and nebulizing gas were elucidated using an ablation chamber in which laser ablated analytes were carried via the nebulizing gas flow through the nebulizer sheath to interact with the electrospray Taylor cone, jet, and subsequent droplets. The signal intensity and relative standard deviation (RSD) of an infused Victoria blue solution was used to assess conventional ESI optimization experiments while a mixture of Gly-Gly-His, lactose, adenosine, and vitamin B12 was laser ablated within the ablation chamber for the optimization of the remote ablation device. It was found that a needle protrusion flush with the nebulizing sheath wall, 9 psi nebulizing gas pressure, and 9 µL/min ESI flow rate yielded the highest signal intensity for low and high mass analytes when utilizing the ablation chamber. However, the conventional ESI signal and stability was maximized using a needle protrusion of 0.6 mm from the sheath, 18 psi nebulizing gas pressure, and 9 µL/ min ESI flow rate. The last two chapters describe collaborative efforts with GlaxoSmithKline (GSK) and Temple University’s Lewis Katz School of Medicine with the application of LEMS to real world problems. The first of these chapters explores the preliminary method development results for sampling protocols of LEMS in a pathway to measuring the active ingredient in a formulation when differences in concentration are a percent or less for GSK. The results from the method development and optimization experiments in the previous chapters were applied to the GSK pharmaceutical manufacturing paradigm to test product quality in-line and in real-time instead of testing in a lab at the end of the manufacturing process. The LEMS sampling protocols involved ablation of either powder, compressed form, or solution containing powder using laser ablation. The ablated material was then entrained in an electrospray aerosol and transferred into a mass spectrometer for quantitative measurement of the molecules making up the powder, pill, or solution. Measurement time was on the order of seconds so that thousands of samples can be potentially measured in an hour. Future prospective experiments include additional optimization of the solution phase and compressed form sampling methods and, ultimately, the method validation of LEMS for quantifying active ingredients in pharmaceutical formulations. The last chapter seeks to develop new methods to map all biomarkers in traumatic brain injury (TBI) through mass spectrometry imaging (MSI), serum analysis, and protein derivatization assays. In this work, the Ramirez laboratory employs the controlled cortical impact model of experimental TBI in mice, harvests the brain (post injury) and prepares sections for analytical analysis. TBI is a complex injury involving multiple physiological and biochemical alterations to tissue. The potentially thousands of relevant biomarkers spread over a volume of thousands of mm3 makes the spatially resolved chemical analysis of brain a big data problem to which principal component analysis is applied. / Chemistry