Single-cell-type quantitative proteomic and ionomic analysis of epidermal bladder cells from the halophyte model plant Mesembryanthemum crystallinum to identify salt-responsive proteins.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27160145", "kind": "science-record", "revision": 6, "content_hash": "sha256:7e282f7a755ffe8d24188d07e395eea40a9d009d449a3ee74fe20c30c5587833", "created_at": "2026-11-01T15:40:18Z", "updated_at": "2026-11-01T21:20:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-cell-type quantitative proteomic and ionomic analysis of epidermal bladder cells from the halophyte model plant Mesembryanthemum crystallinum to identify salt-responsive proteins.", "doi": "10.1186/s12870-016-0797-1", "pmid": "27160145", "authors": ["Bronwyn J Barkla", "Rosario Vera-Estrella", "Carolyn Raymond"], "journal": "BMC plant biology", "year": 2016, "abstract": "BACKGROUND: Epidermal bladder cells (EBC) are large single-celled, specialized, and modified trichomes found on the aerial parts of the halophyte Mesembryanthemum crystallinum. Recent development of a simple but high throughput technique to extract the contents from these cells has provided an opportunity to conduct detailed single-cell-type analyses of their molecular characteristics at high resolution to gain insight into the role of these cells in the salt tolerance of the plant.\nRESULTS: In this study, we carry out large-scale complementary quantitative proteomic studies using both a label (DIGE) and label-free (GeLC-MS) approach to identify salt-responsive proteins in the EBC extract. Additionally we perform an ionomics analysis (ICP-MS) to follow changes in the amounts of 27 different elements. Using these methods, we were able to identify 54 proteins and nine elements that showed statistically significant changes in the EBC from salt-treated plants. GO enrichment analysis identified a large number of transport proteins but also proteins involved in photosynthesis, primary metabolism and Crassulacean acid metabolism (CAM). Validation of results by western blot, confocal microscopy and enzyme analysis helped to strengthen findings and further our understanding into the role of these specialized cells. As expected EBC accumulated large quantities of sodium, however, the most abundant element was chloride suggesting the sequestration of this ion into the EBC vacuole is just as important for salt tolerance.\nCONCLUSIONS: This single-cell type omics approach shows that epidermal bladder cells of M. crystallinum are metabolically active modified trichomes, with primary metabolism supporting cell growth, ion accumulation, compatible solute synthesis and CAM. Data are available via ProteomeXchange with identifier PXD004045.", "claims": [{"id": "claim-method", "statement": "To evaluate the significance of comparative quantification by each of the spectral count methods Student’s t-test was performed on the data as this has been shown to be most appropriate when comparing three or more replicates as was the case in this study [17], and differences were assigned to be significant at either a p value of ≤ 0.05 (*) or a p value of ≤ 0.01 (**), and the fold change of abundance of salt-treated to control was selected as greater than ± 2 (Table 2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27160145", "locator": "sections[3] \"Quantitative proteomic analysis\" paragraph 7", "quote": "To evaluate the significance of comparative quantification by each of the spectral count methods Student’s t-test was performed on the data as this has been shown to be most appropriate when comparing three or more replicates as was the case in this study [17], and differences were assigned to be significant at either a p value of ≤ 0.05 (*) or a p value of ≤ 0.01 (**), and the fold change of abundance of salt-treated to control was selected as greater than ± 2 (Table 2)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD004045.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27160145", "locator": "sections[22] \"Availability of data and materials section\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD004045."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper’s headline result was that salt treatment produced statistically significant changes in 54 EBC proteins and nine elements; it used an “Unpaired two-tailed Student’s t-test (p ≤ 0.05)” for western-blot validation, and the underlying mass-spectrometry proteomics data are available through ProteomeXchange under identifier PXD004045.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27160145", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Using these methods, we were able to identify 54 proteins and nine elements that showed statistically significant changes in the EBC from salt-treated plants."