Comparative Label-Free Quantitative Proteomics Analysis Reveals the Essential Roles of N-Glycans in Salt Tolerance by Modulating Protein Abundance in Arabidopsis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34276718", "kind": "science-record", "revision": 4, "content_hash": "sha256:f429a59ae839e8f030d7cf310c5f7ff1a17e8dbc004d9bf241b5dc60d38322ec", "created_at": "2026-11-01T15:41:44Z", "updated_at": "2026-11-01T21:25:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comparative Label-Free Quantitative Proteomics Analysis Reveals the Essential Roles of N-Glycans in Salt Tolerance by Modulating Protein Abundance in Arabidopsis.", "doi": "10.3389/fpls.2021.646425", "pmid": "34276718", "authors": ["Chuanfa Liu", "Guanting Niu", "Xiaowen Li", "Huchen Zhang", "Huawei Chen", "Dongxia Hou", "Ping Lan", "Zhi Hong"], "journal": "Frontiers in plant science", "year": 2021, "abstract": "Many pieces of evidence show that the adaptive response of plants to salt stress requires the maturation of N-glycan on associated proteins. However, it is still little known about the salt-responsive glycoproteins that function in this process. In the present study, we identified salt-responsive glycoproteins in wild-type (WT) Arabidopsis and two mutants defective in N-glycan maturation, mns1 mns2 and cgl1. A total of 97 proteins with abundance changes of >1.5- or <0.67-fold were identified against salt stress by label-free liquid chromatography coupled mass spectrometry (LC-MS/MS) quantitative analyses. A comparison of differentially abundant glycoproteins (DAGs) indicated the substrate preferences regulated by MNS1/MNS2 and CGL1. In addition, the DAGs in mns1 mns2 hardly form functional regulatory networks in STRING analysis. Comparably, the regulatory network in cgl1 was visible and shared overlapping with that in WT. Such difference may supply the evidence to partially explain the lower salt sensitivity of mutant cgl1 than mns1 mns2. We further confirmed that two N-glycosylation clients, peroxidases PRX32 and PRX34, were involved in the salt stress response since the double mutants showed enhanced salt sensitivity. Together, our study provided proteomic evidence that N-glycans are crucial for modulating stress-responsive protein levels, and several novel glycoproteins responsible for salt stress tolerance in Arabidopsis were listed. Data are available via ProteomeXchange with identifier PXD006893.", "claims": [{"id": "claim-method", "statement": "**Indicated a significant difference from the value of the WT (NaCl) with p < 0.001, n > 20 (Student’s t-test).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34276718", "locator": "sections[21] \"Biological Validation of Quantitative Proteomics Results\" paragraph 4", "quote": "**Indicated a significant difference from the value of the WT (NaCl) with p < 0.001, n > 20 (Student’s t-test)."}], "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 at: http://www.proteomexchange.org/, PXD006893.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34276718", "locator": "sections[23] \"Data Availability Statement\" paragraph 2", "quote": "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 at: http://www.proteomexchange.org/, PXD006893."