← All .science files
pmid:28820483
A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses.
May Alqurashi · Ludivine Thomas · Chris Gehring · Claudius Marondedze
Proteomes · 2017 doi:10.3390/proteomes5030022
Paper
complete
Experiment
partial
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 4 items
claims array · 2 items
[0] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
data object · 3 fields
assets array · 5 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
[2] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 99 items
[0] array · 5 items
[1] array · 1 item
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 5 items
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 1 item
[14] array · 5 items
[15] array · 5 items
[16] array · 5 items
[17] array · 5 items
[18] array · 5 items
[19] array · 5 items
[20] array · 5 items
[21] array · 5 items
[22] array · 5 items
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 5 items
[27] array · 1 item
[28] array · 5 items
[29] array · 5 items
[30] array · 5 items
[31] array · 1 item
[32] array · 5 items
[33] array · 1 item
[34] array · 5 items
[35] array · 5 items
[36] array · 5 items
[37] array · 5 items
[38] array · 5 items
[39] array · 5 items
[40] array · 5 items
[41] array · 5 items
[42] array · 5 items
[43] array · 5 items
[44] array · 5 items
[45] array · 5 items
[46] array · 1 item
[47] array · 5 items
[48] array · 5 items
[49] array · 5 items
[50] array · 5 items
[51] array · 5 items
[52] array · 1 item
[53] array · 5 items
[54] array · 5 items
[55] array · 5 items
[56] array · 5 items
[57] array · 5 items
[58] array · 5 items
[59] array · 5 items
[60] array · 5 items
[61] array · 5 items
[62] array · 5 items
[63] array · 5 items
[64] array · 5 items
[65] array · 5 items
[66] array · 5 items
[67] array · 5 items
[68] array · 1 item
[69] array · 5 items
[70] array · 5 items
[71] array · 5 items
[72] array · 5 items
[73] array · 5 items
[74] array · 1 item
[75] array · 5 items
[76] array · 5 items
[77] array · 5 items
[78] array · 5 items
[79] array · 5 items
[80] array · 5 items
[81] array · 1 item
[82] array · 5 items
[83] array · 5 items
[84] array · 5 items
[85] array · 1 item
[86] array · 5 items
[87] array · 5 items
[88] array · 5 items
[89] array · 5 items
[90] array · 1 item
[91] array · 5 items
[92] array · 5 items
[93] array · 5 items
[94] array · 5 items
[95] array · 5 items
[96] array · 5 items
[97] array · 5 items
[98] array · 5 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 64 items
[0] array · 5 items
[1] array · 1 item
[2] array · 5 items
[3] array · 5 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 5 items
[9] array · 1 item
[10] array · 5 items
[11] array · 5 items
[12] array · 5 items
[13] array · 5 items
[14] array · 5 items
[15] array · 5 items
[16] array · 1 item
[17] array · 5 items
[18] array · 1 item
[19] array · 5 items
[20] array · 5 items
[21] array · 5 items
[22] array · 1 item
[23] array · 5 items
[24] array · 5 items
[25] array · 5 items
[26] array · 5 items
[27] array · 5 items
[28] array · 5 items
[29] array · 5 items
[30] array · 5 items
[31] array · 5 items
[32] array · 5 items
[33] array · 1 item
[34] array · 5 items
[35] array · 5 items
[36] array · 5 items
[37] array · 5 items
[38] array · 1 item
[39] array · 5 items
[40] array · 5 items
[41] array · 5 items
[42] array · 5 items
[43] array · 5 items
[44] array · 5 items
[45] array · 1 item
[46] array · 5 items
[47] array · 5 items
[48] array · 1 item
[49] array · 5 items
[50] array · 5 items
[51] array · 5 items
[52] array · 5 items
[53] array · 5 items
[54] array · 5 items
[55] array · 5 items
