Abstract: ECD (Electron Capture Dissociation) FTMS (Fourier-Transform Mass Spectrometry) induced fragmentation is employed to generate sequence information for a protein enzymatic digest. The digest is initially separated by liquid chromatography, e.g., reversed phase &mgr;HPLC, and then ionized “on-line”. The ions thus formed may be accumulated in the interface hexapole prior to injection and trapping in the FTMS cell. Typically, no parent ion isolation is performed. The trapped ions are subjected to a pulse of electrons to induce fragmentation. Broad band spectra are acquired continuously to produce a three-dimensional LC/MS data set. The spectra are dominated by c and to a lesser degree z ions, which provide nearly complete sequence coverage. External calibration provides good mass accuracy and resolution, typical of FTMS. Thus, LC/ECD-FTMS is shown to be a highly informative method for the analysis of enzymatic protein digests.