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pmid:33816558
In vivo N-Terminomics Highlights Novel Functions of ADAMTS2 and ADAMTS14 in Skin Collagen Matrix Building.
Cédric Leduc · Laura Dupont · Loïc Joannes · Christine Monseur · Dominique Baiwir · Gabriel Mazzucchelli · Christophe Deroanne · Alain Colige · Mourad Bekhouche
Frontiers in molecular biosciences · 2021 doi:10.3389/fmolb.2021.643178
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Complete file
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Previous work using N-terminomic approach (N-TAILS) in vitro led to the identification of new substrates, including some molecules involved in TGF-β signaling. Here, N-TAILS was used to investigate the substrates of these two enzymes in vivo, by comparing the N-terminomes of the skin of wild type mice, mice deficient in ADAMTS2, in ADAMTS14 and in both ADAMTS2 and ADAMTS14. This study identified 68 potential extracellular and cell surface proteins, with the majority of them being cleaved by both enzymes. These analyses comfort their role in collagen matrix organization and suggest their implication in inflammatory processes. Regarding fibrillar collagen, this study demonstrates that both ADAMTS2 and ADAMTS14 are involved in the processing of the aminopropeptide of alpha1 and alpha2 type V collagen. It also revealed the existence of several cleavage sites in the Col1 domain and in the C-propeptide of type I collagens. In addition to collagens and other extracellular proteins, two major components of the cell cytoskeleton, actin and vimentin, were also identified as potential substrates. The latter data were confirmed in vitro using purified enzymes and could potentially indicate other functions for ADAMTS2 and 14. This original investigation of mouse skin degradomes by N-terminomic highlights the essential role of ADAMTS2 and ADAMTS14 in collagen matrix synthesis and turnover, and gives clues to better understand their functions in skin pathophysiology. Data are available via ProteomeXchange with identifier PXD022179.", "claims": [{"id": "claim-method", "statement": "Then, Clipper software was used to determine the upper and lower cutoffs corresponding to 3-sigma calculated from the normal distribution of the log2(P:C ratio) from natural mature N termini.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33816558", "locator": "sections[6] \"Proteomic Data Analysis\" paragraph 3", "quote": "Then, Clipper software was used to determine the upper and lower cutoffs corresponding to 3-sigma calculated from the normal distribution of the log2(P:C ratio) from natural mature N termini."