}, {"asset": "source:pmid:27160145", "locator": "sections[4] \"Western blot validation of proteomics results\" paragraph 3", "quote": "Unpaired two-tailed Student’s t-test (p ≤ 0.05) was performed on the mean band intensity data to determine the significance difference"}, {"asset": "source:pmid:27160145", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Data are available via ProteomeXchange with identifier PXD004045."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper’s headline result was that salt treatment produced statistically significant changes in 54 EBC proteins and nine elements; it used an “Unpaired two-tailed Student’s t-test (p ≤ 0.05)” for western-blot validation, and the underlying mass-spectrometry proteomics data are available through ProteomeXchange under identifier PXD004045.", "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:27160145"], "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:PXD004045"], "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:PXD004045"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27160145", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12870-016-0797-1", "sha256": "sha256:6773f075f8650f05b89a078d22c83528799ea94ae7e314aff68a9d68f49181f4", "bytes": 64038, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12870-016-0797-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4862212", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD004045", "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=PXD004045", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD004045", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD004045.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD004045.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Epidermal Bladder Cell Quantitative Proteomics", "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:27160145:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:be8b599b446d3b5c03ca6f23a093ab9883619bb5b65100c6d8d5949cfa9745cb", "bytes": 3189, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#Tab1", "version": null, "note": "Results from DIGE analysis of control vs salt treated EBC extract", "structure": {"pmcid": "PMC4862212", "section_index": 3, "section_title": "Quantitative proteomic analysis", "row_count": 30, "column_count": 10}, "table": {"label": "Table 1", "caption": "Results from DIGE analysis of control vs salt treated EBC extract", "rows": [["DIGE", "", "", "", "", "", "", ""], ["Spot No.", "t-testa", "Av. Ratiob", "Protein(s) in Spotc", "GO locationd", "GO biological processe", "Uniprot #", "Species", "SignifcantUniquepeptidesf", "M.W./pIg"], ["664", "0.00013", "2.48", "V-ATPase A subunit", "TP", "transport", "Q9AVU8", "M. crystallinum", "12", "69/5.09"], ["740-1", "", "", "Nitrite reductase", "CP", "nitrogen metabolism", "B9RYH9", "R. communis", "4", "66/6.04"], ["", "9.70E-05", "2.61", "", "", "", "", "", "", ""], ["740-2", "", "", "Beta-hexosaminidase 1", "V", "carbohydratemetabolism", "A7WM73", "A. thaliana", "3", "61/5.88"], ["760", "0.00031", "2.93", "V-ATPase B subunit", "TP", "transport", "Q8GUB5", "M. crystallinum", "31", "54/4.96"], ["765", "0.0002", "2.68", "NADP-dependent malic enzyme", "Cyt", "CAM", "P37223", "M. crystallinum", "46", "64/6.06"], ["767", "0.00062", "2.30", "NADP-dependent malic enzyme", "Cyt", "CAM", "P37223", "M. crystallinum", "49", "64/6.06"], ["774", "0.0033", "1.67", "NADP-dependent malic enzyme", "Cyt", "CAM", "P37223", "M. crystallinum", "48", "64/6.06"], ["775", "0.0071", "1.58", "NADP-dependent malic enzyme", "Cyt", "CAM", "P37223", "M. crystallinum", "54", "64/6.06"], ["923", "0.0016", "−1.79", "no proteins identified", "", "", "", "", "", ""], ["1062", "0.00053", "−1.59", "Alpha-1,4-glucan protein synthase", "AP", "cell wall metabolism", "I1J637", "G. max", "16", "42/5.52"], ["1064", "0.0014", "2.00", "no proteins identified", "", "", "", "", "", ""], ["1065", "0.0026", "1.96", "Beta-D-galactosidase", "AP", "cell wall metabolism", "Q5CCQ1", "P. pyrifolia", "3", "41/5.5"], ["1071-1", "", "", "2-phosphoglycerate hydrolase", "Cyt", "glycolysis", "Q43130", "M. crystallinum", "12", "48/5.62"], ["", "0.001", "2.00", "", "", "", "", "", "", ""], ["1071-2", "", "", "Alpha-1,4-glucan protein", "Cyt", "cell wall metabolism", "I1J637", "G. max", "9", "42/5.52"], ["1095", "0.0034", "1.69", "Malate dehydrogenase", "Cyt", "CAM", "Q645N1", "S. lycopersicum", "4", "36/8.87"], ["1123-1", "", "", "Malate dehydrogenase", "Cyt", "CAM/", "Q645N1", "S. lycopersicum", "5", "36/8.87"], ["", "0.00049", "2.13", "", "", "", "", "", "", ""], ["1123-2", "", "", "Proline iminopeptidase", "Cyt", "proteolysis", "B9G1Q0", "P. trichocarpa", "4", "37/8.96"], ["1153", "3.20E-07", "6.20", "V-ATPase E subunit", "TP", "transport", "Q40272", "M.crystallinum", "26", "26/6.52"], ["1290", "0.032", "−1.43", "no proteins