Herein we report the first application of Fourier transform mass spectrometry for the analysis of neuropeptides directly from neuronal tissues. Sample preparation protocols and instrumentation conditions are developed to allow in situ neuropeptide analysis of the neuroendocrine organs freshly isolated from a marine organism Cancer borealis. The utility of a previously developed in-cell accumulation (ICA) technique is extended for peptide analysis in complex tissue samples. With the ICA procedure, ion signals from multiple laser shots are accumulated in the analyzer cell prior to detection. This procedure allows the accumulation of ion signals without accumulating noise, thus improving the signal-to-noise ratio and enhancing the sensitivity for the detection of trace-level endogenous neuropeptides. De novo sequencing of peptides directly from tissue samples becomes more feasible through this improvement. Additionally, an integrated pulse sequence is constructed to cover a wide mass range from m/z 215 to 9000 by centering quadrupole collection of ions at different masses for successive laser shots. Finally, improved mass measurement accuracy (2 ppm) for tissue peptide analysis is achieved using ICA by incorporating calibrants on a separate spot from the sample of interest without premixing calibration standards with the analytes.