Suppression effects in peptide mapping by plasma desorption mass spectrometry

Suppression effects observed in plasma desorption (PD) mass spectrometry have been studied and compared to those found in fast atom bombardment mass spectrometry. A basic difference in the mechanism of suppression in the two techniques is demonstrated. In positive ion mode PD mass spectrometry, peptides carrying net positive charges are preferentially detected when analysed together with peptides carrying net negative charges, and in negative ion mode PD mass spectrometry, the situation is generally reversed. Based on this complementarity, PD mapping carried out by enzymatic digestion of a nitrocellulose‐bound sample can in many cases yield almost complete coverage of smaller proteins.