PepShop

PepShop combines database and bioinformatic and proteomic tools to facilitate annotation and identification of neuropeptides and prohormones across multiple species. Neuropeptides are involved in a wide variety of biological processes including memory, learning, growth, development and metabolism, and disorders such as depression, Parkinson’s disease, and eating and sleeping disorders. Neuropeptides are small peptides (typically less than 50 amino acids) that are derived by cleavage of large prohormone proteins that lack the signal peptide found in the DNA/RNA sequence. The cleavage is considered due to the family of prohormone or proprotein convertases noteably furin, PC1 and PC2 that cleavage at basic amino acids sites (lysine and arginine). After cleavage, C-terminal basic amino acids are removed by carboxypeptidases. The biological active peptides or neuropeptides typically contain post-translational modifications such as amidation, pyroglutamination, acetylation and sulfation.

Discovery of neuropeptides is complex due to cleavage and other post-translational modifications and the dynamic range. NeuroPred was developed to provide various cleavage prediction using models trained on mollusk, insect and mammalian species. Mass spectrometry (MS) is a well-established technology that is well-suited to identify neuropeptides and other peptides derived from prohormones. In order facilitate peptide identification in MS experiments, NeuroPred provided sequence and mass of possible peptides including user-selected PTMs. This permits users to find specific interesting MS peaks that are likely to be neuropeptide but cannot identify if a specific neuropeptide is present or matches known peptide derived from a cleaved prohormone.

PepShop overcomes previous limitations by providing an integrated framework of database and bioinformatics. Sequence and mass spectra data from SwePep has been integrated with cleavage prediction data used in model training from NeuroPred. Additional annotation and sequence information has been extracted from UniProt and NCBI databases. Bioinformatics tools for single sequence search (BLAST) and multiple sequence alignment tool (MUSCLE) have been included. Annotation of single tandem mass spectrometry spectrum has been enabled using the X! Tandem, OMSSA and Crux search engines.

Species

PepShop supports the identification based on the availability of sequenced genomes. Currently only human, mouse, rat, cow, pig, dog and rhesus monkey information is available. Existing NeuroPred information from Mollusk (Aplysia californica), insect (Drosophila melanogaster, Apis mellifera, and Tribolium castaneum), avian (Gallus gallus and Taeniopygia guttata), and planaria (Schmidtea mediterranea) will be added.

Similar to the NeuroPred recommendation, We recommend the prediction model selected be one that is derived from the species most closely related to the one you are studying. Please contact us to add other species with genome sequences.