This thesis is focusing on the development of new analytical strategies for MS-based targeted proteomics. Most analytical proteomics workflows rely mainly on carved in stone procedures such as the overnight tryptic digestion and the one hour chromatographic gradient performed on a nano liquid chromatography separation followed by mass spectrometric detection using ion traps (nanoLC-ESI-ITMS) which has proven to be perfectly suited for discovery experiments. However, in the field of quantitative analysis of biopharmaceuticals, when hundreds of samples need to be quantified with accuracy on a daily basis, or in system biology, when large sets of proteins need to be monitored consistently between altered biological states, new analytical strategies need to be put in place. Our research group develops new applications of mass spectrometry, sample preparation and separation techniques dedicated to analytical proteomics and metabolomics. The development of alternative analytical methods for the rapid and sensitive quantification of proteins is an essential key of this thesis work.