MS (mass spectrometry) has been developed as an important analytical tool to study large molecules including polymer macromolecules and proteins. Its instrumentation technique including ionization methods, mass analyzer and detector systems has been greatly improved from last century to present. Bio-molecules and organic macromolecules tend to be fragile and fragment when they are ionized by conventional ionization methods. ESI (electrospray ionization) and MALDI (matrix assisted laser desorption/ionization) are two relatively tender ionization methods and suitable for the ionization of big molecules. The study on mechanism surround these two ionization methods is a hot issue. For MALDI, one wants to figure out what exactly happens when the laser irradiates the analyte, where in-plume reaction occurs. As an example, the photo-triggered reaction can induce the fragmentation of peptides or proteins. Proteolysis is a key step for proteomic study especially bottom-up proteomic strategy. Porous materials have been developed in last decades. The catalysis of porous materials to enzymatic reaction is a hot issue, and has been demonstrated in much published works. But the mechanism of how different porous materials affect the reaction is not completely clear yet. We compared several different porous material influences for the reaction efficiencies. A kinetic model was proposed to explain and foresee the proteolysis. The model was verified by integrated CE (capillary electrophoresis)/MS detection system, where a custom-designed CE-MS interface was utilized to collect the fraction of digests for off-line MALDI TOF (time-of-flight) MS analysis. From an instrumental point, we then introduce Al-foil as disposable and once-used MALDI-target substitute, by which the sample preparation for MALDI TOF MS analysis is greatly simplified. The regeneration procedure of typical target in each run and attrition of target-plate can be neglected after holding this Al-foil on a commercially available target plate. This substrate provides comparable detection limits (LOD) of protein and digests (peptides) as the typical stainless steel MALDI target plate. The pliability of Al-foil makes it easy to be printed. While nano-scale semiconductor materials such as TiO2 have been widely used for dye-sensitized solar cell study. Following the MALDI target holder study, TiO2 nanoparticles were prepared as optimized ink and fabricated on the Al-foil via screen- and rotogravure- printing procedures. The woven mesh and engraved image carrier can be designed and controlled for different print pattern. The given apparatus here can provide two different TiO2 functionalized Al-foil. The functionalized foil then was then taken for the analysis of matrix free LDI (laser desorption ionization) and the study of protein phosphorylation, which is one of the most common and important protein post-translational modifications that occur in animal cells. Since the typical organic matrix interference always makes noise signals in low mass/charge on a mass spectrum, especially below 1000 or 700 Th, matrix free LDI is introduced to study the low mass molecules or small molecules. In this context, besides TiO2 nanoparticles, we also investigate CdSe semiconductor quantum dots, and electrochemically polymerized film of an aromatic diamine for the LDI analysis. A standard peptide was applied for the feasibility study of LDI based on these substrates. Semiconductor quantum dots are also hot target molecules for the dye-sensitized solar cell. By comparing the photocurrents on different quantum dots fabricated electrodes, the electron transfer process inside was simulated to understand the kinetics, which is also expected to guide the LDI study including the mechanism involved.