Liquid chromatography (LC) has been used extensively for the separation and isolation of peptides due to its high selectivity and peak capacity. An approach combining microbore LC with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-MS) detection is described to identify peptides in cells and guide the purification of peptides from the marine mollusc Aplysia californica. Direct MALDI-MS of neurons and processes provides molecular mass information for unknown peptides with almost no sample preparation, and LC-MALDI-MS allows the isolation and purification of these peptides from pooled samples, thus enabling new putative neuropeptides to be isolated from complex cellular samples. Both direct MALDI-MS and LC-MALDI-MS are compared in terms of detecting peptides from neuronal samples. Using both approaches, two peaks from Aplysia californica connectives having molecular masses of 5013 and 5021 have been isolated, partially sequenced and identified as novel collagen-like peptides.