Radioactive assays are commonly employed to monitor protein or peptide phosphorylation. They not only have all the disadvantages related to radioactivity, but also require large amounts of sample. An alternative is the use of mass spectrometric peptide mapping with sensitivities in the fmole range. We demonstrate here that desalting is a requirement for reproducible results, and we optimized the method for very hydrophilic peptide substrates. The method is very efficient with respect to time and effort.