Prohormone convertase (PC) 1/3 and 2 are involved in the generation of neuropeptides from their precursors. A quantitative peptidomic approach was used to explore the role PC2 plays in the processing of hypothalamic peptides. In this approach, extracts from mice lacking PC2 activity and from wildtype littermates were labeled with isotopic tags, combined, fractionated on a reverse phase HPLC column, and analyzed by electrospray ionization mass spectrometry. Altogether, 53 neuropeptides or other peptides derived from secretory pathway proteins were identified and sequenced using tandem mass spectrometry. These peptides arise from 21 distinct proteins: proenkephalin, proopiomelanocortin, prodynorphin, protachykinin A and B, procholecystokinin, promelanin-concentrating hormone, proneurotensin, proneuropeptide Y, provasopressin, pronociceptin/orphanin, prothyrotropinreleasing hormone, cocaine-and amphetamine-regulated transcript, chromogranin A and B, secretogranin II, prohormone convertase 1 and 2, propeptidyl-amidating monooxygenase, and proteins designated proSAAS and VGF. Approximately one third of the peptides found in wild-type mice were not detectable in PC2 knock-out mice, and another third were present at levels ranging from 25 to 75% of wild-type levels.Comparison of the cleavage sites suggests that sequences with a Trp, Tyr and/or Pro in the P1¢ or P2¢ position, or a basic residue in the P3 position, are preferentially cleaved by PC2 and not by other enzymes present in the secretory pathway. Keywords: carboxypeptidase E, neuropeptide biosynthesis, peptidase, prohormone convertase, proteomics, protease. Neuropeptides are generated from relatively large precursor molecules through limited proteolysis. The first step of proteolysis usually involves endoproteolytic cleavages at sites containing multiple basic amino acids such as KR, RR or RXXR (Rouille et al. 1995;Steiner 1998;Seidah et al. 1999;Zhou et al. 1999). After this step, peptide intermediates with basic C-terminal residues are further processed by a carboxypeptidase (Fricker 1988). In some cases, the resulting peptides are biologically active after the peptidase cleavages, while in other cases, additional post-translational modifications are required. These modifications include phosphorylation, acetylation, sulfation and C-terminal amidation (Mains et al. 1983).The endoproteolytic cleavages involved in the generation of neuroendocrine peptides are carried out by prohormone convertase 1 (PC1, also referred to as PC3 or PC1/3) and prohormone convertase 2 (PC2), which are members of a calcium-dependent, subtilisin-like serine protease family (Rouille et al. 1995;Seidah et al. 1999). These two enzymes are specifically expressed in neuroendocrine tissues and are enriched in peptide-containing secretory vesicles (Zheng et al. 1994;Rouille et al. 1995;Steiner 1998;Zhou et al. 1999). The enzymatic activities of both PC1/3 and PC2 have been extensively studied using in vitro and cell-line based approaches (Mathis and Lindberg 1992;Breslin et al. 1993...