{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:26909372", "kind": "science-record", "revision": 8, "content_hash": "sha256:f717ce48b8eb58ec058b8715e610da7f30e98dbfe60504dcd31f52ed0035864a", "created_at": "2026-11-01T15:40:16Z", "updated_at": "2026-11-01T22:42:34Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Supporting data for the MS identification of distinct transferrin glycopeptide glycoforms and citrullinated peptides associated with inflammation or autoimmunity.", "doi": "10.1016/j.dib.2015.12.045", "pmid": "26909372", "authors": ["A Rosal-Vela", "A Barroso", "E Giménez", "S García-Rodríguez", "V Longobardo", "J Postigo", "M Iglesias", "A Lario", "J Merino", "R Merino", "M Zubiaur", "V Sanz-Nebot", "J Sancho"], "journal": "Data in brief", "year": 2016, "abstract": "This data article presents the results of all the statistical analyses applied to the relative intensities of the detected 2D-DiGE protein spots for each of the 3 performed DiGE experiments. The data reveals specific subsets of protein spots with significant differences between WT and CD38-deficient mice with either Collagen-induced arthritis (CIA), or with chronic inflammation induced by CFA, or under steady-state conditions. This article also shows the MS data analyses that allowed the identification of the protein species which serve to discriminate the different experimental groups used in this study. Moreover, the article presents MS data on the citrullinated peptides linked to specific protein species that were generated in CIA(+) or CFA-treated mice. Lastly, this data article provides MS data on the efficiency of the analyses of the transferrin (Tf) glycopeptide glycosylation pattern in spleen and serum from CIA(+) mice and normal controls. The data supplied in this work is related to the research article entitled \"identification of multiple transferrin species in spleen and serum from mice with collagen-induced arthritis which may reflect changes in transferrin glycosylation associated with disease activity: the role of CD38\" [1]. All mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with identifiers PRIDE: PXD002644, PRIDE: PXD002643, PRIDE: PXD003183 and PRIDE: PXD003163.", "claims": [{"id": "claim-method", "statement": "Spleen protein species that differ in abundance by 2-ANOVA-Arthritis test in Col II-immunized CIA+ versus CIA− mice.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26909372", "locator": "sections[5] \"Data\" paragraph 8", "quote": "Spleen protein species that differ in abundance by 2-ANOVA-Arthritis test in Col II-immunized CIA+ versus CIA− mice."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is within this article. Data also available at the ProteomeXchange Consortium via the PRIDE partner repository, PRIDE: PXD002644, PRIDE: PXD002643, PRIDE: PXD003183 and PRIDE: PXD003163.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:26909372", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "Data is within this article. Data also available at the ProteomeXchange Consortium via the PRIDE partner repository, PRIDE: PXD002644, PRIDE: PXD002643, PRIDE: PXD003183 and PRIDE: PXD003163."