The VILIP-1 Degradome Foundation Atlas (Version 1) is an open-access, fully reproducible reference dataset that provides the first comprehensive in silico reconstruction of the proteolytic degradome of Visinin-like protein-1 (VILIP-1), a neuronal calcium-sensor protein encoded by VSNL1. VILIP-1 participates in intracellular calcium signalling and contributes to neuronal survival, synaptic plasticity, and intracellular signalling pathways. Elevated concentrations of VILIP-1 have been reported in neurodegenerative disorders, where the protein has been investigated as a biomarker of neuronal injury and synaptic dysfunction.Proteins undergoing physiological turnover and stress-related modification generate complex populations of proteolytic fragments. The potential repertoire of VILIP-1-derived peptides has not previously been systematically characterized. The VILIP-1 Degradome Foundation Atlas addresses this gap by enumerating the theoretical peptide landscape that can arise from proteolytic and chemical cleavage of the VILIP-1 primary sequence.Each predicted fragment is annotated with a rich panel of physicochemical and biochemical properties relevant to proteomics, biomarker discovery, and computational peptide analysis.Scope and ContentThe dataset comprises every predicted proteolytic fragment derived from the human VILIP-1 primary sequence based on defined cleavage boundaries. The resulting fragment space includes overlapping peptides spanning the entire protein sequence.For each peptide, the dataset provides:Peptide identifier and coordinates (start and stop positions)Amino acid sequenceCalculated mass-to-charge ratio (m/z)Molecular weight (Da)Boman indexNet chargeIsoelectric point (pI)HydrophobicityInstability indexAliphatic indexThese features provide a unified, feature-rich representation suitable for mass-spectrometry analysis, biomarker discovery, and computational proteomics workflows.Methods SummaryThe Degradome Atlas was generated using a reproducible Python workflow:Definition of cleavage sitesExperimentally reported and computationally defined cleavage positions were specified along the full-length VILIP-1 amino-acid sequence.Fragment enumerationAll pairwise subsequences between cleavage boundaries were generated, producing the complete theoretical fragment space of the protein.Peptide property calculationPhysicochemical properties were calculated using the peptides Python library.Structured data exportAll peptide information was exported as structured CSV files.Dataset consolidationOutput files were merged and compressed into a single FAIR-compliant archive (TAR.XZ format) to facilitate efficient distribution and reproducibility.The complete Python workflow is included in the repository to enable transparent re-execution and extension to additional proteins or sequence variants.Data Format and AccessPrimary file:VILIP1_Degradome_Foundation_Atlas_v1.tar.xzContentsCSV tables containing all predicted peptide fragments and calculated propertiesPython scripts used to generate the degradome datasetDocumentation describing the workflow and dataset structureFile Type:ASCII comma-separated values (CSV)Compression:xz -9 -T0 (maximum parallel compression for efficient distribution)CompatibilityThe dataset can be used directly in:Python (pandas, NumPy)RMATLABSASExcel / LibreOfficeIt can also be integrated into proteomics workflows, including:SkylineMaxQuant preprocessingMS/MS spectral library constructioncomputational peptide modelling pipelinesFAIR PrinciplesThis dataset follows FAIR data principles:FindableRich metadata, persistent DOI, and search-optimized dataset description.AccessiblePublicly available through present open-access Figshare repository.InteroperableStandard CSV format and widely used physicochemical descriptors.ReusableFully reproducible Python workflow and transparent data generation pipeline.ApplicationsThe VILIP-1 Degradome Foundation Atlas enables research across several biomedical and computational domains:Biomarker discovery in neurodegenerative diseaseMass-spectrometry assay developmentComputational proteomics and peptide modellingNeo-epitope discovery and immunological studiesProteolytic pathway analysisSystems-level degradomicsThe dataset may also serve as a reference framework for interpreting peptide-level signals detected in cerebrospinal fluid or blood proteomic studies.Versioning and Future WorkThis release represents Version 1 of the VILIP-1 Degradome Foundation Atlas.Future updates will incorporate:additional experimentally validated cleavage sitesdisease-associated sequence variants of VILIP-1experimentally detected peptide fragmentsintegration with other degradome atlases to support systems-level biomarker researchThese developments will progressively refine modelling of VILIP-1 proteolysis in health and neurodegenerative disease.CitationIf you use this dataset, please cite the associated Figshare DOI:10.5522/04/32054535and:Petzold A. Proteolysis-Based Biomarker Repertoires in Protein Degradomics.Journal of Neurochemistry. 2025;169(3):e70023.doi:10.1111/jnc.70023