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33816558", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33816558", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmolb.2021.643178", "sha256": "sha256:09cb11e316a5393d28828f1e523a61b9b6fb047c18ed6c254c4a028181a419f2", "bytes": 56092, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmolb.2021.643178", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8017238", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:33816558:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9bcf344e4960feb45300a974d1a8ec70288a0155cef936bb52c5d78ad4e09e8b", "bytes": 4253, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T1", "version": null, "note": "Potential extracellular substrates specific or common of ADAMTS2 and/or ADAMTS14.", "structure": {"pmcid": "PMC8017238", "section_index": 13, "section_title": "N-Terminomic Analysis of ADAMTS2 and ADAMTS14 Skin Degradome", "row_count": 35, "column_count": 8}, "table": {"label": "TABLE 1", "caption": "Potential extracellular substrates specific or common of ADAMTS2 and/or ADAMTS14.", "rows": [["Name", "TS2", "TS14", "TS2TS14", "Name", "TS2", "TS14", "TS2TS14"], ["Inter alpha-trypsin inhibitor", "1.2 ± 0.7", "1.9 ± 0.7", "1.6 ± 0.5", "Galectin-1", "1.3 ± 0.3", "1.9 ± 0.4", "2.1 ± 0.4"], ["AE-binding protein 1", "0.7 ± 0.2", "2.0 ± 0.5", "1.2 ± 0.3", "Galectin-7", "2.0 ± 0.6", "2.8 ± 0.8", "4.8 ± 1.4"], ["Alpha-2-HS-glycoprotein", "0.7 ± 0.3", "2.2 ± 1.3", "0.9 ± 0.3", "Gc-globulin", "1.7 ± 0.8", "4.1 ± 2.0", "6.0 ± 3.7"], ["Alpha-2-macroglobulin", "1.7 ± 1.0", "2.0 ± 0.6", "2.2 ± 0.6", "Gelsolin", "2.6 ± 0.7", "2.4 ± 0.9", "5.0 ± 1.7"], ["Annexin-8", "6.4 ± 2.2", "5.5 ± 1.9", "15.0 ± nd a", "H2-Q9", "1.9 ± 1.3", "2.7 ± 1.1", "2.9 ± 1.1"], ["Apolipoprotein A-I", "2.7 ± 1.8", "3.3 ± 1.9", "4.5 ± 1.8", "Hemopexin", "1.0 ± 0.4", "1.9 ± 0.5", "1.5 ± 0.5"], ["Apolipoprotein H", "1.6 ± 0.8", "2.6 ± 1.2", "2.3 ± 0.8", "Ig gamma-2B", "1.8 ± 0.5", "2.3 ± 0.8", "3.5 ± 1.2"], ["Beta-globin", "2.2 ± 0.6", "2.9 ± 1.1", "6.7 ± 3.3", "Ig gamma-3", "1.1 ± 0.4", "1.9 ± 0.4", "1.8 ± 0.4"], ["Biglycan", "2.8 ± 2.4", "3.0 ± 1.6", "3.6 ± 1.8", "Ig kappa chain V-V", "1.2 ± 0.8", "5.1 ± 2.7", "2.9 ± 1.1"], ["Carboxypeptidase A3", "1.6 ± 0.4", "2.1 ± 0.5", "3.2 ± 1.1", "Kallikrein j", "2.0 ± 0.8", "2.4 ± 0.6", "5.1 ± 0.6"], ["Cathepsin B heavy chain", "1.3 ± 0.6", "1.9 ± 0.6", "1.6 ± 0.3", "Kininogen-1", "2.2 ± 0.5", "2.9 ± 0.6", "5.5 ± 0.2"], ["Cathepsin H", "1.2 ± 0.6", "2.4 ± 0.8", "2.0 ± 0.6", "Lumican", "1.6 ± 0.7", "2.6 ± 1.3", "2.3 ± 0.4"], ["Cathepsin S", "1.0 ± 0.5", "2.2 ± 0.7", "1.5 ± 0.4", "Mast cell protease 4", "1.5 ± 0.2", "1.7 ± 0.2", "2.4 ± 0.5"], ["Caveolin-1", "2.0 ± 0.8", "3.1 ± 1.4", "3.1 ± 0.0", "MIF", "1.1 ± 0.6", "2.7 ± 1.1", "1.8 ± 0.5"], ["Cavin-1", "2.1 ± 0.4", "3.5 ± 0.9", "8.7 ± 0.4", "Myelin protein zero", "1.6 ± 0.7", "2.1 ± 1.1", "1.7 ± 0.4"], ["Coagulation factor XIIIa", "2.5 ± 1.0", "3.8 ± 1.5", "7.8 ± nd a", "Osteoglycin", "2.3 ± 0.7", "2.3 ± 0.9", "4.5 ± 1.6"], ["Collagen alpha-1(I) chain", "4.2 ± 0.5", "1.7 ± 0.2", "6.8 ± 1.0", "p24 gamma-1", "2.1 ± 1.1", "3.3 ± 1.7", "1.4 ± 1.0"], ["Collagen alpha-1(III) chain", "3.7 ± 2.2", "2.8 ± 1.3", "5.8 ± 2.7", "p35/Annexin A1", "2.7 ± 1.2", "2.7 ± 0.9", "7.4 ± 3.7"], ["Collagen alpha-1(IV) chain", "1.6 ± 0.6", "1.8 ± 0.6", "2.2 ± 0.4", "p36/Annexin A2", "2.7 ± 1.2", "2.7 ± 0.9", "7.4 ± 3.7"], ["Collagen alpha-1(V) chain", "3.9 ± 1.7", "4.1 ± 1.6", "9.3 ± 0.8", "PCPE-1", "2.2 ± 0.4", "1.9 ± 0.4", "3.6 ± 0.5"], ["Collagen alpha-1(VI) chain", "2.2 ± 0.8", "1.9 ± 0.6", "3.4 ± 0.9", "PDI A6", "1.8 ± 0.7", "2.1 ± 0.7", "2.9 ± 0.9"], ["Collagen alpha-1 (XIV) chain", "3.6 ± 0.7", "2.3 ± 0.5", "8.2 ± 2.5", "Periostin", "1.0 ± 0.5", "2.2 ± 0.8", "1.3 ± 0.4"], ["Collagen alpha-2(I) chain", "3.1 ± 0.7", "1.6 ± 0.2", "4.6 ± 0.6", "Proapolipoprotein A-II", "3.5 ± 2.5", "4.9 ± 3.2", "11.9 ± 7.9"], ["Collagen alpha-2(V) chain", "1.8 ± 0.3", "1.7 ± 0.3", "2.8 ± 0.3", "Prolargin", "2.9 ± 0.9", "2.6 ± 0.8", "5.8 ± 1.3"], ["Collagen alpha-2(VI) chain", "2.5 ± 0.7", "2.2 ± 0.6", "4.1 ± 0.0", "Protein unc-80 homolog", "1.8 ± 0.6", "2.0 ± 0.2", "3.5 ± 1.4"], ["Collagen alpha-3(VI) chain", "4.7 ± 1.3", "2.1 ± 0.6", "8.0 ± 1.2", "Serpin A1c", "1.1 ± 0.3", "2.4 ± 1.0", "2.1 ± 0.5"], ["Complement C3", "1.8 ± 1.4", "4.3 ± 3.4", "2.3 ± 0.8", "Serpin A1d", "0.8 ± 0.5", "2.8 ± 1.3", "1.0 ± 0.4"], ["Complement C4-B", "0.3 ± 0.1", "2.7 ± 1.0", "0.6 ± 0.2", "Serpin B6", "4.7 ± 2.5", "3.9 ± 2.4", "8.0 ± 1.9"], ["Complement factor B", "0.9 ± 0.2", "2.0 ± 0.4", "1.8 ± 0.5", "Protein serpinb6e", "1.3 ± 0.3", "2.3 ± 0.6", "2.5 ± 0.1"], ["Complement factor H", "1.0 ± 0.3", "1.8 ± 0.5", "1.7 ± 0.6", "Serum albumin", "3.2 ± 1.7", "4.2 ± 2.4", "12.6 ± 9.7"], ["Corneodesmosin", "1.5 ± 0.4", "1.7 ± 0.4", "2.2 ± 0.4", "Siderophilin", "2.2 ± 0.7", "2.8 ± 1.1", "5.2 ± 2.5"], ["Cystatin-3", "2.4 ± 0.6", "2.7 ± 0.8", "7.0 ± 3.7", "Stromelysin-1/MMP3", "0.4 ± 0.1", "1.5 ± 0.3", "0.5 ± 0.1"], ["Dermatopontin", "2.0 ± 0.4", "1.6 ± 0.2", "3.1 ± 0.6", "Susd 4", "2.3 ± 0.7", "2.4 ± 1.1", "3.9 ± 1.1"], ["Dermokine", "1.1 ± 0.3", "1.4 ± 0.3", "1.4 ± 0.2", "Transcobalamin II", "0.8 ± 0.5", "2.2 ± 1.1", "0.8 ± 0.2"]], "row_count": 35, "column_count": 8, "numeric_cells": 238, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33816558:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0ce6673d11fba03fb85ac3f07cd39487986e2d4e013d37cc82098945d307b135", "bytes": 