By using electrospray ionization mass spectrometry (ESI-MS), protein complexes of cytochrome c with amino acids were studied. Different amino acids were investigated to explore these complexes. Using these amino acids, a strategy for probing the structure of cytochrome c was established. It was found that L-Arg and L-Glu could bind with cytochrome c to form noncovalent complexes. At low pH solution, complexes between the cytochrome c molecule with several L-Arg molecules (multiple L-Arg adducts) were formed, and the number of binding ligands depended on the charge state of cytochrome c. While in neutral solution, the cytochrome c molecule complexed with only one L-Arg molecule (single L-Arg adducts). As for L-Glu, only single L-Glu adducts were formed in both acidic and neutral solutions.