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34276718"], "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": "complete", "blocked_on": null, "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": ["data:geo:PXD006893"], "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": ["data:geo:PXD006893"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34276718", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fpls.2021.646425", "sha256": "sha256:f3f98ace9028e96224b698e479a0984d1e13dd4dc84176755b586d415db9f805", "bytes": 64017, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fpls.2021.646425", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8283305", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD006893", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD006893", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD006893", "version": null, "note": "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 at: http://www.proteomexchange.org/, PXD006893.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "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 at: http://www.proteomexchange.org/, PXD006893.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Arabidopsis thaliana seedling lectin enriched LC-MS", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34276718:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1d476a1df8bcd63d50be6dd648c881de5b144f4edc4069db0824d4a497564445", "bytes": 597, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#tab1", "version": null, "note": "Statistical analysis of differentially abundant N-glycopeptides and N-glycoproteins in response to salt stress.", "structure": {"pmcid": "PMC8283305", "section_index": 18, "section_title": "Global Changes of Protein Abundance in Response to Salt Stress", "row_count": 5, "column_count": 7}, "table": {"label": "Table 1", "caption": "Statistical analysis of differentially abundant N-glycopeptides and N-glycoproteins in response to salt stress.", "rows": [["NaCl: control", "# of quantified", "# of regulated (fold changes > 1.5, p < 0.05)"], ["N-glyco-peptides", "N-glyco-proteins", "N-glycopeptides*", "N-glycoproteins*"], ["WT", "163", "141", "40 ↑", "4 ↓", "32 ↑", "5 ↓"], ["mns1 mns2", "340", "236", "36 ↑", "17 ↓", "33 ↑", "12 ↓"], ["cgl1-3", "294", "207", "12 ↑", "51 ↓", "13 ↑", "29 ↓"]], "row_count": 5, "column_count": 7, "numeric_cells": 20, "header_rows": 2, "locator": "section[18]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:34276718:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2badcb6f1046e741645610166bb8406f97569c7d97391510ca649b11bc25648d", "bytes": 8432, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[2]#tab2", "version": null, "note": "Differentially abundant glycoproteins were identified in the WT, mns1 mns2, and cgl1-3 in response to salt stress.", "structure": {"pmcid": "PMC8283305", "section_index": 18, "section_title": "Global Changes of Protein Abundance in Response to Salt Stress", "row_count": 109, "column_count": 5}, "table": {"label": "Table 2", "caption": "Differentially abundant glycoproteins were identified in the WT, mns1 mns2, and cgl1-3 in response to salt stress.", "rows": [["Accession number", "Protein descriptions", "Ratio* (T/NT)", "Ratio* (D/ND)", "Ratio* (C/NC)"], ["Post-translational modification, protein folding, and chaperones (10)"], ["AT1G56340", "Calreticulin 1a, CRT1a", "2.14 ± 0.19", "-", "-"], ["AT1G09210", "Calreticulin 1b, CRT1b", "0.13 ± 0.02", "-", "-"], ["AT2G38960", "Endoplasmic reticulum oxidoreductins 2, ERO2", "2.17 ± 0.03", "-", "-"], ["AT3G07770", "Heat shock protein 89.1, Hsp89.1", "-", "3.60 ± 1.30", "-"], ["AT3G54960", "PDIL1-3, a protein disulfide isomerase-like protein", "1.91 ± 0.28", "-", "-"], ["AT4G27080", "PDI-like 5-4, PDI7, PDIL5-4", "-", "-", "0.24 ± 0.03"], ["AT5G19690", "Staurosporin and temperature sensitive 3-like A, STT3A", "2.03 ± 0.22", "0.56 ± 