Picomole samples of the linear peptide gramicidin D and cyclic peptide gramicidin S are shown to be impure by the laser-desorption formation of multiple groups of molecular adduct peaks by using Fourier-transform mass spectrometry. Selective excitation of the molecular peaks of the major sample component followed by collisionally activated dissociation provides complete sequence information for the cyclic decapeptide and for 12 of the 15 amino acids of the linear peptide. This instrumentation shows striking advantages in sensitivity, resolution, and mass accuracy in comparison to tandem mass spectrometers used previously.Mass spectrometry (MS) provides information complementary to conventional techniques for the molecular characterization of peptides and other important macromolecules (1-3). For oligopeptides, MS can utilize picomole samples, determine exact molecular weights, identify unusual amino acids or terminal groups (1-4), and detect frameshift errors in Maxam-Gilbert sequencing of the gene encoding an enzyme (5). MS characterization of larger peptides is now possible by using powerful methods for the ionization of nonvolatile molecules, such as fast atom bombardment (FAB) (2, 6-10), laser desorption (LD) (11-14), and particle-induced desorption (15, 16). The latter has recently been used to measure molecular ions of 23,406 ± 140 daltons from porcine trypsin (16). However, sequence information for larger peptides is often limited by the small degree of fragmentation observed (6-8, 11-13, 15, 16) and by misleading fragments arising from impurities; sample purity is also a critical limitation in conventional methods of peptide sequencing. Tandem mass spectrometry (MS/MS) offers a possible solution to both problems (17,25,26,30). In MS/MS the molecular ion species of a mixture component can be separated by MS-I, fragmented by collisionally activated dissociation (CAD) (17) or laser photodissociation (18,19) to produce fragments measured in MS-II indicating the peptide sequence (7, 8, 17-21, 25, 26, 30).However, the few examples in which MS/MS has been applied to larger peptides (ionized by FAB) gave only limited sequence information of poor resolution (peak widths, >3 daltons), sensitivity (nmol samples), and mass accuracy (7,8,17,25,26). This arises because primary ion dissociations are accompanied by translational energy release, causing both broadening and shifting of peaks in magnetic sector instruments (17). Fourier-transform mass spectrometry (FTMS) (22-24) offers a promising alternative for such studies. The measured cyclotron frequency only depends on the magnetic field and ion's mass, not on its translational energy. Further, the masses of nearly all (e.g., m/z 100-16,000, broad-band recording) ions can be measured simultaneously, so that pulsed ionization is feasible; scanning instruments require continuous ionization, at any instant wasting all ions formed except those of the exact mass measured. For modem FTMS instrumentation we have recently demonstrated high (>16,000) mass range and ...