[56] array · 1 item
[57] array · 5 items
[58] array · 5 items
[59] array · 1 item
[60] array · 5 items
[61] array · 5 items
[62] array · 5 items
[63] array · 5 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 31 items
[0] array · 6 items
[1] array · 1 item
[2] array · 6 items
[3] array · 6 items
[4] array · 1 item
[5] array · 6 items
[6] array · 6 items
[7] array · 1 item
[8] array · 6 items
[9] array · 1 item
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 1 item
[14] array · 6 items
[15] array · 6 items
[16] array · 1 item
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 1 item
[21] array · 6 items
[22] array · 1 item
[23] array · 6 items
[24] array · 6 items
[25] array · 6 items
[26] array · 6 items
[27] array · 6 items
[28] array · 1 item
[29] array · 6 items
[30] array · 6 items
gaps array · 2 items
analysis object · 4 fields
methods array · 1 item
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 1 item
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 5 items
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 8 items
assays array · 2 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28820483", "kind": "science-record", "revision": 7, "content_hash": "sha256:93bead2563f2a68c52aeafe6e8d76794c956b3f1d7b0e19374eddf8d61b9e20a", "created_at": "2026-11-01T15:40:27Z", "updated_at": "2026-11-01T21:59:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses.", "doi": "10.3390/proteomes5030022", "pmid": "28820483", "authors": ["May Alqurashi", "Ludivine Thomas", "Chris Gehring", "Claudius Marondedze"], "journal": "Proteomes", "year": 2017, "abstract": "The plant hormone abscisic acid (ABA) modulates a number of plant developmental processes and responses to stress. In planta, ABA has been shown to induce reactive oxygen species (ROS) production through the action of plasma membrane-associated nicotinamide adenine dinucleotide phosphate (NADPH)-oxidases. Although quantitative proteomics studies have been performed to identify ABA- or hydrogen peroxide (H₂O₂)-dependent proteins, little is known about the ABA- and H₂O₂-dependent microsomal proteome changes. Here, we examined the effect of 50 µM of either H₂O₂ or ABA on the Arabidopsis microsomal proteome using tandem mass spectrometry and identified 86 specifically H₂O₂-dependent, and 52 specifically ABA-dependent proteins that are differentially expressed. We observed differential accumulation of proteins involved in the tricarboxylic acid (TCA) cycle notably in response to H₂O₂. Of these, aconitase 3 responded to both H₂O₂ and ABA. Additionally, over 30 proteins linked to RNA biology responded significantly to both treatments. Gene ontology categories such as 'response to stress' and 'transport' were enriched, suggesting that H₂O₂ or ABA directly and/or indirectly cause complex and partly overlapping cellular responses. Data are available via ProteomeXchange with identifier PXD006513.", "claims": [{"id": "claim-method", "statement": "Proteins were deemed responsive to treatment when present in at least two replicates with a fold change (FC) greater or equal to |±2|, verified by Student t-test (p-value ≤ 0.05) in comparison to the mock-treated samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28820483", "locator": "sections[5] \"2.3. Trypsin Digestion and Protein Identification by Tandem Mass Spectrometry\" paragraph 2", "quote": "Proteins were deemed responsive to treatment when present in at least two replicates with a fold change (FC) greater or equal to |±2|, verified by Student t-test (p-value ≤ 0.05) in comparison to the mock-treated samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with identifier PXD006513.