0.05", "0.26 ± 0.05"], ["AT1G76400", "Ribophorin I, an oligosaccharyl transferase subunit", "2.23 ± 0.47", "-", "-"], ["AT1G67490", "Glucosidase 1, GCS1, KNF", "-", "2.54 ± 0.28", "-"], ["AT1G71220", "UDP-glucose:glycoprotein glucosyltransferases, EBS1", "2.78 ± 0.71", "-", "0.41 ± 0.18"], ["Carbohydrate metabolism and energy production (16)"], ["AT3G26650", "GAPDH A subunit, GAPA", "0.29 ± 0.16", "-", "0.25 ± 0.02"], ["AT1G42970", "GAPDH B subunit, GAPB", "-", "-", "0.37 ± 0.17"], ["AT1G09780", "Phosphoglycerate mutase", "0.32 ± 0.16", "-", "-"], ["ATCG00680", "Photosystem II reaction center protein B, PSBB", "0.32 ± 0.10", "-", "0.08 ± 0.00"], ["ATCG00480", "ATP synthase subunit beta, ATPB", "-", "3.39 ± 0.38", "-"], ["AT2G28470", "Beta-galactosidase 8, BGAL8", "2.67 ± 0.13", "-", "0.34 ± 0.20"], ["AT5G63810", "Beta-galactosidase 10, BGAL10", "1.85 ± 0.11", "-", "0.42 ± 0.13"], ["AT5G13640", "Phospholipid:diacylglycerol acyltransferase, PDAT", "2.19 ± 0.30", "-", "-"], ["AT1G66970", "SVL2, a member of GDPD-like family", "-", "-", "0.27 ± 0.17"], ["AT1G74380", "Xyloglucan xylosyltransferase 5, XXT5", "-", "0.52 ± 0.06", "0.28 ± 0.02"], ["AT3G26720", "Glycosyl hydrolase family 38 protein", "-", "-", "0.52 ± 0.12"], ["AT2G44450", "Beta glucosidase 15, BGLU15", "-", "0.23 ± 0.09", "-"], ["AT1G52400", "Beta glucosidase 18, BGLU18", "2.57 ± 0.37", "2.21 ± 0.59", "-"], ["AT3G18080", "B-S glucosidase 44, BGLU44", "-", "3.36 ± 0.36", "0.25 ± 0.02"], ["AT1G65590", "Beta-hexosaminidase 3, HEXO3", "-", "-", "4.63 ± 0.97"], ["AT1G07230", "Non-specific phospholipase C1, NPC1", "-", "4.31 ± 0.71", "-"], ["Putative uncharacterized protein (14)"], ["AT5G14030", "TRAPB family protein", "0.54 ± 0.11", "0.49 ± 0.10", "-"], ["AT5G15350", "Early nodulin-like protein 17, ENODL17", "1.52 ± 0.02", "-", "-"], ["AT4G12880", "Early nodulin-like protein 19, ENODL19", "-", "1.55 ± 0.03", "-"], ["AT3G62730", "Unknown protein, desiccation-like protein", "3.99 ± 0.41", "-", "-"], ["AT2G12400", "Unknown protein, plasma membrane fusion protein", "4.22 ± 0.60", "-", "-"], ["AT1G19370", "Unknown protein, membrane protein", "-", "0.07 ± 0.00", "-"], ["AT5G58100", "Unknown protein, transmembrane protein", "-", "0.28 ± 0.05", "-"], ["AT3G56750", "Unknown protein, transferase activity", "-", "2.38 ± 0.23", "-"], ["AT1G05070", "Protein of unknown function (DUF1068)", "-", "1.76 ± 0.15", "-"], ["AT2G01310", "Hypothetical protein", "-", "-", "3.60 ± 0.32"], ["AT3G13410", "2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase", "-", "2.23 ± 0.35", "-"], ["AT1G10950", "Transmembrane nine 1, TMN1", "-", "-", "0.21 ± 0.15"], ["AT1G09870", "Histidine acid phosphatase family protein", "-", "1.59 ± 0.26", "-"], ["AT1G17100", "HBP1, SOUL heme-binding family protein", "-", "2.30 ± 0.03", "1.59 ± 0.16"], ["Protein transport and metabolism (9)"], ["AT2G35780", "Serine carboxypeptidase-like 26, SCPL26", "1.67 ± 0.37", "-", "-"], ["AT5G23210", "Serine carboxypeptidase-like 34, SCPL34", "-", "2.83 ± 0.96", "-"], ["AT2G33530", "Serine carboxypeptidase-like 46, SCPL46", "-", "1.86 ± 0.23", "0.62 ± 0.09"], ["AT1G78680", "Gamma-glutamyl hydrolase 2, GGH2", "2.73 ± 0.71", "-", "-"], ["AT3G62020", "Germin-like protein 10, GLP10", "3.74 ± 0.59", "3.85 ± 1.27", "3.56 ± 0.06"], ["AT1G59970", "Matrixin family protein", "-", "0.55 ± 0.00", "0.60 ± 0.04"], ["AT1G13900", "PAP2, a dual-localized acid phosphatase that modulates protein targeting to mitochondrion", "3.77 ± 0.01", "2.27 ± 0.45", "0.47 ± 0.16"], ["AT3G52850", "Vacuolar sorting receptor homolog 1, VSR1", "-", "3.22 ± 0.68", "-"], ["AT4G20110", "Vacuolar sorting receptor 7, VSR7", "-", "2.55 ± 0.02", "-"], ["Defense response (11)"], ["AT1G79340", "Metacaspase 4, MC4, MCP2d", "2.02 ± 0.32", "3.17 ± 0.40", "-"], ["AT1G52410", "TSK-associating protein 1, TSA1", "2.88 ± 0.63", "-", "-"], ["AT2G39730", "Rubisco activase, RCA", "3.02 ± 0.05", "-", "-"], ["AT5G06860", "Polygalacturonase inhibiting protein 1, PGIP1", "-", "-", "0.49 ± 0.04"], ["AT5G06870", "Polygalacturonase inhibiting protein 2, PGIP2", "-", "3.53 ± 0.70", "-"], ["AT3G11650", "NDR1/HIN1-like 2, NHL2", "-", "-", "1.59 ± 0.11"], ["AT5G37780", "CAM1, calmodulin 1", "-", "-", "11.11 ± 2.63"], ["AT5G26000", "Thioglucoside glucohydrolase 1, TGG1, BGLU38", "1.80 ± 0.17", "-", "-"], ["AT5G25980", "Glucoside glucohydrolase 2, TGG2, BGLU37", "-", "2.84 ± 0.34", "-"], ["AT3G14210", "Epithiospecifier modifier 1, ESM1", "2.13 ± 0.24", "1.50 ± 0.17", "-"], ["AT1G08470", "Strictosidine synthase-like 3, SSL3", "-", "-", "0.43 ± 0.15"], ["Cell wall biosynthesis and modification (14)"], ["AT5G49720", "Endo-1,4-glucanase, GH9A1, KORRIGAN/RSW2", "2.13 ± 0.15", "-", "0.28 ± 0.15"], ["AT3G14310", "Pectin methylesterase 3, PME3", "-", "-", "2.45 ± 0.43"], ["AT4G33220", "Pectin methylesterase 44, PME44", "-", "2.32 ± 0.43", "-"], ["AT2G35610", "Xyloglucanase 113, XEG113", "-", "0.27 ± 0.02", "-"], ["AT4G37800", "Xyloglucan endotransglucosylase/hydrolase 7, XTH7", "-", "0.10 ± 0.03", "-"], ["AT3G16860", "COBRA-like protein 8 precursor, COBL8", "-", "-", "0.50 ± 0.11"], ["AT1G68560", "Alpha-xylosidase 1, XYL1", "-", "-", "0.46 ± 0.03"], ["AT5G64570", "Beta-D-xylosidase 4, XYL4", "-", "-", "0.49 ± 0.04"], ["AT4G01080", "TRICHOME BIREFRINGENCE-LIKE 26, TBL26", "-", "2.34 ± 0.35", "-"], ["AT5G55730", "FASCICLIN-like arabinogalactan 1, FLA1", "-", "1.83 ± 0.10", "-"], ["AT2G04780", "FASCICLIN-like arabinogalactan 7, FLA7", "-", "2.36 ± 0.36", "-"], ["AT1G03870", "FASCICLIN-like arabinogalactan 9, FLA9", "-", "3.38 ± 0.17", "1.97 ± 0.14"], ["AT1G28290", "Arabinogalactan protein 31, AGP31", "-", "2.90 ± 0.36", "-"], ["AT3G09090", "Defective in exine formation protein, DEX1", "-", "-", "0.46 ± 0.13"], ["Signal transduction (8)"], ["AT1G28340", "Receptor like protein 4, RLP4", "2.35 ± 0.37", "-", "-"], ["AT1G73080", "PEP1 receptor 1, PEPR1, LRR receptor kinase", "1.79 ± 0.29", "-", "-"], ["AT3G51740", "Inflorescence meristem receptor-like kinase 2, IMK2", "3.34 ± 0.74", "-", "-"], ["AT4G33430", "BRI1-associated receptor kinase, BAK1", "3.07 ± 0.87", "-", "0.54 ± 0.06"], ["AT5G48380", "BAK1-interacting receptor-like kinase 1, BIR1", "-", "-", "0.48 ± 0.14"], ["AT3G17840", "Receptor-like kinase 902, RLK902", "-", "-", "2.16 ± 0.03"], ["AT1G21270", "Wall-associated kinase 2, WAK2", "-", "0.64 ± 0.06", "-"], ["AT4G22130", "STRUBBELIG-receptor family 8, SRF8", "-", "1.80 ± 0.28", "-"], ["Oxidation-reduction process (11)"], ["AT5G62630", "hipl2 protein precursor, HIPL2", "3.72 ± 0.70", "-", "-"], ["AT5G63910", "Farnesylcysteine lyase, FCLY", "4.26 ± 0.81", "3.11 ± 0.62", "-"], ["AT5G21105", "Plant L-ascorbate oxidase", "2.11 ± 0.28", "-", "1.95 ± 0.03"], ["AT3G32980", "Peroxidase 32, PRX32", "-", "-", "2.04 ± 0.33"], ["At3g49120", "Peroxidase 34, PRX34", "-", "1.35 ± 0.05", "1.34 ± 0.03"], ["AT5G67400", "Root hair specific 19, RHS19", "-", "0.27 ± 0.16", "0.16 ± 0.03"], ["AT1G74790", "Catalytics", "2.96 ± 0.18", "-", "-"], ["AT2G01270", "Quiescin-sulfhydryl oxidase 2, QSOX2", "-", "-", "0.29 ± 0.04"], ["AT1G76160", "SKU5 similar 5, SKS5", "-", "-", "0.31 ± 0.08"], ["AT1G41830", "SKU5-similar 