Almost two decades after the introduction of the electrospray ionization (ESI) and the matrix-assisted laser desorption ionization (MALDI) techniques, mass spectrometry (MS) has become a key technology in the emerging field of proteomics. MS-based procedures combined with various affinity-trapping methods allowed massive identification of constitutive elements in multi-protein complexes from different organisms. Similarly, various MS-based strategies have been developed and applied to low-resolution structural studies on protein and protein complex. In fact, products generated either by limited proteolysis, selective chemical modification or radical probe reactions performed on isolated proteins have been characterized by ESI and MALDI techniques, providing information on the location of residues accessible on molecular surface. Differential experiments performed before and following complex formation allowed the identification of masked regions in each component of the complex after binding, generated as a result of macromolecular interaction. Similarly, MS analysis of protein complex cross-linking products has led to the identification of spatially closed amino acids occurring at molecular interface. Nowadays, these methodologies are used for experimental validation of insilico generated models and verification of interface regions predicted by bioinformatics computations. Accordingly, these approaches present a fundamental resource when severe limitations using high-resolution methods, such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, which arise from the amount of sample required, difficulties in crystallization or solubilization, may hinder a definitive structural characterization. In this review, the combined use of chemical cross-linking, limited proteolysis, selective chemical modification or radical probe reactions with MS analysis is reviewed and discussed in the point of view of structural biology studies on protein and protein complexes.