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:26909372"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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:26909372", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.dib.2015.12.045", "sha256": "sha256:dcd7ea645bff339f963189a79f1f8de2c5fe3eab474b5505357122763101392d", "bytes": 22652, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.dib.2015.12.045", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4731419", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "asset:table:pmid:26909372:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cdb59b6252143fd6a1a8fc1c64a4f0433d4a2a9f5d6a716ff593fd53f9899b9d", "bytes": 3060, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[1]#t0005", "version": null, "note": "Protein spots from mouse spleen identified by MS/MS using the 4800 MALDI-TOF/TOF (AB Sciex).", "structure": {"pmcid": "PMC4731419", "section_index": 5, "section_title": "Data", "row_count": 27, "column_count": 11}, "table": {"label": "Table 1", "caption": "Protein spots from mouse spleen identified by MS/MS using the 4800 MALDI-TOF/TOF (AB Sciex).", "rows": [["Spot numbera", "Identification", "Accession", "Accension numberb", "Protein score", "Protein score CI%c", "Pep.count", "Total ion scored", "Total %ion CI", "MW (theorical)e", "IEP (theorical)e"], ["533", "Serotransferrin", "TRFE_MOUSE", "Q921I1", "119", "100", "11", "69", "100.000", "78840.5", "6.94"], ["537", "Serotransferrin", "TRFE_MOUSE", "Q921I1", "217", "100", "18", "109", "100.000", "78840.5", "6.94"], ["539", "Serotransferrin", "TRFE_MOUSE", "Q921I1", "461", "100", "25", "266", "100.000", "78840.5", "6.94"], ["614", "Stress-induced-phosphoprotein 1", "STIP1_MOUSE", "Q60864", "277", "100", "19", "146", "100", "63,170", "6.40"], ["692", "Fibrinogen beta chain", "FIBB_MOUSE", "Q8K0E8", "800", "100", "25", 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"13", "518", "100.000", "17310.9", "6.84"], ["", "Nucleoside diphosphate kinase B", "NDKB_MOUSE", "Q01768", "330", "100", "7", "278", "100.000", "17,466", "6.97"], ["1184", "Protein S100-A9", "S10A9_MOUSE", "P31725", "95", "100", "1", "89", "100", "13,211", "6.64"], ["1313", "Protein S100-A8", "S10A8_MOUSE", "P27005", "146", "100", "3", "119", "100.000", "10345.1", "5.43"], [""]], "row_count": 27, "column_count": 11, "numeric_cells": 229, "header_rows": 1, "locator": "section[5]/table-wrap[1]#t0005"}}, {"id": "asset:table:pmid:26909372:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0e7d2be5d5b9700a1d4008dd00840e4b5aa7725012e595200f3bd72940816578", "bytes": 2463, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[2]#t0010", "version": null, "note": "Protein spots identified by MS/MS using the MALDI-TOF/TOF UltrafleXtreme (Bruker).", "structure": {"pmcid": "PMC4731419", "section_index": 5, "section_title": "Data", "row_count": 22, "column_count": 9}, "table": {"label": "Table 2", "caption": "Protein spots identified by MS/MS using the MALDI-TOF/TOF UltrafleXtreme (Bruker).", "rows": [["Spot numbera", "Identification", "Accession", "Accession numberb", "Protein score", "Sequence coverage (%)", "No. of peptides", "MW (theorical)c", "IEP (theorical)c"], ["501", "Aconitate hydratase, mitochondrial", "ACON_MOUSE", "Q99KI0", "93.05", "3.60", "2", "85,400", "8.08"], ["538", "Serotransferrin", "TRFE_MOUSE", "Q921I1", "96.65", "4", "3", "78,841", "6.94"], ["539", "Serotransferrin", "TRFE_MOUSE", "Q921I1", "190.90", "5.9", "4", "78,841", "6.94"], ["554", "Far upstream element-binding protein 1", "FUBP1_MOUSE", "Q91WJ8", "32.75", "2.00", "1", "68,668", "7.74"], ["633", "Fibrinogen alpha chain", "FIBA_MOUSE", "E9PV24", "123.51", "4.20", "3", "88,117", "5.77"], ["638", "Heterogeneous nuclear ribonucleoprotein