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28820483", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD006513."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "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:28820483"], "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:PXD006513"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:PXD006513"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28820483", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/proteomes5030022", "sha256": "sha256:10ba204b6ee0649a538f43bc1c7619d0e6eae98666528d018d69ddcde68b2fed", "bytes": 46421, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/proteomes5030022", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5620539", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD006513", "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=PXD006513", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD006513", "version": null, "note": "Data are available via ProteomeXchange with identifier PXD006513.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data are available via ProteomeXchange with identifier PXD006513.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "A microsomal proteomics view of H2O2- and ABA-dependent responses", "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:28820483:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:65a172c7045d86de7002ccf06427edc4ea59ee36720cf9784953a68cd71dc779", "bytes": 6001, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#proteomes-05-00022-t001", "version": null, "note": "Proteins responsive to H2O2 treatment.", "structure": {"pmcid": "PMC5620539", "section_index": 8, "section_title": "3. Results", "row_count": 99, "column_count": 5}, "table": {"label": "Table 1", "caption": "Proteins responsive to H2O2 treatment.", "rows": [["Accession Number", "Protein Name", "ANOVA (p-Value)", "FC 5 min", "FC 20 min"], ["1. Metabolism"], ["AT1G17745", "D-3-phosphoglycerate dehydrogenase 2", "0.0089", "0.1", "0.1"], ["AT5G26780", "Serine hydroxymethyltransferase 2", "0.036", "2.1", "13"], ["AT3G61440", "Cysteine synthase C1", "0.00074", "ns", "5"], ["AT4G14880", "O-acetylserine (thiol) lyase isoform A1", "0.015", "0.1", "7.9"], ["AT5G23300", "Pyrimidine d", "0.013", "0.2", "ns"], ["AT3G09820", "Adenosine kinase 1", "0.0042", "0.1", "14.0"], ["AT5G17770", "NADH:cytochrome B5 reductase 1", "0.017", "0.4", "2.5"], ["AT1G74790", "Catalytics", "0.045", "5.7", "4.6"], ["AT4G23850", "AMP-dep. synthetase and ligase protein", "0.017", "0.5", "ns"], ["AT1G65290", "Mitochondrial acyl carrier protein 2", "0.044", "2.9", "ns"], ["AT3G47930", "L-galactono-1,4-lactone dehydrogenase", "0.019", "0.2", "ns"], ["2. Energy"], ["AT1G79550", "Phosphoglycerate kinase", "0.0069", "0.2", "2.0"], ["AT1G24180", "Pyruvate dehydrogenase E1 comp. α-2", "0.014", "0.1", "0.2"], ["AT3G48000", "Aldehyde dehydrogenase 2B4", "0.022", "4.3", "7.1"], ["AT3G60750", "Transketolase", "0.0087", "0.5", "4.5"], ["AT2G05710", "Aconitase 3", "0.0002", "2.5", "12.0"], ["AT2G20420", "ATP citrate lyase", "0.022", "ns", "5.0"], ["AT5G08300", "Succinyl-CoA ligase, alpha subunit", "0.006", "2.4", "2.5"], ["AT2G44350", "Citrate synthase family protein", "0.026", "ns", "5.9"], ["AT1G65930", "Cyt. NADP+-dep. isocitrate dehydrogenase", "0.033", "0.1", "2.9"], ["AT1G15120", "Ubiquinol-cytochrome C reductase hinge", "0.016", "19", "20"], ["AT3G03100", "NADH:ubiquinone oxidoreductase,17.2kDa", "0.0029", "0.5", "ns"], ["AT5G13430", "Ubiquinol-cytochrome C reductase, Fe-S", "0.02", "0.2", "ns"], ["AT3G14610", "Cytochrome