Qualitative and quantitative analyte analysis is omnipresent: from quality control in food, pharmaceutical, biotechnology industries, to new molecular syntheses, detection of explosives and drugs, as well as natural compound mixture analysis, such as crude oils or animal fluids. Of particular interest are analytes associated with human health and energy, both of synthetic and natural origin. Thus, a selection of synthetic analytes related to ongoing efforts in drug design and alternative energy sources, has been made for this Thesis. Additionally, for natural analytes, peptides and crude oil were selected as analytes of choice due to their central role in human health and energy sources, respectively. Mass spectrometry was chosen as the method of choice for analyte investigation (elemental composition and structural feature determination) due to its sensitivity, ability to obtain data on thousands of analytes simultaneously, and use of radical and photo chemistry to probe molecular structure. The thesis is split into three major parts, first investigating synthetic analytes, then peptides and, finally, crude oil fractions. In the first part, use of photoionization is discussed as an alternative to other common analyte ionization methods as most selected synthetic targets do not ionize with the latter. A rough guideline, based on analyte structural composition, is proposed to determine analyte photoionization response. In-source analyte reactions are analysed and used as indicators of various functional group presence. Finally, upper mass boundary on analytes is considered and extended with photoionization. In the second part, peptide-ion/electron and ion/radical anion interactions in tandem mass spectrometry experiments, along with in silico modelling are used to put forth a new mechanistic proposal, which is fundamentally different to all the other mechanistic proposals related to this type of fragmentation process. The proposal involves charge-driven, rather than radical driven peptide radical fragmentation. It is also additionally significantly influenced by the local 3D structure of the peptide. The proposal may be of particular interest when considering radiation damage effects on key biological systems. In the third part, several methods are proposed aimed at enhancing crude oil (and other complex mixture) analysis on a new type of high resolution mass spectrometer, the Orbitrap Elite FTMS, including maximising number of identifiable analytes and evaluating key parameters of mass spectra of complex mixtures. Additionally, a data visualization method is proposed, based on analyte heteroatom content, which creates a graphical representation of all the identified components in the complex mixture and how changes in bulk properties of the sample get reflected on its compositional makeup.