L", "HNRPL_MOUSE", "Q8R081", "69.55", "4.60", "2", "64,550", "8.33"], ["732", "Coronin-1", "CORO1A_MOUSE", "gi|4895037", "102.3", "2.2", "1", "51,627", "6.05"], ["738", "Vimentin", "VIME_MOUSE", "P20152", "286.83", "16.10", "5", "53,712", "5.06"], ["770", "Protein disulfide-isomerase A6 precursor", "PDIA6_MOUSE", "gi|58037267", "117.78", "10.6", "3", "49,058", "5.05"], ["898", "Actin, cytoplasmic 1", "ACTB_MOUSE", "P60710", "177.47", "9.10", "2", "42,052", "5.29"], ["", "Beta-actin-like protein 2", "ACTBL_MOUSE", "Q8BFZ3", "129.62", "9.00", "2", "42,319", "5.30"], ["", "F-actin-capping protein subunit alpha-1", "CAZA1_MOUSE", "P47753", "92.04", "9.80", "2", "33,090", "5.34"], ["972", "Tropomyosin alpha-1 chain", "TPM1_MOUSE", "P58771", "59.03", "4.90", "1", "32,718", "4.69"], ["981", "Proteasome subunit alpha type-1", "PSA1_MOUSE", "Q9R1P4", "133.78", "13.7", "3", "29,813", "6.00"], ["1001", "Proteasome subunit alpha type-6", "PSA6_MOUSE", "Q9QUM9", "177.79", "16.3", "4", "27,811", "6.34"], ["1049", 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Differences in spleen protein species abundance compared between CFA/IFA-treated CD38 KO mice (test group) and CFA/IFA-treated B6 WT mice (control group).", "structure": {"pmcid": "PMC4731419", "section_index": 5, "section_title": "Data", "row_count": 15, "column_count": 4}, "table": {"label": "Table 8", "caption": "Chronic inflammation model. Differences in spleen protein species abundance compared between CFA/IFA-treated CD38 KO mice (test group) and CFA/IFA-treated B6 WT mice (control group).", "rows": [["DeCyder spot no.", "Protein namea", "Average ratiob", "P value (t-test)"], ["", "", "Decreased abundance", ""], ["1049", "Proteasome subunit beta type-10", "−1.18", "4.06E−03"], ["", "Growth factor receptor-bound protein 2", "", ""], ["1330", "Not identified", "−1.31", "0.0106"], ["972", "Tropomyosin alpha-1 chain", "−1.11", "0.0163"], ["1173", "Ubiquitin-conjugating enzyme E2 N", "−1.13", "0.0217"], ["1103", "Ferritin light chain 1", "−1.62", "0.0343"], ["", "Ferritin light chain 2", "", ""], ["738", "Vimentin", "−1.22", "0.0351"], ["1104", "Low molecular weight phosphotyrosine", "", ""], ["", "protein phosphatase (PMF)", "−1.28", "0.0384"], ["732", "Coronin-1", "−1.1", "0.0434"], ["", "", "Increased abundance", ""], ["1313", "Protein S100-A8", "1.37", "0.0236"]], "row_count": 15, "column_count": 4, "numeric_cells": 34, "header_rows": 1, "locator": "section[5]/table-wrap[8]#t0040"}}, {"id": "asset:table:pmid:26909372:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:34fc9b41e3eae819c79ef97a310209081b177a0365b3627bec371f704237a6f7", "bytes": 822, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[9]#t0045", "version": null, "note": "Non-immunized control mice. Differences in spleen protein species abundance compared between non-immunized CD38 KO mice (test group) and non-immunized B6 WT mice (control group).", "structure": {"pmcid": "PMC4731419", "section_index": 5, "section_title": "Data", "row_count": 10, "column_count": 4}, "table": {"label": "Table 9", "caption": "Non-immunized control mice. Differences in spleen protein species abundance compared between non-immunized CD38 KO mice (test group) and non-immunized B6 WT mice (control group).", "rows": [["DeCyder spot no.", "Protein namea", "Average ratiob", "Pvalue (t-test)"], ["", "", "Decreased abundance", ""], ["538", "Serotransferrin", "−1.26", "4.04E−03"], ["539", "Serotransferrin", "−1.23", "0.0185"], ["537", "Serotransferrin", "−1.22", "0.0221"], ["638", "Heterogeneous