P450, 72A, polypeptide 7", "0.0026", "0.1", "5.4"], ["3. Cell growth/division"], ["AT5G52240", "Membrane steroid binding protein 1", "0.02", "0.1", "7.5"], ["AT1G10930", "DNA helicase (RECQl4A)", "0.0036", "4.6", "0.1"], ["AT3G44310", "Nitrilase 1", "0.023", "2.9", "ns"], ["4. Transcription"], ["AT1G14850", "Nucleoporin 155", "0.00094", "ns", "0.3"], ["5. Protein synthesis"], ["AT1G01100", "60S acidic ribosomal", "0.022", "ns", "0.4"], ["AT3G48930", "Nucleic acid-binding, OB-fold-like protein", "0.024", "2.1", "ns"], ["AT3G10090", "Nucleic acid-binding, OB-fold-like protein", "0.027", "ns", "0.3"], ["AT3G09200", "Ribosomal protein L10", "0.012", "2.9", "ns"], ["AT3G04400", "Ribosomal protein L14p/L23e", "0.0095", "3.8", "3.0"], ["AT1G23290", "Ribosomal protein L18e/L15", "0.017", "ns", "0.5"], ["AT4G02230", "Ribosomal protein L19e", "0.0089", "ns", "0.3"], ["AT2G44120", "Ribosomal protein L30/L7", "0.027", "ns", "0.5"], ["AT5G56710", "Ribosomal protein L31e", "0.013", "4.6", "ns"], ["AT3G45030", "Ribosomal protein S10p/S20e", "0.03", "ns", "2.2"], ["AT5G02960", "Ribosomal protein S12/S23", "0.016", "2.3", "ns"], ["AT3G60245", "Zinc-binding ribosomal protein", "0.036", "2.4", "ns"], ["6. Protein destination and storage"], ["AT1G14980", "Chaperonin 10", "0.022", "ns", "2.9"], ["AT3G02530", "Chaperonin 60 family protein", "0.045", "2.2", "0.4"], ["AT3G03960", "Chaperonin 60 family protein", "0.041", "2.1", "ns"], ["AT5G56030", "Heat shock protein 81-2", "0.012", "0.4", "ns"], ["AT3G52140", "Tetratricopeptide repeat-containing protein", "0.04", "5.3", "ns"], ["7. Transporters"], ["AT4G38580", "Farnesylated protein 6", "0.017", "0.4", "ns"], ["AT3G15660", "Glutaredoxin 4", "0.011", "ns", "6.0"], ["AT1G27950", "Glycosylphosphatidylinositol-anchored lipid protein transfer 1", "0.027", "16.0", "44.0"], ["AT1G07670", "Endomembrane-type CA-ATPase 4", "0.0026", "0.1", "5.0"], ["AT4G27500", "Proton pump interactor 1", "0.006", "ns", "2.4"], ["AT4G39080", "Vacuolar proton ATPase A3", "0.0041", "0.5", "ns"], ["AT3G58730", "Vacuolar proton pump D subunit", "0.044", "0.4", "ns"], ["AT1G15500", "TLC ATP/ADP transporter", "0.0099", "0.3", "ns"], ["AT4G28390", "ADP/ATP carrier 3", "0.014", "0.1", "ns"], ["AT5G60460", "Preprotein translocase Sec, Sec61-β subunit", "0.0081", "4.7", "4"], ["AT3G51890", "Clathrin light chain protein", "0.019", "ns", "0.5"], ["AT3G08530", "Clathrin, heavy chain", "0.0021", "0.5", "0.2"], ["AT3G11130", "Clathrin, heavy chain", "0.00044", "0.5", "0.4"], ["AT5G19760", "Mitochondrial substrate carrier protein", "0.038", "ns", "2.2"], ["AT5G40810", "Cytochrome C1", "0.021", "0.3", "ns"], ["8. Intracellular traffic"], ["AT3G49560", "Mit. import inner membrane translocase Tim17", "0.0031", "0.1", "ns"], ["AT1G61570", "Mit. import inner membrane translocase 13", "0.0044", "17", "23"], ["AT1G27390", "Translocase outer membrane 20-2", "0.0015", "0.1", "2.1"], ["AT3G60600", "Vesicle associated protein", "0.051", "ns", "3"], ["AT4G34660", "SH3 domain-containing protein", "0.039", "4.7", "ns"], ["9. Cell structure"], ["AT5G09810", "Actin 7", "0.0038", "0.5", "ns"], ["AT5G19770", "Tubulin alpha-3", "0.016", "0.1", "ns"], ["AT5G62690", "Tubulin beta chain 2", "0.006", "0.4", "0.4"], ["AT2G29550", "Tubulin beta-7 chain", "0.0034", "0.3", "0.4"], ["AT4G14960", "Tubulin/FtsZ family protein", "0.036", "0.4", "0.5"], ["AT3G08950", "Electron transport SCO1/SenC protein", "0.045", "0.1", "4.3"], ["10. Signal transduction"], ["AT3G14840", "LRR transmembrane protein kinase", "0.025", "ns", "11"], ["AT5G59840", "Ras-related small GTP-binding