S100 is a family of small, acidic, calcium binding proteins involved in the control of a multitude of intra- and extracellular processes, including many pathologies. The application of the analytical methodology based on the combination of RP HPLC and ESI-MS allowed for the characterization of S-nitrosylation and S-glutathionylation in two representative S100 proteins: S100A1 and S100B. The GSNO related S-nitrosylation of the conserved C-terminal cysteine is strongly activated by the binding of Ca(II) to S100A1 and of Ca(II) and Zn(II) to S100B. This modification results in a global alteration of protein structure, as demonstrated by a variety of techniques. The presented results provide a mechanistic basis for further studies of the function of S100 proteins in the control of redox-based and metal-based signal transduction.