nuclear ribonucleoprotein L", "−1.13", "0.0266"], ["770", "Protein disulfide-isomerase A6", "−1.11", "0.0437"], ["532", "Not identified", "−1.2", "0.0477"], ["", "", "Increased abundance", ""], ["1295", "Not identified", "1.33", "0.0162"]], "row_count": 10, "column_count": 4, "numeric_cells": 21, "header_rows": 1, "locator": "section[5]/table-wrap[9]#t0045"}}, {"id": "asset:table:pmid:26909372:10", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a2bdd4109b56a310171ca7bb2268fec7a5ab960352ddfc73613b7c8a8f06c6b8", "bytes": 1967, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[10]#t0050", "version": null, "note": "Citrullinated protein species and peptidesa detected in spleen from collagen-induced arthritis, or CFA-treated mice. TOF/TOF 4800.", "structure": {"pmcid": "PMC4731419", "section_index": 5, "section_title": "Data", "row_count": 16, "column_count": 11}, "table": {"label": "Table 10a", "caption": "Citrullinated protein species and peptidesa detected in spleen from collagen-induced arthritis, or CFA-treated mice. TOF/TOF 4800.", "rows": [["Spot number", "Identification", "Accesion", "Accension number", "Protein score", "Protein score CI%", "Pep. count", "Total ion score", "Total % ion CI", "MW (theoretical)", "IEP (theoretical)"], [""], ["537", "Serotransferrin", "TRFE_MOUSE", "Q921I1", "172", "100", "20", "107", "100.00", "78840.50", "6.94"], ["614", "Stress-induced-phosphoprotein 1", "STIP1_MOUSE", "Q60864", "238", "100", "27", "145", "100.00", "63169.60", "6.40"], ["697", "Catalase", "CATA_MOUSE", "Q8C6E3", "174", "100", "15", "131", "100.00", "60082.80", "7.73"], ["778", "Alpha enolase", "ENOA_MOUSE", "P17182", "940", "100", "33", "675", "100.00", "47453.30", "6.37"], ["", "Beta enolase", "ENOB_MOUSE", "P21550", "260", "100", "12", "224", "100.00", "47337.40", "6.73"], ["", "Gamma enolase", "ENOG_MOUSE", "P17183", "102", "100", "10", "75", "100.00", "47609.10", "4.99"], ["981", "Proteasome subunit alpha type-1", "PSA1_MOUSE", "Q9R1P4", "415", "100", "14", "350", "100.00", "29812.90", "6.00"], ["", "Proteasome subunit alpha type", "PSMA1_MOUSE", "Q8BTU5", "399", "100", "12", "349", "100.00", "29732.80", "5.78"], ["1001", "Proteasome subunit alpha type-6", "PSA6_MOUSE", "Q9QUM9", "325", "100", "13", "264", "100.00", "27811.00", "6.34"], ["", "Pyridoxine-5׳-phosphate oxidase", "PNPO_MOUSE", "Q91XF0", "81", "99.999", "5", "57", "100.00", "30437.10", "8.46"], ["1103", "Ferritin light chain 2", "FRIL2_MOUSE", "P49945", "251", "100", "10", "202", "100.00", "20886.90", "6.39"], ["1136", "Peptidyl-prolyl cis–trans isomerase A", "PPIA_MOUSE", "P17742", "320", "100", "11", "249", "100.00", "18130.90", "7.74"], ["1171", "Nucleoside diphosphate kinase A", "NDKA_MOUSE", "P15532", "726", "100", "17", "591", "100.00", "17310.90", "6.84"], ["", "Nucleoside diphosphate kinase B", "NDKB_MOUSE", "Q01768", "321", "100", "9", "278", "100.00", "17466.00", "6.97"]], "row_count": 16, "column_count": 11, "numeric_cells": 122, "header_rows": 0, "locator": "section[5]/table-wrap[10]#t0050"}}, {"id": "asset:table:pmid:26909372:11", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:f13552d9a447325194dcc14712924fda4d8c1ba2225f5fe871d88b51854a9036", "bytes": 863, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[11]#t0100", "version": null, "note": "Citrullinated protein species and peptidesa detected in spleen from collagen-induced arthritis, or CFA-treated mice. TOF/TOF