2026-10-11T06:58:26Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33993784 2026-09-25T11:29:08Z category_25270 category_24829 category_24748 portal_549 item_type_3 month_year_09_2026

Collagen-alpha-1(XVIII)-chain Degradome Foundation Atlas Axel Petzold (7076261) Theoretical and computational chemistry not elsewhere classified Ophthalmology and optometry not elsewhere classified Neurosciences not elsewhere classified retinal pigment epithelium Bruch's membrane Knobloch syndrome cerebral small vessel disease diabetic retinopathy AMD liver fibrosis pial membrane, endothelial cell proliferation This Figshare repository hosts the Collagen Alpha-1(XVIII) Chain Degradome Foundation Atlas (Version 1), a comprehensive in silico reconstruction of the theoretical peptide landscape generated through the proteolytic cleavage of human collagen alpha-1(XVIII) chain (COL18A1).Designed as an open-access reference resource for researchers in proteomics, degradomics, mass spectrometry, extracellular matrix biology, basement membrane research, vascular biology, ophthalmology, and biomarker discovery, this dataset systematically maps the potential fragment landscape of Type XVIII collagen. Rather than treating COL18A1 as a single static structural protein, the atlas adopts a degradome-centred perspective in which extracellular matrix turnover, basement-membrane remodeling, and enzymatic cleavage generate dynamic populations of collagen-derived peptide fragments.Collagen XVIII is a multiplexin collagen and an important component of basement membranes throughout the body. COL18A1 contributes to extracellular matrix organization and tissue architecture and is expressed in basement membranes associated with the vasculature and multiple organs, including the eye, liver, kidney, and nervous system. Importantly, the C-terminal region of collagen XVIII contains endostatin, a biologically active fragment generated by proteolytic processing that has been extensively studied in relation to angiogenesis and vascular biology. Pathogenic variants in COL18A1 cause Knobloch syndrome, a rare disorder associated with ocular and neurological abnormalities. Characterizing the proteolytic fragment landscape of COL18A1 may therefore provide valuable insights into basement-membrane turnover, angiogenesis, vascular remodeling, ocular and neurological biology, tissue injury, and the development of peptide-based biomarkers.<h3 dir="ltr">Key Features of the Proteomics Dataset</h3>Using predicted enzymatic and chemical cleavage sites, the atlas systematically generates and annotates possible COL18A1 peptide fragments. Each fragment is characterized using physicochemical features relevant to mass spectrometry, proteomics, and computational peptide analysis.Mass Spectrometry and Peptide Metrics:<ul><li>Molecular weight</li><li>Mass-to-charge ratio (m/z)</li><li>Net charge</li><li>Isoelectric point (pI)</li></ul>Biochemical and Biophysical Features:<ul><li>Hydrophobicity</li><li>Boman index</li><li>Instability index</li><li>Aliphatic index</li></ul>Together, these annotations provide a feature-rich computational reference for exploring the detectability, physicochemical behaviour, and potential analytical relevance of COL18A1-derived peptides.<h3 dir="ltr">Applications in Biomarker Discovery and Biomedical Research</h3>The Collagen Alpha-1(XVIII) Chain Degradome Foundation Atlas can support a broad range of experimental and computational applications, including:<ul><li>Targeted Proteomics: Identification and prioritization of candidate COL18A1-derived peptides for mass-spectrometry assays.</li><li>Biomarker Discovery: Exploration of collagen-derived peptide candidates associated with basement-membrane remodeling, angiogenesis, vascular biology, ocular disease, neurological disorders, and tissue injury.</li><li>Discovery Proteomics: Interpretation and annotation of COL18A1-derived signals detected in mass-spectrometry datasets and biological fluids.</li><li>Degradomics: Investigation of potential proteolytic processing patterns, extracellular matrix protease activity, and basement-membrane-derived fragment populations.</li><li>Endostatin Research: Exploration of the theoretical peptide landscape surrounding the endostatin-containing C-terminal region of COL18A1 and its potential proteolytic products.</li><li>Clinical Proteomics: Computational exploration of Type XVIII collagen turnover in physiological conditions and disease-associated extracellular matrix remodeling.</li><li>Vascular and Angiogenesis Research: Investigation of COL18A1 processing in vascular extracellular matrix organization, angiogenic signalling, and basement-membrane biology.</li><li>Ocular and Neurological Research: Exploration of COL18A1-derived fragments in tissues and disease contexts relevant to Knobloch syndrome and other disorders affecting basement-membrane integrity.</li><li>Computational Biology: Generation of reference features for peptide-level modelling, degradome analysis, and machine-learning applications.</li><li>Assay Development: Prioritization of candidate COL18A1 peptides for future experimental validation.</li></ul><h3 dir="ltr">Data Inclusion and Reproducibility</h3>The atlas provides a systematic computational representation of the wild-type COL18A1 degradome, including the complete set of theoretically generated contiguous peptide fragments and their calculated physicochemical properties.Importantly, this Foundation Atlas represents a theoretical fragment space rather than a catalogue of experimentally confirmed collagen peptides. Experimental proteomic and mass-spectrometry studies will be required to establish which predicted fragments are generated and detectable under physiological or disease-associated conditions.Future releases will expand the resource through the incorporation of disease-associated COL18A1 variants, alternative protein isoforms, post-translational and extracellular matrix modifications, experimentally validated cleavage products, and complementary experimental proteomics data, progressively extending the atlas from a theoretical reference framework toward an experimentally informed representation of the COL18A1 degradome. 2026-09-25T11:29:08Z Dataset Dataset 10.5522/04/33993784.v1 https://figshare.com/articles/dataset/Collagen-alpha-1_XVIII_-chain_Degradome_Foundation_Atlas/33993784 CC0