In Unit 2 (items 2.1 to 2.8) are discussed deeply the two most commonly used methodologies in the study of proteins in proteomics that have higher resolution and allow analysis of samples in high throughput assays: two-dimensional electrophoresis and multidimensional liquid chromatography coupled to mass spectrometry. First, the principles of electrophoretic techniques, processing of biological samples for this technique and the quantitative evaluation of the results obtained by imaging techniques are described. Subsequently the different types of protein separation by liquid chromatography are referred. Then, a review is shown on the different methods of sequence determination of proteins by mass spectrometry using the main types of ionization (ionization by matrix assisted laser desorption, electrospray ionization) and ion separation (Time-of-flight analyzer, triple quadrupole analyzer and ion trap) mass spectrometry and their possible combinations. Finally, the unit describes the various techniques utilized for the interpretation of the protein sequence using peptide mass fingerprinting.