In the context of proteome analysis, matrix-assisted laser desorption/ionization (MALDI) mass spectrometry can fulfil the two tasks of primary structure verification and protein identification. As an illustration of the first of these tasks, the sequence of E. coli isoleucyl-tRNA synthetase, a protein with 15 reported sequence conflicts, has been established by means of MALDI mass mapping. The identification of mitochondrial proteins participating 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 (PSD) analysis for confident protein identification.