Neuropeptides regulate most, if not all, biological processes in the animal kingdom, but only seven have been isolated and sequenced from Drosophila melanogaster. In analogy with the proteomics technology, where all proteins expressed in a cell or tissue are analyzed, the peptidomics approach aims at the simultaneous identification of the whole peptidome of a cell or tissue, i.e. all expressed peptides with their posttranslational modifications. Using nanoscale liquid chromatography combined with tandem mass spectrometry and data base mining, we analyzed the peptidome of the larval Drosophila central nervous system at the amino acid sequence level. We were able to provide biochemical evidence for the presence of 28 neuropeptides using an extract of only 50 larval Drosophila central nervous systems. Eighteen of these peptides are encoded in previously cloned or annotated precursor genes, although not all of them were predicted correctly. Eleven of these peptides were never purified before. Eight other peptides are entirely novel and are encoded in five different, not yet annotated genes. This neuropeptide expression profiling study also opens perspectives for other eukaryotic model systems, for which genome projects are completed or in progress.The most common approach in proteomic studies is to separate and visualize as many proteins as possible of an organism, tissue, or cell, by two-dimensional electrophoresis and to subsequently identify differentially expressed proteins by mass spectrometric techniques. One of the major constraints of this technology is that proteins of a molecular mass lower than 10 kDa are generally not retained and overlooked in most of the proteomic studies. Nevertheless this mass region contains a group of very important proteins, the peptide hormones and neurotransmitters.To date, many neuropeptides have been purified from vertebrate and invertebrate sources. Peptide physiology in the pregenomic era (before the realization of the genome projects) was time-consuming as a peptide present in tissue extracts had to be purified to homogeneity prior to sequencing, synthesis, and functional analysis.Drosophila is an outstanding model system for the molecular genetics and developmental biology in higher eukaryotes. Yet, its molecular endocrinology is poorly documented because only seven neuropeptides have been identified by traditional purification. Recently, a milestone was reached with the completion of the Drosophila genome project (1). Through the BLAST program, one can screen the genome of an organism for candidate-neuropeptides based on sequence homology with known neuropeptides from other organisms. In this way, 31 (neuro)peptide genes were found in Drosophila melanogaster (2-5). These findings, however, give no information on the temporal and spatial expression nor on the physiological relevance of these (neuro)peptide genes. Often, the precursors of biologically active peptides encode several peptides. In general, these peptides can be predicted from the precursor gene as it is assume...