Analysis of protein sequences and protein complexes by matrix-assisted laser desorption/ionization mass spectrometry

In the context of proteome analysis, matrix-assisted laser desorption/ioniz ation (MALDI) mass spectrometry can fulfil the two tasks of primary structu re verification and protein identification. As an illustration of the first of these tasks, the sequence of E. coli isoleucyl-tRNA synthetase, a prote in with 15 reported sequence conflicts, has been established by means of MA LDI mass mapping. The identification of mitochondrial proteins participatin g in a yeast supramolecular complex exhibiting NADH dehydrogenase activity highlights the performance of MALDI mass spectrometry for the second task. The spectral suppression phenomenon occurring for complex peptide mixtures analyzed by MALDI is discussed, as well as the role of post-source decay (P SD) analysis for confident protein identification.