identified", "", "", "", "", "", ""], ["1307", "0.0019", "2.20", "Ascorbate peroxidase", "Cyt", "stress response", "C5J0H6", "S. nigrum", "5", "18/4.83"], ["1325", "0.0082", "−1.66", "Fructose bisphosphate aldolase,", "Cyt", "glycolysis", "O04975", "M. crystallinum", "8", "38/6.49"], ["1501", "2.40E-07", "−2.51", "Alpha-galactosidase-like protein", "AP", "cell wall metabolism", "D7LVE6", "A. lyrata", "3", "48/4.79"], ["1502", "0.003", "1.63", "5-methyltetrahydropteroyltri-glutamate-homocysteine methyltransferase", "Cyt", "amino acid metabolism", "P93263", "M. crystallinum", "62", "85/5.9"], ["1503", "0.03", "−1.4", "Triosephosphate isomerase", "Cyt", "glycolysis", "I3SN66", "M. tribuloides", "5", "33/6.54"], ["1508", "4.40E-05", "2.4", "V-ATPase A subunit", "TP", "transport", "Q9AVU8", "M. crystallinum", "54", "69/5.09"]], "row_count": 30, "column_count": 10, "numeric_cells": 132, "header_rows": 2, "locator": "section[3]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:27160145:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:138595da222fd27cdaa33bb5bb83b38b1ee11eca8e525e33cedbc09bb8ed8e69", "bytes": 230, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#Tab2", "version": null, "note": "Salt-responsive proteins identified by GeLC-MS Label Free Quantitative Proteomics", "structure": {"pmcid": "PMC4862212", "section_index": 3, "section_title": "Quantitative proteomic analysis", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "Salt-responsive proteins identified by GeLC-MS Label Free Quantitative Proteomics", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[3]/table-wrap[2]#Tab2"}}], "gaps": ["asset:data:geo:PXD004045 not downloaded", "asset:data:geo:PXD004045 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "GO enrichment"}}, {"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": "To evaluate the significance of comparative quantification by each of the spectral count methods Student’s t-test was performed on the data as this has been shown to be most appropriate when comparing three or more replicates as was the case in this study [17], and differences were assigned to be significant at either a p value of ≤ 0.05 (*) or a p value of ≤ 0.01 (**), and the fold change of abundance of salt-treated to control was selected as greater than ± 2 (Table 2)."}}], "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": ["pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pathway_enrichment."}, "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": ["PXD004045"], "resolved_accessions": ["PXD004045"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD004045."], "basis": "The paper names PXD004045 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pathway_enrich"], "assets": ["source:pmid:27160145", "data:geo:PXD004045", "asset:table:pmid:27160145:1", "asset:table:pmid:27160145:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD004045"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:28:31Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 132610, "completion_tokens": 3890, "cached_tokens": 2088}}, "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:27160145", "type": "paper", "label": "pmid:27160145"}, {"id": "source:pmid:27160145", "type": "manuscript", "label": "PMID 27160145 full text"}, {"id": "data:geo:PXD004045", "type": "dataset", "label": "GEO PXD004045"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:27160145", "type": "paper", "label": "pmid:27160145"}, {"id": "source:pmid:27160145", "type": "manuscript", "label": "PMID 27160145 full text"}, {"id": "data:geo:PXD004045", "type": "dataset", "label": "GEO PXD004045"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27160145", "type": "extraction", "used": ["source:pmid:27160145"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD004045", "type": "accession_resolution", "used": ["data:geo:PXD004045"], "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:27160145", "parent_hash": "sha256:c9f1ec648b25f5d73879ff6f182c6f7249838b2ee40092ec50eae119f41f47b0", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:PXD004045 licence not read", "asset:data:geo:PXD004045 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["d metabolism (CAM). Validation of results by western blot, confocal microscopy and enzyme analysis hel"], "order_basis": "paper_text_order:1314", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_imaging", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["CAM). Validation of results by western blot, confocal microscopy and enzyme analysis helped to strengthen fin", "idation of results by western blot, confocal microscopy and enzyme analysis helped to strengthen fin"], "order_basis": "paper_text_order:1328", "id": "assay:2"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["GO enrichment"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}