Over the years, mass spectrometry has increasingly become an analytical tool of choice in the field of natural products chemistry owing to its high throughput nature, quantitative capability and the facility to integrate with chromatographic separation methods. This study enhances the capacity of mass spectrometry in the analysis of wide variety of complex mixtures with the development of novel MALDI matrices as well as optimizing the existing hyphenated techniques, and thereby cast new light on some pharmacological and ecological aspects that have not been successfully addressed yet. The initial success in development of 1,14-diaza[5]helicene as a novel MALDI matrix for the analysis of acidic analytes demonstrates the applicability of MALDI-MS in small molecule analysis and challenges the perception of MALDI-MS to be a “high molecular mass tool only”. Furthermore, it confirms the recently introduced strategy for the selection of “ionless” matrices based on the Brønsted-Lowry acid-base theory and signifies the importance of rational matrix design. These findings indicate a tremendous potential for studying biological systems and opens up new venues for high throughput targeted metabolomics work. Apart from MALDI-MS, the thesis demonstrates the immense contribution of hyphenated techniques in the study of secondary metabolites as indicated in the chemical profiling of two phytochemically unexplored medicinal plants in Sri Lanka. In comparison to the extracts of other medicinal plants reported in literature, the lipophilic extracts of Plectranthus zeylanicus and Munronia pinnata have exhibited extremely potent 5-lipoxygenase inhibitory activity suggesting a high pharmacological potential of these plants for intervention with 5-lipoxygenase related disorders. This observation was reinforced by UHPLC-ESI-MS and GC-MS analysis of the active extracts and fractions, which have revealed the presence of several bioactive secondary metabolites together with some compounds for which the knowledge regarding bioactivities are rare. In particular, the identification of coleone P for the first time in P. zeylanicus, would spotlight the pharmacological community for future comprehensive studies, due to the high possibility of this compound to exhibit anti-inflammatory or anti-proliferative properties. The hidden phytochemistry in M. pinnata has been unveiled for the first time and the platform laid by this study will be indispensable for further phytochemical and bioactivity research on this precious and rare medicinal plant in future. Therefore, the MS-based rapid screening of medicinal plants substantiates the traditional use of these plants as anti-inflammatory remedy, while ensures that phytochemical screening is no longer as cumbrous as it was a few years ago. The applications of novel hyphenated techniques could be expanded beyond the discovery of pharmaceuticals, as reflected by the study on complex surface lipids extracts in Drosophila melanogaster. The identification of female specific 9-(3-methyl-5-pentylfuran-2-yl)nonanoic acid and its triglyceide by UHPLC-APCI-MS and GC-MS analysis contradicts the decades-old concept of the absence of qualitative differences between cuticular fatty acid profiles in male and female flies. Despite its occurrence in several other biological sources, the biosynthesis of this fatty acid is not clear yet, however, it was suggested that the putative biosynthetic pathway starts from cis-vaccenic acid, a common precursor of the pheromones in D. melanogaster. Therefore, the detection of this female specific fatty acid for first time in an insect would have a great significance and inspire the biologists for detailed study of its biosynthesis and physiological functions. In conclusion, the thesis breaks new grounds in several aspects of natural product chemistry with the development and optimization of high throughput, efficient and robust mass spectrometric approaches.