Cys-SH based quantitative redox proteomics of salt induced response in sugar beet monosomic addition line M14.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34661775", "kind": "science-record", "revision": 4, "content_hash": "sha256:fb6e569a2cfbf8b51187b1346a24ee5fa91f807f578f4691ab558d22f796e502", "created_at": "2026-11-01T17:36:19Z", "updated_at": "2026-11-01T22:04:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Cys-SH based quantitative redox proteomics of salt induced response in sugar beet monosomic addition line M14.", "doi": "10.1186/s40529-021-00320-x", "pmid": "34661775", "authors": ["Jinna Li", "Kun Wang", "Meichao Ji", "Tingyue Zhang", "Chao Yang", "He Liu", "Sixue Chen", "Hongli Li", "Haiying Li"], "journal": "Botanical studies", "year": 2021, "abstract": "BACKGROUND: Salt stress is a major abiotic stress that limits plant growth, development and productivity. Studying the molecular mechanisms of salt stress tolerance may help to enhance crop productivity. Sugar beet monosomic addition line M14 exhibits tolerance to salt stress.\nRESULTS: In this work, the changes in the BvM14 proteome and redox proteome induced by salt stress were analyzed using a multiplex iodoTMTRAQ double labeling quantitative proteomics approach. A total of 80 proteins were differentially expressed under salt stress. Interestingly, A total of 48 redoxed peptides were identified for 42 potential redox-regulated proteins showed differential redox change under salt stress. A large proportion of the redox proteins were involved in photosynthesis, ROS homeostasis and other pathways. For example, ribulose bisphosphate carboxylase/oxygenase activase changed in its redox state after salt treatments. In addition, three redox proteins involved in regulation of ROS homeostasis were also changed in redox states. Transcription levels of eighteen differential proteins and redox proteins were profiled. (The proteomics data generated in this study have been submitted to the ProteomeXchange and can be accessed via username: reviewer_pxd027550@ebi.ac.uk, password: q9YNM1Pe and proteomeXchange# PXD027550.) CONCLUSIONS: The results showed involvement of protein redox modifications in BvM14 salt stress response and revealed the short-term salt responsive mechanisms. The knowledge may inform marker-based breeding effort of sugar beet and other crops for stress resilience and high yield.", "claims": [{"id": "claim-method", "statement": "We used student’s t-test conducted between the fold change of iodoTMT labeled peptides and the fold change of the corresponding proteins based on iTRAQ.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34661775", "locator": "sections[8] \"Data analysis\" paragraph 2", "quote": "We used student’s t-test conducted between the fold change of iodoTMT labeled peptides and the fold change of the corresponding proteins based on iTRAQ."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data and materials used and analyzed in the current study can be provided by the corresponding author for scientific, non‐profit purposes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34661775", "locator": "sections[29] \"notes\" paragraph 1", "quote": "The data and materials used and analyzed in the current study can be provided by the corresponding author for scientific, non‐profit purposes."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 80 proteins were differentially expressed under salt stress.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34661775", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "A total of 80 proteins were differentially expressed under salt stress."}, {"asset": "source:pmid:34661775", "locator": "sections[12] \"Identification of differential proteins and different redox proteins in response to salt stress\" paragraph 3", "quote": "Based on iodoTMT reporter intensities, we identified 42 proteins with significant redox changes in response to salt stress (Additional file 5: Table S3)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 80 proteins were differentially expressed under salt stress.", "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:34661775"], "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:PXD027550"], "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:PXD027550"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34661775", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40529-021-00320-x", "sha256": "sha256:af8b400ff7068bd71b8494a1d0ab55184f21a9d8c76445d293fd2c27cd3b9279", "bytes": 45838, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40529-021-00320-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8523603", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD027550", "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=PXD027550", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD027550", "version": null, "note": "The data and materials used and analyzed in the current study can be provided by the corresponding author for scientific, non‐profit purposes.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data and materials used and analyzed in the current study can be provided by the corresponding author for scientific, non‐profit purposes.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Cys-SH based quantitative redox proteomics of salt induced response in sugar beet monosomic addition line M14", "resolution_checked_at": "2026-11-01T17:30:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD027550 not downloaded", "asset:data:geo:PXD027550 licence not read"]}, "analysis": {"state": "partial", "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": 0.8, "band": "high", "quote": "ANOVA"}}, {"id": "method-2", "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": "We used student’s t-test conducted between the fold change of iodoTMT labeled peptides and the fold change of the corresponding proteins based on iTRAQ."}}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "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": "R1", "reachable": true, "accessions": ["PXD027550"], "resolved_accessions": ["PXD027550"], "statements": ["The data and materials used and analyzed in the current study can be provided by the corresponding author for scientific, non‐profit purposes."], "basis": "The paper names PXD027550 in ProteomeXchange and the accession resolves in the repository. 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:34661775", "data:geo:PXD027550"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD027550"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:04:29Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 13607, "completion_tokens": 1687, "cached_tokens": 188}}, "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:34661775", "type": "paper", "label": "pmid:34661775"}, {"id": "source:pmid:34661775", "type": "manuscript", "label": "PMID 34661775 full text"}, {"id": "data:geo:PXD027550", "type": "dataset", "label": "GEO PXD027550"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34661775", "type": "paper", "label": "pmid:34661775"}, {"id": "source:pmid:34661775", "type": "manuscript", "label": "PMID 34661775 full text"}, {"id": "data:geo:PXD027550", "type": "dataset", "label": "GEO PXD027550"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34661775", "type": "extraction", "used": ["source:pmid:34661775"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD027550", "type": "accession_resolution", "used": ["data:geo:PXD027550"], "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:34661775", "parent_hash": "sha256:4f0081a40ffc2a1dafd0af1db96fb7916976900ce054575748f94023ed8d8a55", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:PXD027550 licence not read", "asset:data:geo:PXD027550 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["heir gene transcriptional level changes. The Real-time PCR primer sequences can be found in Additional"], "order_basis": "paper_text_order:3041", "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": 0.8, "evidence": ["ANOVA"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}