The effect of sample extraction and preparation on neuropeptidomic analysis of brain tissue by capillary liquid chromatography with tandem mass spectrometry was investigated. In agreement with previous reports, analysis of peptide extracts of brain tissue from animals sacrificed by microwave irradiation, which fixes tissue, allows identification of neuronally derived peptides whereas similar analysis of tissue from animals sacrificed without fixation does not. A comparison of a physical method for cell lysis (sonication) to physical combined with chemical cell lysis (sonication with detergent treatment) revealed that the latter method increased the number of neuronally derived peptides positively identified by approximately 3-fold, from 16 to 44, for analysis of microwave-fixed rat striatum. Use of synaptosome preparations also allowed detection of neuronally derived peptides (23 positively identified) without a requirement of microwave fixation, suggesting that this method may be a useful alternative for sample preparation. Although numerous peptides were identified in these experiments, several known neuropeptides were not detected including neuropeptide Y and neurotensin. Chemical properties such as hydrophobicity and atypical gas-phase fragmentation were found to account for the inability to detect these peptides. These results suggest that further improvement in sample preparation and automated spectral interpretation are needed to provide better coverage of neuropeptides in mammalian tissues. A total of 39 novel neuronally derived peptides, including some originating from proenkephalin and phosphatidylethanolamine binding protein, were identified in striatum and synaptosome.