protein", "0.0084", "0.1", "2.7"], ["AT3G51800", "Metallopeptidase M24", "0.0015", "5.1", "ns"], ["11. Disease/Defence"], ["AT3G57280", "Transmembrane proteins 14C", "0.014", "0.1", "ns"], ["AT3G12500", "Basic chitinase", "0.035", "ns", "2.1"], ["AT3G32980", "Peroxidase superfamily protein", "0.012", "ns", "3"], ["AT4G36430", "Peroxidase superfamily protein", "0.015", "0.1", "ns"], ["12. Unclassified"], ["AT2G40765", "Unknown protein", "0.019", "2", "ns"], ["AT2G46540", "Unknown protein", "0.033", "ns", "3.5"], ["AT4G12590", "Transmembrane protein, DUF106", "0.033", "0.3", "ns"], ["AT1G08480", "Unknown protein", "0.048", "0.2", "0.4"], ["AT3G20370", "TRAF-like family protein", "0.0058", "0.2", "3"], ["AT3G49720", "Unknown protein", "0.016", "0.1", "0.3"], ["AT4G24330", "DUF1682, unknown protein", "0.0077", "0.1", "2.2"], ["AT2G33585", "Unknown protein", "0.019", "0.1", "13"]], "row_count": 99, "column_count": 5, "numeric_cells": 353, "header_rows": 1, "locator": "section[8]/table-wrap[1]#proteomes-05-00022-t001"}}, {"id": "asset:table:pmid:28820483:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7026578a3d9b8c4ad78965d5c2b77a9432c9e11f75b26965192842224d248f9d", "bytes": 3796, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[2]#proteomes-05-00022-t002", "version": null, "note": "Proteins responsive to abscisic acid (ABA) treatment.", "structure": {"pmcid": "PMC5620539", "section_index": 8, "section_title": "3. Results", "row_count": 64, "column_count": 5}, "table": {"label": "Table 2", "caption": "Proteins responsive to abscisic acid (ABA) treatment.", "rows": [["Accession Number", "Protein Name", "ANOVA (p-Value)", "FC 5 min", "FC 20 min"], ["1. Metabolism"], ["AT2G26400", "Acireductone dioxygenase 3", "0.035", "3.9", "6.8"], ["AT4G34200", "D-3-phosphoglycerate dehydrogenase 1", "0.017", "0.5", "ns"], ["AT1G17745", "D-3-phosphoglycerate dehydrogenase 2", "0.029", "0.1", "0.2"], ["AT4G13940", "S-adenosyl-L-homocysteine hydrolase", "0.028", "2.5", "2.0"], ["AT3G17820", "Glutamine synthetase 1.3", "0.023", "3.7", "3.5"], ["AT5G17770", "NADH cytochrome B5 reductase 1", "0.046", "2.3", "2.3"], ["AT3G15730", "Phospholipase D α 1", "0.014", "3.2", "3.8"], ["2. Energy"], ["AT2G01140", "Aldolase superfamily protein", "0.0075", "5.0", "5.1"], ["AT5G43940", "GroES-like zinc-binding dehydrogenase", "0.014", "4.5", "5.2"], ["AT4G34870", "Rotamase cyclophilin 5", "0.0015", "3.1", "2.7"], ["AT2G05710", "Aconitase 3", "0.035", "8.0", "9.9"], ["AT1G15120", "Ubiquinol-cytochrome C reductase hinge", "0.041", "15.0", "11.0"], ["AT2G33220", "GRIM-19 protein", "0.017", "2.9", "7.1"], ["3. Cell growth/division"], ["AT5G43070", "WPP domain protein 1", "0.042", "0.4", "0.2"], ["4. Transcription"], ["AT2G18740", "Small nuclear ribonucleoprotein", "0.02", "7.7", "4.3"], ["AT5G40480", "Embryo defective 3012", "0.0084", "5.6", "7.9"], ["AT1G14850", "Nucleoporin 155", "0.0058", "0.1", "0.2"], ["5. Protein synthesis"], ["AT1G08360", "Ribosomal protein L1p/L10e", "0.037", "3.1", "ns"], ["AT4G10450", "Ribosomal protein L6", "0.00092", "12.0", ">0.1"], ["AT5G08180", "Ribosomal protein L7Ae", "0.022", "11.0", "8.7"], ["AT3G04400", "Ribosomal protein L14p", "0.016", "3.5", "2.6"], ["AT3G14600", "Ribosomal protein L18ae", "0.033", "3.4", "3.3"], ["AT3G45030", "Ribosomal protein S10p/S20e", "0.0041", "2.3", "ns"], ["AT5G47930", "Zinc-binding ribosomal protein", "0.027", "8.6", "7.0"], ["AT4G00810", "60S acidic ribosomal protein family", "0.042", "0.4", "0.4"], ["AT1G01100", "60S acidic ribosomal protein family", "0.045", "0.4", "0.4"], ["AT5G47700", "60S acidic ribosomal protein family", "0.0085", "0.3", "0.4"], ["6. Protein