5385, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T2", "version": null, "note": "Type I collagen processing in mouse skin.", "structure": {"pmcid": "PMC8017238", "section_index": 15, "section_title": "Cleavage of the Aminopropeptide of Fibrillar Collagens", "row_count": 43, "column_count": 8}, "table": {"label": "TABLE 2", "caption": "Type I collagen processing in mouse skin.", "rows": [["Collagen α1(I) chain", "Collagen α2(I) chain"], ["Peptide Sequence", "TS2", "TS14", "TS2TS14", "Peptide Sequence", "TS2", "TS14", "TS2TS14"], ["NC2 (A150-P167)", "NC2 (A75-P96)"], ["NFAS(151).(152)QMSYGYDEKSAGVSVPGPMGPSGPR", "4.2 ± 0.5", "1.7 ± 0.2", "6.8 ± 1.0", "NFAA(85).(86)QYSDKGVSSGPGPMGLMGPR", "3.1 ± 0.7", "1.6 ± 0.2", "4.6 ± 0.6"], ["FASQ(152).(153)MSYGYDEKSAGVSVPGPMGPSGPR", "2.0 ± 0.3", "1.5 ± 0.2", "2.9 ± 0.4", "FAAQ(86).(87)YSDKGVSSGPGPMGLMGPR", "2.0 ± 0.3", "2.0 ± 0.3", "1.5 ± 0.2"], ["QMSY(155).(156)GYDEKSAGVSVPGPMGPSGPR", "2.4 ± 1.0", "1.6 ± 0.3", "3.3 ± 1.1", "YSDK(90).(91)GVSSGPGPMGLMGPR", "2.9 ± 0.4", "1.4 ± 0.2", "2.9 ± 0.6"], ["SYGY(157).(158)DEKSAGVSVPGPMGPSGPR", "3.0 ± 1.0", "1.8 ± 0.3", "5.2 ± 2.0", "SDKG(91).(92)VSSGPGPMGLMGPR", "1.9 ± 0.3", "1.4 ± 0.2", "2.6 ± 0.3"], ["DEKS(161).(162)AGVSVPGPMGPSGPR", "2.0 ± 0.3", "1.5 ± 0.2", "2.9 ± 0.5", "DKGV(92).(93)SSGPGPMGLMGPR", "1.9 ± 0.2", "1.5 ± 0.1", "2.8 ± 0.1"], ["EKSA (162).(163)GVSVPGPMGPSGPR", "1.9 ± 0.3", "1.4 ± 0.1", "2.6 ± 0.4", "Triple helix (G97-G1113)"], ["KSAG(163).(164)VSVPGPMGPSGPR", "3.7 ± 0.3", "1.4 ± 0.1", "5.1 ± 0.2", "SSGP(96).(97)GPMGLMGPR", "1.9 ± 0.3", "1.5 ± 0.2", "2.7 ± 0.5"], ["Triple helix (<I>G168-P1181</I>)", "GPGP(98).(99)MGLMGPR", "2.5 ± 0.8", "1.8 ± 0.5", "3.9 ± 1.6"], ["VSVP(167).(168)GPMGPSGPR", "1.8 ± 0.5", "1.6 ± 0.4", "2.5 ± 0.6", "RGIP(336).(337)GPAGAAGATGAR", "2.5 ± 0.7", "1.7 ± 0.4", "3.6 ± 1.0"], ["VPGP(169).(170)MGPSGPR", "1.8 ± 0.5", "1.5 ± 0.4", "2.6 ± 1.0", "RPGP(485).(486)IGPAGPR", "2.4 ± 0.7", "1.6 ± 0.4", "3.5 ± 1.3"], ["TGPP(332).(333)GFPGAVGAKGEAGPQGAR", "2.1 ± 0.6", "1.7 ± 0.3", "3.5 ± 1.1", "RGTP(600).(601)GESGAAGPSGPIGSR", "2.1 ± 0.6", "1.6 ± 0.3", "3.2 ± 1.1"], ["PPGF(334).(335)PGAVGAKGEAGPQGAR", "2.3 ± 0.8", "1.7 ± 0.5", "3.5 ± 1.7", "GESG(604).(605)AAGPSGPIGSR", "2.0 ± 0.2", "1.3 ± 0.1", "2.5 ± 0.4"], ["PGFP(335).(336)GAVGAKGEAGPQGAR", "2.4 ± 0.8", "1.9 ± 0.5", "4.0 ± 1.3", "ESGA(605).(606)AGPSGPIGSR", "2.0 ± 0.4", "1.4 ± 0.2", "2.7 ± 0.5"], ["RGFP(485).(486)GADGVAGPKGPSGER", "2.6 ± 1.0", "1.7 ± 0.4", "3.8 ± 1.5", "VGAP (636).(637)GSAGASGPGGLPGER", "2.3 ± 0.8", "1.7 ± 0.4", "3.5 ± 1.2"], ["GFPG(486).