Investigation of the applicability of a sequential digestion protocol using trypsin and leucine aminopeptidase M for protein identification by matrix-assisted laser desorption/ionization - time of flight mass spectrometry

An investigation of the applicability of a sequential digestion procedure i nvolving endo-and exoprotease digestion of proteins is reported. The proced ure involves the digestion of a protein sample with trypsin, yielding pepti de fragments characteristic of the protein. The resulting mixture of peptid e fragments is then subjected to N-terminal sequencing with leucine aminope ptidase M (LAP), with matrix-assisted laser desorption ionization-time of f light mass spectrometric analysis of the various digestion products. Severa l proteins in solution, as well as gel extracted proteins were subjected to this sequential enzyme digestion procedure. The results of these experimen ts reveal that LAP will preferentially cleave specific peptides of the tryp sin digested sample with high efficiency, while leaving other peptides undi gested. Also, the length of the amino acid sequence tags that can be genera ted with this method is limited; the longest sequence tag generated from a single tryptic peptide was four amino acids, even though the digestion was allowed to proceed for long times. In the experiments, N-terminal digestion products were detected as early as two minutes, or as late as 90 minutes, following the addition of LAP to the sample. The method was shown to be eff ective for subpicomole starting quantities of protein, although with some l oss in digestion efficiency at lower concentrations of starting material. T his method is useful in providing additional sequence information to increa se the level of confidence in protein identification, as illustrated in the identification of bacterial proteins fractionated by high-performance liqu id chromatography. In some instances, this method can provide additional se quence information where post source decay and nanospray mass spectrometry failed to generate fragment ion spectra. This is illustrated in an example where the procedure was applied to a membrane protein, CD9, that had been i solated by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Altho ugh the sequential digestion procedure requires more human intervention, it is a straightforward method and can be readily implemented.