destination and storage"], ["AT1G14980", "Chaperonin 10", "0.0061", "2.5", "3.0"], ["AT3G16420", "PYK10-binding protein 1", "0.017", "0.3", "0.5"], ["AT5G56030", "Heat shock protein 81-2", "0.0038", "0.4", "0.5"], ["AT1G03220", "Eukaryotic aspartyl protease", "0.0045", "2.3", "2.5"], ["7. Transporters"], ["AT3G53420", "Plasma membrane intrinsic protein 2A", "0.031", "0.3", "ns"], ["AT3G42050", "Vacuolar ATP synthase subunit H", "0.045", "4.4", "4.2"], ["AT4G27500", "Proton pump interactor 1", "0.0048", "ns", "2.3"], ["AT2G34250", "SecY protein transport", "0.011", "2.5", "3.9"], ["AT3G08530", "Clathrin, heavy chain", "0.0019", "0.2", "0.4"], ["AT3G11130", "Clathrin, heavy chain", "0.00054", "0.3", "0.4"], ["8. Intracellular traffic"], ["AT2G29530", "TIM10 zinc finger protein", "0.021", "6.0", "5.0"], ["AT1G61570", "Mit. import inner membrane 13 translocase", "0.042", "19.0", "11.0"], ["9. Cell structure"], ["AT4G30270", "Xyloglucan endotransglucosylase", "0.045", "ns", "3.0"], ["AT3G18780", "Actin 2", "0.016", "0.3", "ns"], ["AT5G09810", "Actin 7", "0.00073", "0.5", "0.5"], ["AT5G19770", "Tubulin alpha-3", "0.044", "0.5", "0.3"], ["AT5G62690", "Tubulin beta chain 2", "0.003", "0.3", "0.4"], ["AT2G29550", "Tubulin beta-7 chain", "0.0072", "0.3", "0.4"], ["AT4G14960", "Tubulin/FtsZ family protein", "0.019", "0.4", "0.3"], ["10. Signal transduction"], ["AT3G14840", "LRR transmembrane protein kinase", "0.014", "8.3", "14.0"], ["AT3G51800", "Metallopeptidase M24", "0.027", "3.4", "ns"], ["11. Disease/Defence"], ["AT1G78850", "D-mannose binding lectin protein", "0.0013", "14.0", "18.0"], ["AT2G43610", "Chitinase family protein", "0.05", "ns", "0.3"], ["AT4G38740", "Rotamase CYP 1", "0.02", "2.6", "ns"], ["AT1G20620", "Catalase 3", "0.0064", "3.5", "2.1"]], "row_count": 64, "column_count": 5, "numeric_cells": 245, "header_rows": 1, "locator": "section[8]/table-wrap[2]#proteomes-05-00022-t002"}}, {"id": "asset:table:pmid:28820483:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:44de3bf261db64b8ca950888ca99709786b25f7370f2a42f2ce7523dfbae36db", "bytes": 1895, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[3]#proteomes-05-00022-t003", "version": null, "note": "Comparison differential protein accumulation in response to ABA and H2O2.", "structure": {"pmcid": "PMC5620539", "section_index": 8, "section_title": "3. Results", "row_count": 31, "column_count": 6}, "table": {"label": "Table 3", "caption": "Comparison differential protein accumulation in response to ABA and H2O2.", "rows": [["Accession Number", "Protein Name", "H2O2 5 min", "H2O2 20 min", "ABA 5 min", "ABA 20 min"], ["1. Metabolism"], ["AT1G17745", "D-3-phosphoglycerate dehydrogenase 2", "0.1", "0.1", "0.1", "0.2"], ["AT5G17770", "NADH:cytochrome B5 reductase 1", "0.4", "2.5", "2.3", "2.3"], ["2. Energy"], ["AT2G05710", "Aconitase 3", "2.5", "12", "8", "9.9"], ["AT1G15120", "Ubiquinol-cytochrome C reductase hinge", "19", "20", "15", "11"], ["3. Transcription"], ["AT1G14850", "Nucleoporin 155", "ns", "0.3", "0.1", "0.2"], ["4. Protein synthesis"], ["AT3G04400", "Ribosomal protein L14p/L23e", "3.8", "3", "3.5", "2.6"], ["AT3G45030", "Ribosomal protein S10p/S20e", "ns", "2.2", "2.3", "ns"], ["AT1G01100", "60S acidic ribosomal protein family", "ns", "0.4", "0.4", "0.4"], ["5. Protein destination and storage"], ["AT1G14980", "Chaperonin 10", "ns", "2.9", "2.5", "3"], ["AT5G56030", "Heat shock protein 81-2", "0.4", "ns", "0.4", "0.5"], ["6. Transporters"], ["AT4G27500", "Proton pump interactor 1", "ns", "2.4", "ns", "2.3"], ["AT3G08530", "Clathrin, heavy