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Neuropeptides are signaling molecules of intermediate size that are involved in neurotransmission and endocrine regulation. Complete monitoring of neuropeptides using neuropeptidomics approaches remains an important goal for describing targeted physiological regulation pathways. Considerable effort has been expended, particularly in terms of technique and methodology development, to extend the scope of neuropeptidomics. The capability of peptide characterization has been gradually improved, thus responding to increasing demands for broad detection and determination of various peptides. In this review, we discuss some achievements for the improvement of peptide identification coverage and their application for brain diseases and studying consequences of drug applications.