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As part of the ongoing effort to substitute finite fuel and chemical resources with renewable ones, biomass is emerging as one of the most promising sources. Biomass consists of three main components of cellulose, hemicellulose, and lignin. Traditionally, cellulose has been used extensively in pulping industry, while lignin has been considered waste and is burned to generate heat. Lignin, a complex aromatic polymer component of biomass, has the potential to be used as a source of aromatic chemicals and pharmaceutical synthons. The recalcitrant nature of lignin, the lack of effective lignin breakdown methods and analytical techniques to analyze it are the main obstacles to obtaining high-yield chemicals from lignin. Mass spectrometry has proven to be one of the most promising analytical techniques and it is widely used in the pharmaceutical and chemical industries. The goal of this work is to develop analytical methods using mass spectrometry and lignin model compounds. Additionally, this work focused on the development and application of quantitative Derivatization Followed by Reductive Cleavage(q-DFRC) for the evaluation of various biomass pretreatment methods. Since most commercially available lignin model compounds fail to mimic the structure of native lignin, it is necessary to develop compounds that more closely reflect the functionality of native lignin. The first project of this dissertation is focused on developing precursors for synthesizing b-O-4 model compounds and modifying their functional groups. The precursors have been synthesized and analyzed using gas chromatography-mass spectrometry. These precursors were used to synthesize b-O-4 model compounds that exhibit all characteristics of the native lignin. The second project involved the synthesis and mass spectral analysis of a mixed linkage trimer containing both b-O-4 and b-5 bond types. A detailed analysis of the mass spectral fragmentation of lignin trimer with lithium adduct ionization is presented. The developed analysis of the lignin trimer facilitates the structural elucidation of lignin breakdown products. The third project involved the application of q-DFRC as one of the lignin breakdown techniques to evaluate different biomass pretreatment methods. Ethanosolv, dioxosolv, co-solvent enhanced lignocellulosic fractionation (CELF), hydrotropic, and acetic acid/formic acid pretreatments were evaluated by q-DFRC with deuterium-labeled acylated monolignols internal standard. An evaluation and comparison of the quality of lignin obtained from each of these pretreatments was conducted. This dissertation provides valuable information for the advancement of mass spectrometric analysis of lignin, and it can be applied to lignin oligomer analysis. Furthermore, the q-DFRC results provide insight into how various pretreatments are related to the extent of condensation in extracted lignin.