2026-10-14T07:24:24Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33972067 2026-09-23T09:13:31Z category_25270 category_24829 category_24748 portal_549 item_type_3 month_year_09_2026

Collagen-alpha-1(XII)-chain Degradome Foundation Atlas Axel Petzold (7076261) Theoretical and computational chemistry not elsewhere classified Ophthalmology and optometry not elsewhere classified Neurosciences not elsewhere classified collagen FACIT Ehlers-Danlos-like myopathic syndrome hypermobility muscular dystrophy This Figshare repository hosts the Collagen Alpha-1(XII) 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(XII) chain (COL12A1).Designed as an open-access reference resource for researchers in proteomics, degradomics, mass spectrometry, extracellular matrix biology, connective-tissue research, musculoskeletal biology, and biomarker discovery, this dataset systematically maps the potential fragment landscape of Type XII collagen. Rather than treating COL12A1 as a single static structural protein, the atlas adopts a degradome-centred perspective in which extracellular matrix turnover, tissue remodeling, and enzymatic cleavage generate dynamic populations of collagen-derived peptide fragments.Collagen XII is a FACIT (fibril-associated collagen with interrupted triple helices) that associates with fibrillar collagens and contributes to the organization and mechanical properties of the extracellular matrix. It is particularly associated with connective tissues, including tendons, ligaments, skin, skeletal muscle, and other mechanically stressed tissues, where it participates in interactions between collagen fibrils and surrounding matrix components. COL12A1 has also been implicated in extracellular matrix organization, tissue development, and musculoskeletal function, with pathogenic variants associated with congenital connective-tissue and myopathic phenotypes. Characterizing the proteolytic fragment landscape of COL12A1 may therefore provide valuable insights into collagen fibril organization, matrix remodeling, tendon and muscle biology, connective-tissue pathology, 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 COL12A1 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 COL12A1-derived peptides.<h3 dir="ltr">Applications in Biomarker Discovery and Biomedical Research</h3>The Collagen Alpha-1(XII) Chain Degradome Foundation Atlas can support a broad range of experimental and computational applications, including:<ul><li>Targeted Proteomics: Identification and prioritization of candidate COL12A1-derived peptides for mass-spectrometry assays.</li><li>Biomarker Discovery: Exploration of collagen-derived peptide candidates associated with extracellular matrix remodeling, tendon and ligament injury, muscle pathology, connective-tissue disorders, fibrosis, and tissue repair.</li><li>Discovery Proteomics: Interpretation and annotation of COL12A1-derived signals detected in mass-spectrometry datasets and biological fluids.</li><li>Degradomics: Investigation of potential proteolytic processing patterns, extracellular matrix protease activity, collagen fibril-associated cleavage events, and fragment populations.</li><li>Clinical Proteomics: Computational exploration of Type XII collagen turnover in physiological conditions and disease-associated extracellular matrix remodeling.</li><li>Musculoskeletal Research: Investigation of COL12A1 processing in tendon, ligament, skeletal muscle, skin, and other mechanically active connective tissues.</li><li>Connective-Tissue Research: Exploration of COL12A1-derived fragments in disorders affecting collagen organization, extracellular matrix integrity, and tissue development.</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 COL12A1 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 COL12A1 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 COL12A1 variants, 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 COL12A1 degradome. 2026-09-23T09:13:31Z Dataset Dataset 10.5522/04/33972067.v1 https://figshare.com/articles/dataset/Collagen-alpha-1_XII_-chain_Degradome_Foundation_Atlas/33972067 CC0