This dissertation focuses on the analysis of plant and animal extracts utilizing MS and FTIR-PAS. Chapter 2 details the use of high resolution TOF MS to analyze metabolites extracted from rat cecal and distal colon contents. The goal of the study is to determine whether rats fed four different starch diets have metabolic profiles that could be considered significantly different using partial least squares-discriminate analysis (PLS-DA) software. Chapter 3 delves into a comprehensive identification of alpha-zein proteins using LC separation coupled to a high resolution TOF MS. This is the first study to have comprehensively identified alpha-zein proteins with accurate mass capabilities. The study aims at determining whether alpha-zein protein extract profiles are different when extracted from corn gluten mean and dried distillers grains with solubles in combination with varying extraction conditions. Chapter 4 revisits the analysis of rat cecal and distal colon contents; however, the analysis focuses on starch determination utilizing FTIR-PAS. Many starch analysis techniques are time consuming and expensive, FTIR-PAS is explored to speed up analysis time and decrease cost on large sample runs. FTIR-PAS spectra of the cecal and distal colon contents are processed using PLS to determine quantitative starch values and principal component analysis (PCA) is applied to determine qualitative starch differences.