Vacuum UV matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance mass spectrometry (FTMS) has been applied to the direct analysis of crustacean neuronal tissues using in-cell accumulation techniques to improve sensitivity. In an extension of previous work by Li and co-workers (Kutz, K. K.; Schmidt, J. J.; Li, L. Anal. Chem. 2004, 76, 5630-5640), and with a focus on the Maine lobster, Homarus americanus, we report that many peaks appearing in direct tissue spectra from crustaceans result from the metastable decay of aspartate-containing neuropeptides with localized protonation sites. We report on mass spectral characteristics of crustacean neuropeptides under MALDI-FTMS conditions and show how fragments formed by Asp-Xxx cleavages can be used to advantage for the identification of orcokinin peptides, a ubiquitous family of crustacean neuropeptides with a highly conserved N-terminus sequence. We show that predicted fragment ion fingerprints (FIFs) can be used to screen internally calibrated direct tissue spectra to provide high-confidence identification of previously identified orcokinin peptides. We use FIFs, identified based upon characteristic neutral losses, to screen for new members of the orcokinin family. Sustained off-resonance irradiation of y-series fragment ions is used to sequence the variable C-terminus. We apply these techniques to the analysis of CoG tissues from Cancer borealis and Panulirus interruptus and show that orcokinins in P. interruptus were misidentified in a previous MALDI-TOF study.