(487)ADGVAGPKGPSGER", "1.8 ± 0.3", "1.4 ± 0.2", "2.3 ± 0.2", "SGDR(699).(700)GEAGAAGPSGPAGPR", "1.9 ± 0.4", "1.6 ± 0.3", "3.0 ± 0.7"], ["AGAQ(608).(609)GAPGPAGPAGER", "2.2 ± 0.4", "1.6 ± 0.3", "3.1 ± 0.3", "GDRG(700).(701)EAGAAGPSGPAGPR", "1.9 ± 0.3", "1.5 ± 0.2", "2.8 ± 0.3"], ["PGPI(842).(843)GNVGAPGPKGPR", "2.4 ± 0.3", "1.9 ± 0.3", "4.3 ± 0.2", "DRGE(701).(702)AGAAGPSGPAGPR", "2.4 ± 0.6", "1.7 ± 0.4", "3.8 ± 1.1"], ["PPGP(889).(890)VGKEGGKGPR", "2.4 ± 0.6", "1.4 ± 0.3", "3.1 ± 0.8", "GEAG(703).(704)AAGPSGPAGPR", "2.0 ± 0.2", "1.3 ± 0.1", "2.5 ± 0.4"], ["AGSP(935).(936)GTPGPQGIAGQR", "2.2 ± 0.6", "1.6 ± 0.3", "3.1 ± 1.0", "EAGA(704).(705)AGPSGPAGPR", "2.1 ± 0.4", "1.5 ± 0.2", "3.0 ± 0.7"], ["PGTP(938).(939)GPQGIAGQR", "2.6 ± 0.8", "1.6 ± 0.4", "3.8 ± 1.3", "AGAP(969).(970)GPHGSVGPAGKHGNR", "2.2 ± 0.5", "1.6 ± 0.3", "3.4 ± 0.7"], ["KNGD(1,054).(1,055)RGETGPAGPAGPIGPAGAR", "2.1 ± 0.5", "2.0 ± 0.4", "3.6 ± 0.1", "RGEP(987).(988)GPAGSVGPVGAVGPR", "2.5 ± 0.8", "1.6 ± 0.4", "3.7 ± 1.4"], ["NGDR(1,055).(1,056)GETGPAGPAGPIGPAGAR", "2.0 ± 0.4", "1.4 ± 0.2", "2.6 ± 0.5", "EPGP(989).(990)AGSVGPVGAVGPR", "2.2 ± 0.6", "1.5 ± 0.3", "3.2 ± 1.1"], ["RGET (1,058).(1,059)GPAGPAGPIGPAGAR", "1.7 ± 0.2", "1.2 ± 0.1", "2.1 ± 0.1", "PGPA(990).(991)GSVGPVGAVGPR", "1.9 ± 0.2", "1.3 ± 0.1", "2.4 ± 0.4"], ["ETGP(1,060).(1,061)AGPAGPIGPAGAR", "2.4 ± 0.7", "1.6 ± 0.4", "3.5 ± 1.1", "AGSV(993).(994)GPVGAVGPR", "2.3 ± 0.5", "1.5 ± 0.2", "3.3 ± 0.9"], ["PAGP(1,063).(1,064)AGPIGPAGAR", "2.6 ± 0.8", "1.5 ± 0.4", "3.7 ± 1.5", "SVGP(995).(996)VGAVGPR", "1.7 ± 0.2", "1.6 ± 0.2", "2.6 ± 0.3"], ["NC1 (S1182-V1453)", "LKGY(1,031).(1,032)SGLQGLPGLAGLHGDQGAPGPVGPAGPR", "2.2 ± 0.6", "1.9 ± 0.5", "3.6 ± 1.1"], ["GYDF(1,187).(1,188)SFLPQPPQEKSQDGGR", "4.4 ± 0.4", "9.5 ± 3.6", "24.3 ± 7.6", "YSGL(1,034).(1,035)QGLPGLAGLHGDQGAPGPVGPAGPR", "2.6 ± 1.2", "1.7 ± 0.5", "3.1 ± 1.0"], ["DTTL(1,224).(1,225)KSLSQQIENIR", "2.5 ± 0.9", "2.0 ± 0.9", "3.4 ± 0.8", "GLPG (1,039).(1,040)LAGLHGDQGAPGPVGPAGPR", "2.9 ± 0.6", "1.9 ± 0.5", "5.6 ± 2.4"], ["LKSL(1,227).(1,228)SQQIENIR", "2.3 ± 0.6", "1.7 ± 0.5", "3.2 ± 0.8", "LPGL(1,040).(1,041)AGLHGDQGAPGPVGPAGPR", "2.3 ± 0.4", "1.3 ± 0.2", "2.8 ± 0.3"], ["", "", "", "", "PGLA(1,041).(1,042)GLHGDQGAPGPVGPAGPR", "2.8 ± 1.2", "2.5 ± 1.2", "6.1 ± 2.9"], ["", "", "", "", "LAGL(1,043).(1,044)HGDQGAPGPVGPAGPR", "2.0 ± 0.3", "1.6 ± 0.2", "2.9 ± 0.5"], ["", "", "", "", "GLHG(1,045).(1,046)DQGAPGPVGPAGPR", "1.5 ± 0.4", "1.8 ± 0.2", "2.7 ± 0.9"], ["", "", "", "", "LHGD(1,046).(1,047)QGAPGPVGPAGPR", "2.2 ± 0.3", "1.5 ± 0.2", "3.2 ± 0.1"], ["", "", "", "", "HGDQ(1,047).(1,048)GAPGPVGPAGPR", "1.8 ± 0.2", "1.3 ± 0.1", "2.4 ± 0.4"], ["", "", "", "", "GDQG(1,048).