Mass spectrometry (MS) is an analytical instrument used to determine the mass-to-charge ratio of ions. In the last decade, MS emerged as a powerful method for the analysis of biological molecules, in order to obtain the chemical composition of a compound and the amount of a compound in a sample. An important field of application for this technique is proteomics, where protein structure determination and biomarkers detecting are two major issues. Tandem mass spectrometry (MS/MS) involves multiple step of mass selection or analysis, after a fragmentation of a specific peptide ion, and permits to elucidate the composition of complex molecules, which cannot be determined by means of MS alone. This presentation will introduce MS and MS/MS, and then focus on the computational problems related to the interpretation of their results, such as dimensionality reduction, peptide identification via database search and de novo peptide sequencing.