Neuropeptidomics is the analysis of the neuropeptides present in a tissue extract. Most neuropeptidomic studies use mass spectrometry to detect and identify the peptides, which provides information on the precise post-translationally-modified form of each peptide. Quantitative peptidomics uses isotopic labels to compare the levels of peptides in extracts from two different samples. This technique is ideal for examining neuropeptide levels in a variety of systems, and is especially suited for studies of mice lacking peptide-processing enzymes. This review is focused on the neuropeptidomics technique and its application to the analysis of mice with a mutation that inactivates carboxypeptidase E, a critical enzyme in the biosynthesis of many neuroendocrine peptides. Mice without carboxypeptidase E activity are overweight, and a key question is the identification of the peptide or peptides responsible. The quantitative peptidomics approach has provided some insights towards the answer to this question.