A practical ion trap mass spectrometer for the analysis of peptides by matrix-assisted laser desorption/ionization.

The present paper describes the performance of a newly configured matrix-assisted laser desorption/ionization quadrupole ion trap mass spectrometer (MALDI-ITMS), designed for biological applications that require the determination of the primary structures of proteins, e.g., the rapid identification of proteins and the elucidation of posttranslational modifications. The strategy used for solving problems of this type involves enzymatic digestion of the protein, followed by MALDI ion trap mass spectrometric analysis of the components of the resulting complex mixture of peptide ions. The new instrument is demonstrated to be a highly practical tool for analyzing proteins. In particular, mixtures containing as many as 30 peptide components can be rapidly and sensitively analyzed without prior chromatographic separation of the components. Informative tandem mass spectra can be obtained from the peptide components with m/z values up to 3500. A single subpicomole sample loading of a complex peptide mixture is more than sufficient for a complete set of experiments that includes both low- and high-resolution molecular mass determinations as well as a complete MS/MS study of the various components present in the sample. Extensive use is made of improved methods for trapping, isolating, fragmenting, and detecting ions in the ITMS (details are to be provided in two future papers).