Fragmentation of protein and peptide ions generated by matrix-assisted laser desorption has been investigated using a modified LAMMA 1000 reflecting time-of-flight (TOF) mass spectrometer. Whereas fragmentation of covalent bonds prior to ion acceleration (i.e., within several ns after the laser pulse) in general is not observed using the matrix technique, extensive fragmentation on a longer time scale can be studied in our instrument. The high mass resolution (M/ΔM≈1200–1800 for insulin and peptides) permits the investigation of even small mass losses from parent molecular ions (occuring in the first section of the field-free drift region) by measuring flight time differences of daughter ions acquired during passage through a two-stage reflection. The kind and extent of this metastable decay has been found to depend strongly on the substance under investigation. Typical fragmentations are loss of ammonia and parts of the amino acid side-chains. The large abundances of peaks due to such metastable fragmentation, observed for most of the peptides and proteins investigated, may, at least in part, explain peak broadening (and, hence, poor mass resolution) typical in matrix-assisted laser-desorption TOF mass spectra.