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Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool to investigate large molecules. Miniaturized microchips, as a goal of ‘Lab-on-chip’, allow various integrated analysis quickly. The coupling of functional microchips and ESI-MS is capable of providing a sensitive and fast analysis of all products generated in various functional microchips. Beta-amyloid (Aβ) peptides are the main component of senile plaques, a hallmark of Alzheimer’s disease. Copper binding is an important factor to induce soluble Aβ peptides aggregation and generates reactive oxygen species (ROS). By using a sacrificial copper electrode as the anode in positive ionization mode of ESI-MS, copper (I) and (II) complexes were formed on-line in a microchip electrospray emitter. This approach provides direct information on Cu(I)-Aβ16 complexes generated in solution from metallic copper, and tandem mass spectrometry gives evidence that His13 and His14 are involved in the coordination of both Cu(I)- and Cu(II)-Aβ16 complexes. Since soluble Aβ peptide potentially controls copper homeostasis in human body, the damage by excessive ROS may destroy their functions. Two main types of oxidation products of N-terminal truncated Aβ11 and Aβ16 in the presence of ascorbic acid, i.e., oxygen-addition products and N-terminal loss damages were investigated by ESI-MS. The oxidation sites for both of them were firstly well identified together with the influence of pH value and the reaction time on the generation of oxidation products. Alpha-synuclein (α-syn) plays a central role in the pathogenesis of Parkinson's disease. Post-translational modifications (PTMs) of α-syn occur at the C-terminal region and are in very close proximity to the putative metal binding sites. The interactions between the di- and trivalent cations, Cu(II), Pb(II), Fe(II) and Fe(III) and the C-terminal region of α-syn and its phosphorylated forms were carried out using ESI-MS and fluorescence spectroscopy. Dual-sprayer microchip coupled to ESI-MS, successfully ionized aqueous peptide/protein samples due to a cooperative electrospray from the Taylor cone with assisting solution containing an organic solvent and acids. As an effective and quick mixer in the Taylor cone, dual-sprayer microchip was able to gradually change the conformations of large proteins and quickly investigate the fast reactions such as the complexation reaction of Aβ peptide and phospholipid after direct mixing them in the Taylor cone. Droplet microchip was developed and directly interfaced to ESI-MS. Different sizes of droplets were generated and successfully determined by ESI-MS even at a very low sample concentration. Owing to a high feasibility of microchip fabrication, this droplet microchip can also act as an effective micro-mixer capable of introducing multiple samples into one droplet by the introduction of additional micro-channels for aqueous liquids.