UltrafleXtreme.", "structure": {"pmcid": "PMC4731419", "section_index": 5, "section_title": "Data", "row_count": 6, "column_count": 10}, "table": {"label": "Table 10b", "caption": "Citrullinated protein species and peptidesa detected in spleen from collagen-induced arthritis, or CFA-treated mice. TOF/TOF UltrafleXtreme.", "rows": [["Spot number", "Protein name", "Accession", "Accesion number", "MW (theoretical)", "IEP (theoretical)", "Score", "Sequence coverage (%)", "Queries matched", "Queries searched"], [""], ["633", "Fibrinogen alpha chain", "FIBA_MOUSE", "E9PV24", "87.40", "5.78", "101.00", "17.00", "15", "26"], ["732", "Coronin-1A", "COR1A_MOUSE", "O89053", "51.00", "6.04", "83.40", "36.00", "16", "75"], ["898", "F-actin-capping protein subunit alpha-1", "CAZA1_MOUSE", "P47753", "32.90", "5.34", "77.90", "43.00", "12", "65"], ["972", "Tropomyosin alpha-3 chain", "TPM3_MOUSE", "P21107", "33.00", "4.68", "60.50", "38.60", "10", "40"]], "row_count": 6, "column_count": 10, "numeric_cells": 35, "header_rows": 0, "locator": "section[5]/table-wrap[11]#t0100"}}, {"id": "asset:table:pmid:26909372:12", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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["LCQLCPGCGCSSTQPFFGYV GAFK", "✓"], ["CLK", "✓"], ["DGGGDVAFVK", "✓"], ["HTTIFEVLPEK", "✓"], ["ADR", "✓"], ["DQYELLCLDNTR", "✓"], ["KPVDQYEDCYLAR", "✓"], ["IPSHAVVAR", "✓"], ["K", "✓"], ["NNGK", "X"], ["EDLIWEILK", "✓"], ["VAQEHFGK", "✓"], ["GK", "✓"], ["SK", "✓"], ["DFQLFSSPLGK", "✓"], ["DLLFK", "✓"], ["DSAFGLLR", "✓"], ["VPPR", "✓"], ["MDYR", "✓"], ["LYLGHNYVTAIR", "✓"], ["NQQEGVCPEGSIDNSPVK", "✓"], ["WCALSHLER", "✓"], ["TK", "✓"], ["CDEWSIISEGK", "✓"], ["IECESAETTEDCIEK", "✓"], ["IVNGEADAMTLDGGHAYIAGQCGLVPVMAEYYESSNCAIPSQQGIFPK", "✓"], ["GYYAVAVVK", "✓"], ["ASDTSITWNNLK", "✓"], ["GK", "✓"], ["K", "✓"], ["SCHTGVDR", "✓"], ["TAGWNIPMGMLYNR", "✓"], ["INHCK", "✓"], ["FDEFFSQGCAPGYEK", "✓"], ["CAPNNK", "✓"], ["EEYNGYTGAFR", "✓"], ["CLVEK", "✓"], ["GDVAFVK", "✓"], ["HQTVLDNTEGK", "✓"], ["NPAEWAK", "✓"], ["NLK", "✓"], ["QEDFELLCPDGTR", "✓"], ["KPVK", "✓"], ["DFASCHLAQAPNHVVVSR", "✓"], ["K", "✓"], ["EK", "✓"], ["AAR", "✓"], ["VK", "✓"], ["AVLTSQETLFGGSDCTGNFC LFK", "✓"], ["STTK", "✓"], ["DLLFR", "✓"], ["DDTK", "X"], ["CFVK", "✓"], ["LPEGTTPEK", "✓"], ["YLGAEYMQSVGNMR", "✓"], ["K", "✓"], ["CSTSR", "✓"], ["LLEACTFHK", "✓"], ["H", "✓"], ["Total number of amino acids", "678"], ["Number of amino acids detected", "618"], ["Coverage (%)", "91"]], "row_count": 81, "column_count": 2, "numeric_cells": 3, "header_rows": 1, "locator": "section[5]/table-wrap[12]#t0055"}}, {"id": "asset:table:pmid:26909372:13", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:128c61079258d4bf747bfb4553f144a9fc24837e033509be46a38af2b3cfa18a", "bytes": 985, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[5]/table-wrap[13]#t0060", "version": null, "note": "Normalized peak area and %RSD of Tf glycopeptide glycoforms detected in the spots of spleen protein extracts subjected to 2D electrophoretic separation and in-gel tryptic digestion.", "structure": {"pmcid": "PMC4731419", "section_index": 5, "section_title": "Data", "row_count": 8, "column_count": 11}, "table": {"label": "Table 12", "caption": "Normalized peak area and %RSD of Tf glycopeptide glycoforms detected in the spots of spleen protein extracts subjected to 2D electrophoretic separation and in-gel tryptic digestion.", "rows": [["Glycoforms", "Spot 532", "Spot 533", "Spot 536", "Spot 