chain", "0.5", "0.2", "0.2", "0.4"], ["AT3G11130", "Clathrin, heavy chain", "0.5", "0.4", "0.3", "0.4"], ["7. Intracellular traffic"], ["AT1G61570", "Mit. import inner membrane 13 translocase", "17", "23", "19", "11"], ["8. Cell structure"], ["AT5G09810", "Actin 7", "0.5", "ns", "0.5", "0.5"], ["AT4G14960", "Tubulin/FtsZ family protein", "0.4", "0.5", "0.4", "0.3"], ["AT5G62690", "Tubulin beta chain 2", "0.4", "0.4", "0.3", "0.4"], ["AT2G29550", "Tubulin beta-7 chain", "0.3", "0.4", "0.3", "0.4"], ["AT5G19770", "Tubulin alpha-3", "0.1", "ns", "0.5", "0.3"], ["9. Signal transduction"], ["AT3G51800", "Metallopeptidase M24 family protein", "5.1", "ns", "3.4", "ns"], ["AT3G14840", "LRR transmembrane protein kinase", "ns", "11", "8.3", "14"]], "row_count": 31, "column_count": 6, "numeric_cells": 121, "header_rows": 1, "locator": "section[8]/table-wrap[3]#proteomes-05-00022-t003"}}], "gaps": ["asset:data:geo:PXD006513 not downloaded", "asset:data:geo:PXD006513 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Proteins were deemed responsive to treatment when present in at least two replicates with a fold change (FC) greater or equal to |±2|, verified by Student t-test (p-value ≤ 0.05) in comparison to the mock-treated samples."}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["PXD006513"], "resolved_accessions": ["PXD006513"], "statements": ["Data are available via ProteomeXchange with identifier PXD006513."], "basis": "The paper names PXD006513 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": [], "assets": ["source:pmid:28820483", "data:geo:PXD006513", "asset:table:pmid:28820483:1", "asset:table:pmid:28820483:2", "asset:table:pmid:28820483:3"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD006513"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:10:00Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 38831, "completion_tokens": 919, "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:28820483", "type": "paper", "label": "pmid:28820483"}, {"id": "source:pmid:28820483", "type": "manuscript", "label": "PMID 28820483 full text"}, {"id": "data:geo:PXD006513", "type": "dataset", "label": "GEO PXD006513"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:28820483", "type": "paper", "label": "pmid:28820483"}, {"id": "source:pmid:28820483", "type": "manuscript", "label": "PMID 28820483 full text"}, {"id": "data:geo:PXD006513", "type": "dataset", "label": "GEO PXD006513"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-28820483", "type": "extraction", "used": ["source:pmid:28820483"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD006513", "type": "accession_resolution", "used": ["data:geo:PXD006513"], "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:28820483", "parent_hash": "sha256:6b3e8e802ae0694f2a4a25ec533df41d3747ad38a1604dd5dad822637192339a", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD006513 licence not read", "asset:data:geo:PXD006513 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "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": ["A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses.", "hate (NADPH)-oxidases. Although quantitative proteomics studies have been performed to identify ABA-", "Arabidopsis microsomal proteome using tandem mass spectrometry and identified 86 specifically H₂O₂-dependen"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Proteins were deemed responsive to treatment when present in at least two replicates with a fold change (FC) greater or equal to |±2|, verified by Student t-test (p-value ≤ 0.05) in comparison to the mock-treated samples."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}