Here we report that the addition of HCl or HNO(3) to the matrix at a limited concentration dramatically increases the signal-to-noise ratio of the matrix-assisted laser desorption/ionization mass spectrometry spectrum of phosphate-containing peptide mixtures such as those obtained from an immobilised metal affinity capture eluent or a phosphate-containing tryptic digest. These improved spectra permitted both peptide identification and the determination of protein phosphorylation sites. In comparison to existing methods for removing salts, this method requires less sample manipulation and thus less sample loss is expected.