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oai:figshare.com:article/34021818 2026-09-29T09:25:50Z category_25270 category_24829 category_24748 portal_549 item_type_3 month_year_09_2026

Collagen-alpha-2(VI)-chain-isoform-2C2A Degradome Foundation Atlas Axel Petzold (7076261) Theoretical and computational chemistry not elsewhere classified Ophthalmology and optometry not elsewhere classified Neurosciences not elsewhere classified Ullrich congenital muscular dystrophy 1 Bethlem myopathy 1 peripheral nerve sheath neurovascular adventitia scleral ECM corneal stroma This Figshare repository hosts the Collagen Alpha-2(VI) Chain Isoform 2C2A Degradome Foundation Atlas (Version 1). It is a comprehensive in silico reconstruction of the theoretical peptides that could be generated by proteolytic cleavage of isoform 2C2A of human collagen alpha-2(VI) (COL6A2).The atlas is an open-access computational reference for researchers in proteomics, degradomics, mass spectrometry, extracellular matrix biology, connective tissue research, muscle biology and biomarker discovery. It systematically maps the peptide fragments that could arise from turnover and enzymatic processing of this isoform. This gives an isoform-resolved, degradome-centred view of the peptides that may be generated during extracellular matrix remodeling and tissue-specific proteolysis.<h2 dir="ltr">Biological Context</h2>Collagen alpha-2(VI) is encoded by COL6A2 and is one of the three principal alpha chains of type VI collagen. Type VI collagen is a distinctive extracellular matrix collagen that assembles into beaded microfibrils and mediates interactions between cells and the surrounding matrix.COL6A2 undergoes alternative splicing, which produces isoforms that differ in their C-terminal region. Isoform 2C2A is one of these splice variants. It shares most of its sequence with the canonical isoform (2C2) but has a distinct C-terminal segment. Because proteolysis can generate peptides from any part of a protein, alternative C-terminal sequences can yield fragments that are not present in the canonical degradome. An isoform-specific atlas therefore helps distinguish peptides shared across COL6A2 variants from those that may be unique to isoform 2C2A.COL6A2 is expressed in many connective tissues. It is particularly relevant to skeletal muscle and other tissues where the extracellular matrix helps maintain tissue architecture and cellular function. The ongoing synthesis, assembly, remodeling and proteolytic turnover of type VI collagen can release fragments and peptides that carry information about matrix dynamics beyond what measurements of the intact protein provide.Variants in the genes encoding type VI collagen chains, including COL6A2, are associated with inherited collagen VI-related disorders such as Bethlem myopathy and Ullrich congenital muscular dystrophy. A systematic, isoform-level COL6A2 degradome reference can therefore support work on peptide signatures in muscle and connective-tissue biology.<h3 dir="ltr">Key Features of the Proteomics Dataset</h3>The atlas provides a systematic computational representation of the theoretical peptide space of COL6A2 isoform 2C2A. It includes:<ul><li>Predicted enzymatic and chemical cleavage sites across the isoform 2C2A sequence</li><li>Possible contiguous peptide fragments generated by proteolytic cleavage, including fragments spanning the isoform-specific C-terminal region</li><li>Physicochemical and biochemical characteristics for each fragment</li><li>Sequence-derived properties relevant to peptide characterization and detection by mass spectrometry</li></ul>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 parameters form a feature-rich reference for evaluating peptides derived from isoform 2C2A. They can also help prioritize candidate fragments for downstream proteomic and mass-spectrometric work.<h3 dir="ltr">Applications in Biomarker Discovery and Biomedical Research</h3>The dataset can support a broad range of research applications:<ul><li>Targeted Proteomics: Identifying and prioritizing isoform 2C2A-derived peptides, including isoform-discriminating peptides, for targeted mass-spectrometry assays.</li><li>Isoform-Resolved Proteomics: Distinguishing peptides shared with other COL6A2 isoforms from those that may be specific to isoform 2C2A.</li><li>Biomarker Discovery: Exploring peptide signatures from this isoform that are associated with extracellular matrix turnover and tissue remodeling.</li><li>Discovery Proteomics: Generating candidate peptide lists for untargeted and discovery-based proteomic studies.</li><li>Degradomics: Investigating proteolytic processing of type VI collagen within an isoform-specific degradome framework.</li><li>Clinical Proteomics: Identifying candidate peptide biomarkers associated with extracellular matrix changes in connective tissue and muscle.</li><li>Muscle Biology: Supporting studies of collagen VI turnover and extracellular matrix organization in skeletal muscle.</li><li>Neuromuscular Research: Providing a computational resource for studying COL6A2-derived peptides in collagen VI-related muscle disorders.</li><li>Alternative Splicing Research: Supporting investigation of how COL6A2 splice variation shapes the potential peptide landscape of type VI collagen.</li><li>Connective Tissue Research: Characterizing potential collagen VI fragments generated during extracellular matrix remodeling.</li><li>Fibrosis and Tissue Remodeling: Exploring COL6A2 isoform-derived peptide signatures associated with pathological extracellular matrix changes.</li><li>Computational Biology: Enabling sequence-based degradome profiling, peptide prioritization and comparative analysis across COL6A2 isoforms and other collagens.</li><li>Assay Development: Supporting the selection and characterization of candidate isoform 2C2A peptides for experimental validation.</li></ul><h3 dir="ltr">Data Inclusion and Reproducibility</h3>Version 1 covers the human collagen alpha-2(VI) chain isoform 2C2A reference sequence ([UniProt accession, e.g. P12110-2]). It provides a systematic theoretical representation of this isoform's potential degradome, including contiguous peptide fragments and their calculated physicochemical properties.The dataset represents a theoretical fragment space, not a catalogue of experimentally confirmed peptides. A predicted fragment's presence in the atlas does not establish several things:<ul><li>that the peptide is generated in vivo</li><li>that it remains stable in biological samples</li><li>that a given mass-spectrometric platform can detect it</li><li>that it can be attributed specifically to isoform 2C2A rather than another COL6A2 isoform</li></ul>Experimental proteomics, degradomics and mass-spectrometry studies are needed to establish the generation, stability, abundance, detectability and isoform origin of individual peptides.Future releases may add disease-associated sequence variants, post-translational modifications, experimentally validated cleavage products, tissue-specific degradome profiles and complementary experimental proteomics data. Future releases may also annotate peptides as shared across isoforms or unique to one isoform. These additions will progressively connect the theoretical peptide landscape of isoform 2C2A with experimentally informed models of type VI collagen turnover, splice-variant biology, muscle and connective-tissue biology, and disease-associated matrix remodeling. 2026-09-29T09:25:50Z Dataset Dataset 10.5522/04/34021818.v1 https://figshare.com/articles/dataset/Collagen-alpha-2_VI_-chain-isoform-2C2A_Degradome_Foundation_Atlas/34021818 CC0