peptidome

Peptidome refers to the complete set of endogenous peptides present in a biological sample, such as a cell, tissue, organism, or body fluid. These peptides, typically 2 to 50 amino acids in length, arise from proteolytic processing of larger proteins, from alternative translation, or from post-translational maturation of precursor proteins. The peptidome represents signaling, regulatory, and degradation-related peptides that complement the information provided by the proteome and the transcriptome, and it includes both intracellular fragments and extracellular circulating peptides such as hormones and neuropeptides.

Peptidomics is the study of the peptidome, usually by mass spectrometry-based approaches. Sample preparation aims to preserve native peptides and prevent artifactual generation: rapid quenching, low temperature, and the use of protease inhibitors; selective enrichment for low molecular weight species is common. Analytical workflows combine liquid chromatography with tandem mass spectrometry (LC-MS/MS) and may involve bottom-up peptidomics, targeted assays, or de novo sequencing to identify peptides. Data analysis relies on peptide-centric databases and spectral libraries; results are often deposited in general proteomics repositories.

Applications include biomarker discovery, characterization of proteolytic pathways and peptide signaling networks, and studies of neuropeptides and circulating peptide hormones. Peptidomics informs understanding of diseases where proteolysis and signaling are altered, such as cancer, neurodegeneration, and inflammatory disorders, and supports researchers investigating host-pathogen interactions and aging.

Challenges include the wide dynamic range of peptide abundances, instability of short peptides, and post-translational modifications that complicate identification. Sample handling, standardization of workflows, and interpretation of complex peptidome data remain active areas of methodological development. As techniques improve, the peptidome is increasingly integrated with proteomics, proteogenomics, and systems biology to provide a more complete view of protein processing and signaling.