Colon cancer is a common and deadly disease characterized by aberrant genetic alterations. We are using quantitative tools to measure biological macromolecules that are altered in expression between different states associated with colon cancer. The studies in this thesis relate to comparisons between normal colon tissue versus colon tumor tissue, chemotherapeutic treatment versus non-treated, poor prognosis (relapse) versus good prognosis (disease-free survival), aneuploidy effects and gene silencing.  Transcript data has been collected with microarrays and quantitative real-time polymerase chain reaction (qRT-PCR). Protein level data was collected by bottom-up, global proteomics strategies using ESI-3D ion trap, ESI-Orbitrap, and MALDI-TOF mass spectrometers. As well as through targeted experiments including immunohistochemistry and selected reaction monitoring (SRM) on an ESI-triple quadrupole mass spectrometer. Studies were also conducted to improve and optimize our ability to analyze samples by mass spectrometric techniques include an evaluation of bottom-up sample preparation approaches and a proof of principle method to capture proteins/peptides from a matrix.  Taken as a whole, these studies focus on developing and utilizing quantitative methodology to measure biological species in colon cancer cell lines and primary human samples to enhance our understanding of this complex disease. The results of these studies have implications for improved treatment selection for stage II colon cancer patients, identification of biomarkers and potential targets for therapeutic options, and an overall enhanced understanding of the biology behind microRNA clusters and aneuploidy.