The origin of fluorous interaction was explored and experimentally examined based on both HPLC and CEC data in this project. It was found that the selective fluorous interaction is a kind of reduced instantaneous or induced dipole interaction compared to the hydrophobic interaction. A series of FPPM preparation parameters were optimized. The optimized FPPM column can resolve the components in a manner that was otherwise not possible with its non-fluorous (hydrocarbon) counterpart. Following, the CEC separation of fluorous analytes on FPPM stationary phase based upon fluorous-fluorous interaction was realized for the first time. It was also found that, quantitatively, hydrophobic stationary phases have better methylene selectivity (〖 α〗_(-CH_2-)), while fluorous stationary phases have better perfluoromethylene selectivity (〖 α〗_(-CF_2-)). Thermodynamically, ∆G_(-CF_2- → -CF_2-)^° : ∆G_(-CH_2- → -CH_2-)^° (Gibbs free energy change of transferring a –CF2– unit to pure fluorous stationary phase versus Gibbs free energy change of transferring a –CH2– unit to pure hydrophobic stationary phase) is approximately equal to 8:1. A new concept, hypothetical water percentage (HWP) based on the comparison of 〖 α〗_(-CH_2-) and〖 α〗_(-CF_2-) was proposed for the first time to quantitatively evaluate the hydrophobicity/fluorophilicity of a stationary phase. A stationary phase can be classified as fluorous stationary phase when the HWP is less than 0 (more negative indicates more fluorous), or as a hydrophobic stationary phase when the HWP is larger than 100. For the range between 0 and 100, the stationary phase can be treated as either fluorous or hydrophobic due to the similar values of〖 α〗_(-CH_2-) and〖 α〗_(-CF_2-). Fluorous tagged peptides and proteins (up to 5800 Da) were effectively separated from their non-fluorous counterparts on the FPPM stationary phase in capillary-based columns and detected both on-line with ESI-MS and off-line with MALDI-MS. Finally, the FPPM solid-phase extraction (SPE) stationary phase was transplanted from the capillary to a microchip format. This microchip exhibits the merits of both selective fluorous interaction and micro total analysis system (µTAS). / Thesis (Ph.D, Chemistry) -- Queen's University, 2013-11-19 23:11:16.636