Myristoylated alanine-rich C kinase substrate (MARCKS), a major in vivo substrate protein of protein kinase C, isolated from calf brain contains various species phosphorylated to different degrees. To establish the in vivo phosphorylation sites, the protein was digested with lysyl endoprotease, and the digests were analyzed by the capillary high performance liquid chromatography interfaced on-line to an electrospray mass spectrometer. Six out of 17 peptides were found to be phosphorylated. Of the 7 phosphorylated serine residues identified by Edman degradation, only 1 was within the known phosphorylation domain by protein kinase C. All the other phosphorylated serine residues originated from the N-terminal half of the molecule and were immediately followed by proline. Therefore, MARCKS, a major in vivo substrate of protein kinase C, is also an in vivo substrate of proline-directed protein kinase(s) such as mitogen-activated protein kinase or Cdk5 kinase.