(1,049)APGPVGPAGPR", "2.0 ± 0.2", "1.4 ± 0.2", "2.7 ± 0.5"], ["", "", "", "", "RSGQ(1,076).(1,077)PGPVGPAGVR", "2.2 ± 0.3", "1.5 ± 0.2", "3.2 ± 0.1"], ["", "", "", "", "NC1 (Y1114-K1372)"], ["", "", "", "", "DATL(1,145).(1,146)KSLNNQIETLLTPEGSR", "3.9 ± 3.4", "6.0 ± 5.6", "3.2 ± 1.0"], ["", "", "", "", "LKSL(1,148).(1,149)NNQIETLLTPEGSR", "1.6 ± 0.4", "2.0 ± 0.6", "2.7 ± 0.8"], ["", "", "", "", "RLPF(1,347).(1,348)LDIAPLDIGGADQEFR", "3.0 ± 0.7", "2.0 ± 0.6", "5.3 ± 1.2"]], "row_count": 43, "column_count": 8, "numeric_cells": 272, "header_rows": 2, "locator": "section[15]/table-wrap[1]#T2"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "3-sigma cutoff from the normal distribution of natural N-termini, using the Protease/Control (P/C) ratio", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Then, Clipper software was used to determine the upper and lower cutoffs corresponding to 3-sigma calculated from the normal distribution of the log2(P:C ratio) from natural mature N termini."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (3-sigma cutoff from the normal distribution of natural N-termini, using the Protease/Control (P/C) ratio), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": ["PXD022179 and 10.6019/PXD022179"], "resolved_accessions": [], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article."], "basis": "The paper names PXD022179 and 10.6019/PXD022179, but the accession does not resolve in the repository (no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33816558", "asset:table:pmid:33816558:1", "asset:table:pmid:33816558:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:47Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 42916, "completion_tokens": 1325, "cached_tokens": 792}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33816558", "type": "paper", "label": "pmid:33816558"}, {"id": "source:pmid:33816558", "type": "manuscript", "label": "PMID 33816558 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33816558", "type": "paper", "label": "pmid:33816558"}, {"id": "source:pmid:33816558", "type": "manuscript", "label": "PMID 33816558 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33816558", "type": "extraction", "used": ["source:pmid:33816558"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33816558", "parent_hash": "sha256:98a076f78b96c7785ae5102608ce64db2d5c0e751e13fc1710737aeeff7892f5", "fork_of": null, "generation": 5}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["In vivo N-Terminomics Highlights Novel Functions of", "estigate the substrates of these two enzymes in vivo, by comparing the N-terminomes of the skin o", "AMTS2 and 14. 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