537", "Spot 539"], ["Anorm⁎", "%RSD", "Anorm⁎", "%RSD", "Anorm⁎", "%RSD", "Anorm⁎⁎", "%RSD", "Anorm⁎", "%RSD"], ["2Ant/1NeuGc", "7.7", "6.1", "–", "–", "–", "–", "17.0", "18.1", "15.4", "6.4"], ["2Ant/1NeuGc1Fuc", "5.5", "1.2", "–", "–", "–", "–", "–", "–", "–", "–"], ["2Ant/2NeuGc", "54.7", "3.7", "56.9", "7.1", "54.9", "7.9", "76.5", "5.5", "137.8", "0.8"], ["2Ant/2NeuGc1Fuc", "29.8", "6.7", "25.9", "7.5", "–", "–", "16.2", "20.7", "26.1", "17.1"], ["2Ant/3NeuGc", "17.7", "5.5", "–", "–", "–", "–", "29.8", "15.6", "8.7", "4.9"], ["2Ant/3NeuGc1Fuc", "2.6", "3.3", "–", "–", "–", "–", "–", "–", "–", "–"]], "row_count": 8, "column_count": 11, "numeric_cells": 45, "header_rows": 2, "locator": "section[5]/table-wrap[13]#t0060"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Spleen protein species that differ in abundance by 2-ANOVA-Arthritis test in Col II-immunized CIA+ versus CIA− mice."}}], "targets": [], "gaps": []}, "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": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["PRIDE: PXD002644", "PRIDE: PXD002643", "PRIDE: PXD003183", "PRIDE: PXD003163"], "resolved_accessions": [], "statements": ["Data is within this article. Data also available at the ProteomeXchange Consortium via the PRIDE partner repository, PRIDE: PXD002644, PRIDE: PXD002643, PRIDE: PXD003183 and PRIDE: PXD003163."], "basis": "The paper names PRIDE: PXD002644, PRIDE: PXD002643, PRIDE: PXD003183, PRIDE: PXD003163, but the accession does not resolve in the repository (no reason recorded, no reason recorded, no reason recorded, no reason recorded), so the data cannot be reached from here. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:26909372", "asset:table:pmid:26909372:1", "asset:table:pmid:26909372:2", "asset:table:pmid:26909372:3", "asset:table:pmid:26909372:4", "asset:table:pmid:26909372:5", "asset:table:pmid:26909372:6", "asset:table:pmid:26909372:7", "asset:table:pmid:26909372:8", "asset:table:pmid:26909372:9", "asset:table:pmid:26909372:10", "asset:table:pmid:26909372:11", "asset:table:pmid:26909372:12", "asset:table:pmid:26909372:13"], "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": "2026-10-31T18:27:17Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 50370, "completion_tokens": 4690, "cached_tokens": 7612}}, "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:26909372", "type": "paper", "label": "pmid:26909372"}, {"id": "source:pmid:26909372", "type": "manuscript", "label": "PMID 26909372 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:26909372", "type": "paper", "label": "pmid:26909372"}, {"id": "source:pmid:26909372", "type": "manuscript", "label": "PMID 26909372 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-26909372", "type": "extraction", "used": ["source:pmid:26909372"], "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:26909372", "parent_hash": "sha256:5cda6003b20693e547a65a1c5e1043b4bf696c58681584d1d4661a938b63f01f", "fork_of": null, "generation": 7}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["disease activity: the role of CD38\" [1]. All mass spectrometry data have been deposited to the ProteomeXcha"], "order_basis": "paper_text_order:1381", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Spleen protein species that differ in abundance by 2-ANOVA-Arthritis test in Col II-immunized CIA+ versus CIA− mice."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T03:57:33+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}