This Ph.D. work was focused on the study of surface and pneumatic phenomena occurring in a desorption electrospray ionization-mass spectrometric (DESI) ion source. Another part of the work concerned innovative proteomics-based approaches aimed at the sensitive determination of trace hidden allergens in food. The first part of this Ph.D. work describes the successful use of innovative materials as supports for DESI investigations. A sol-gel mixture of tetraethoxysilane (TEOS) and octyltriethoxysilane (OTES) was used to prepare dip-coated hydrophobic xerogel films and then characterized by means of atomic force microscopy (AFM), ellipsometer, contact angle goniometry (CA) and surface free energy measurements. The DESI process was studied by using as supports functionalized surfaces obtained depositing three different silanes (3-mercaptopropyltriethoxysilane, MTS, octyltriethoxysilane, OTES and 1H,1H,2H,2H-perfluorooctyltriethoxy-silane, FOTES) from toluene solution onto standard glass slides. Surfaces were characterized by CA, AFM and X-ray photoelectron spectroscopy (XPS). Low-molecular weight compounds were used as analytes and surface effects were discussed together with those of sprayer potential in terms of ion formation yield. A study of pneumatic effects with ESI and DESI interfaces was also carried out. For this purpose the sprayer potential was set in such a way that no ESI ionization occurs. Further confirmation about the physico-chemical processes involved in the ion formation mechanism were obtained by exploring effects of ESI parameters on the analyte ionization. In addition, it was demonstrated how different analytical responses were observed as a function of surface free energy when different solvents and applied potentials were investigated. It was confirmed that DESI phenomenon is mainly pneumatically driven and it is related to analyte solubility in the sprayed solvent. It was confirmed also found that in the DESI interface, like in ESI, ion formation is ruled by thermodynamics and proton transfer is preferred toward the species with the highest gas phase basicity. The second part of this manuscript describes a proteomic-based approach for the simultaneous determination of a number of hidden allergens in foods using characteristic peptide markers of the allergens. In detail, an innovative buffer-based extraction method for the simultaneous analysis of five nut allergens in cereals and biscuits using liquid chromatography-electrospray-linear ion trap-tandem mass spectrometry (LC-ESI-LIT-MS) was proposed. Liquid chromatography was used for the analytical separation and MS as detection technique. Chromatographic and mass spectrometric performances were evaluated according to Eurachem validation guidelines, demonstrating the performances of the novel approach in terms of sensitivity, selectivity, limits of detection as well as accuracy.