6, SKS6", "-", "-", "0.24 ± 0.03"], ["AT4G39640", "Gamma-glutamyl transpeptidase 1, GGT1", "-", "1.77 ± 0.27", "-"], ["ER and ribosome biogenesis (2)"], ["AT2G39780", "Ribonuclease 2, RNS2, the main endoribonuclease activity in plant cells.", "2.31 ± 0.33", "-", "-"], ["AT3G15950", "DNA topoisomerase related, NAI2, loss of function mutations lacks ER bodies.", "-", "0.54 ± 0.03", "4.15 ± 0.27"], ["Auxin biosynthesis and signaling (3)"], ["AT3G07390", "Auxin-responsive family protein, AIR12", "-", "-", "6.00 ± 0.39"], ["AT4G24670", "TAR2, auxin biosynthetic process", "-", "2.77 ± 0.28", "-"], ["AT4G02980", "Auxin binding protein 1, ABP1", "-", "2.87 ± 0.72", "-"]], "row_count": 109, "column_count": 5, "numeric_cells": 302, "header_rows": 1, "locator": "section[18]/table-wrap[2]#tab2"}}], "gaps": ["asset:data:geo:PXD006893 not downloaded", "asset:data:geo:PXD006893 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Student’s t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "**Indicated a significant difference from the value of the WT (NaCl) with p < 0.001, n > 20 (Student’s t-test)."}}], "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": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Student’s t-test), 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": "R1", "reachable": true, "accessions": ["PXD006893"], "resolved_accessions": ["PXD006893"], "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 at: http://www.proteomexchange.org/, PXD006893."], "basis": "The paper names PXD006893 in ProteomeXchange and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:34276718", "data:geo:PXD006893", "asset:table:pmid:34276718:1", "asset:table:pmid:34276718:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD006893"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:22Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 52320, "completion_tokens": 1052, "cached_tokens": 784}}, "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:34276718", "type": "paper", "label": "pmid:34276718"}, {"id": "source:pmid:34276718", "type": "manuscript", "label": "PMID 34276718 full text"}, {"id": "data:geo:PXD006893", "type": "dataset", "label": "GEO PXD006893"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34276718", "type": "paper", "label": "pmid:34276718"}, {"id": "source:pmid:34276718", "type": "manuscript", "label": "PMID 34276718 full text"}, {"id": "data:geo:PXD006893", "type": "dataset", "label": "GEO PXD006893"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34276718", "type": "extraction", "used": ["source:pmid:34276718"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD006893", "type": "accession_resolution", "used": ["data:geo:PXD006893"], "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:34276718", "parent_hash": "sha256:b414239eabf9648b20da0b8c69c12eec018bd1a774f88e2dc33fd4ca25da295b", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD006893 licence not read", "asset:data:geo:PXD006893 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "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": 0.99, "evidence": ["Comparative Label-Free Quantitative Proteomics Analysis Reveals the Essential Roles of N-Gl", "lt sensitivity. Together, our study provided proteomic evidence that N-glycans are crucial for modu", "by label-free liquid chromatography coupled mass spectrometry (LC-MS/MS) quantitative analyses. A comparis", "id chromatography coupled mass spectrometry (LC-MS/MS) quantitative analyses. A comparison of diff"], "order_basis": "paper_text_order:0", "id": "assay:1"}]}