Since the introduction of the of Micro Total Analysis Systems concept in 1990, important progress in microfluidic analytical systems has been realized. In many cases, microfluidic systems have shown improved analytical performances over classical methods, while consuming small amounts of sample and reagents, and strongly reducing analysis time. In this thesis, we propose to explore two important topics in analytics in the microchip format: (i) Capillary electrophoresis (CE) on-chip, where we will focus on pressure-based sample injection techniques and (ii) the isolation and quantification of biological molecules, like antibodies, using magnetic nanoparticles as support in a sandwich immunoassay. After a general introduction, we will introduce the theoretical concepts for understanding our work in CE on-chip, followed by the description of the magnetism applied to the manipulation of magnetic nanoparticles in a microchannel. The state-of-the-art of the injection techniques in a CE microchip and the utilization of microfluidic chips for immunoassays will be introduced, followed by the presentation of two intensively used microfabrication techniques: (i) the powder blasting micro-erosion process for the realization of CE microchips, and (ii) deep reactive-ion etching for the microfabrication of microfluidic chips used for the retention of magnetic nanoparticles. As main results of this thesis, we develop a novel and promising concept of pressure-based injection in a CE microchip, where the sample is flowing continuously through the microchip using a single potential that is constant in time, and injected by a pressure pulse in less than one second. Then, we will introduce a new and original concept to retain superparamagnetic nanoparticles in a microfluidic chip, using a microchannel with periodically enlarged sections. We use this retention technique for the detection and quantification of monoclonal antibodies spiked in cell culture medium or directly obtained from the production of a cell culture. Thereby, we perform a complete on-chip sandwich immunoassay, while using only nanoliters of sample and reagents. Finally, we will conclude the thesis by giving an outlook of the expected future developments of our work and propose potential new applications in other area of microfluidic analytical microsystems.