Analysis of the Escherichia coli extracellular vesicle proteome identifies markers of purity and culture conditions.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31275533", "kind": "science-record", "revision": 4, "content_hash": "sha256:352091b8d0949765959d8d17ed1044971a15db4aa333b9efacef940e5c9077f1", "created_at": "2026-11-01T15:40:46Z", "updated_at": "2026-11-01T21:22:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Analysis of the Escherichia coli extracellular vesicle proteome identifies markers of purity and culture conditions.", "doi": "10.1080/20013078.2019.1632099", "pmid": "31275533", "authors": ["Jiwon Hong", "Priscila Dauros-Singorenko", "Alana Whitcombe", "Leo Payne", "Cherie Blenkiron", "Anthony Phillips", "Simon Swift"], "journal": "Journal of extracellular vesicles", "year": 2019, "abstract": "Bacteria release nano-sized extracellular vesicles (EVs) into the extracellular milieu. Bacterial EVs contain molecular cargo originating from the parent bacterium and have important roles in bacterial survival and pathogenesis. Using 8-plex iTRAQ approaches, we profiled the EV proteome of two Escherichia coli strains, uropathogenic (UPEC) 536 and probiotic Nissle 1917. For these strains, we compared the proteome of crude input EVs prepared by ultracentrifugation alone with EVs purified by either density gradient centrifugation (DGC) or size exclusion chromatography (SEC). We further compared the proteome of EVs from bacterial cultures that were grown in iron-restricted (R) and iron-supplemented (RF) conditions. Overall, outer membrane components were highly enriched, and bacterial inner membrane components were significantly depleted in both UPEC and Nissle EVs, in keeping with an outer membrane origin. In addition, we found enrichment of ribosome-related Gene Ontology terms in UPEC EVs and proteins involved in glycolytic processes and ligase activity in Nissle EVs. We have identified that three proteins (RbsB of UPEC in R; YoeA of UPEC in RF; BamA of Nissle in R) were consistently enriched in the DGC- and SEC-purified EV samples in comparison to their crude input EV, whereas conversely the 60 kDa chaperonin GroEL was enriched in the crude input EVs for both UPEC and Nissle in R condition. Such proteins may have utility as technical markers for assessing the purity of E. coli EV preparations. Several proteins were changed in their abundance depending on the iron availability in the media. Data are available via ProteomeXchange with identifier PXD011345. In summary, we have undertaken a comprehensive characterization of the protein content of E. coli EVs and found evidence of specific EV cargos for physiological activity and conserved protein cargo that may find utility as markers in the future. Abbreviation: DGC: density gradient centrifugation; DTT: 1,4-dithiothreitol; EV: extracellular vesicles; FDR: false discovery rate; GO: Gene Ontology; R: iron-restricted; RF: iron-supplemented; iTRAQ: isobaric tags for relative and absolute quantitation; OMV: outer membrane vesicle; SWATH-MS: sequential window acquisition of all theoretical mass spectra; SEC: size exclusion chromatography.", "claims": [{"id": "claim-method", "statement": "For the GO analysis, categories with Bonferroni-corrected p value <0.05 were selected.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31275533", "locator": "sections[10] \"Mass spectrometry and protein identification and quantitation\" paragraph 5", "quote": "For the GO analysis, categories with Bonferroni-corrected p value <0.05 were selected."}], "state": "complete"}, {"id": "claim-data-access", "statement": "ProteomeXchange (ID#PXD011345)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31275533", "locator": "sections[30] \"Data deposition\" paragraph 2", "quote": "ProteomeXchange (ID#PXD011345)"}], "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:31275533"], "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:PXD011345"], "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:PXD011345"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31275533", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1080/20013078.2019.1632099", "sha256": "sha256:4bdb22af5e45b260b1c8bacee71dc5f54155f359895a1ae8a3d7edd02fa840b7", "bytes": 62863, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1080/20013078.2019.1632099", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6598517", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD011345", "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=PXD011345", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD011345", "version": null, "note": "ProteomeXchange (ID#PXD011345)", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "ProteomeXchange (ID#PXD011345)", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Analysis of the Escherichia coli membrane vesicle proteome identifies markers of purity and culture conditions", "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:31275533:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a5da5a4ccfd2f9cf69d4ba2b3baf62389e16126cc0454e6878de2ef487296265", "bytes": 1439, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#T0001", "version": null, "note": "Samples used in two 8-plex iTRAQ experiments.", "structure": {"pmcid": "PMC6598517", "section_index": 13, "section_title": "Comparison of overall EV protein profile between UPEC and Nissle", "row_count": 17, "column_count": 6}, "table": {"label": "Table 1.", "caption": "Samples used in two 8-plex iTRAQ experiments.", "rows": [["iTRAQ experiment#", "iTRAQ tag", "E. coli strain", "Growth medium", "EV sample name", "EV preparation description"], ["1", "117", "UPEC", "R", "DGC-crude input", "Crude input before DGC"], ["113", "UPEC", "R", "DGC-purified", "Pooled fractions from DGC purification"], ["119", "UPEC", "R", "SEC-crude input", "Crude input before SEC"], ["115", "UPEC", "R", "SEC-purified", "Pooled fractions from SEC purification"], ["114", "UPEC", "RF", "DGC-crude input", "Crude input before DGC"], ["116", "UPEC", "RF", "DGC-purified", "Pooled fractions from DGC purification"], ["118", "UPEC", "RF", "SEC-crude input", "Crude input before SEC"], ["121", "UPEC", "RF", "SEC-purified", "Pooled fractions from SEC purification"], ["2", "116", "Nissle", "R", "DGC-crude input", "Crude input before DGC"], ["114", "Nissle", "R", "DGC-purified", "Pooled fractions from DGC purification"], ["121", "Nissle", "R", "SEC-crude input", "Crude input before SEC"], ["118", "Nissle", "R", "SEC-purified", "Pooled fractions from SEC purification"], ["117", "Nissle", "RF", "DGC-crude input", "Crude input before DGC"], ["113", "Nissle", "RF", "DGC-purified", "Pooled fractions from DGC purification"], ["119", "Nissle", "RF", "SEC-crude input", "Crude input before SEC"], ["115", "Nissle", "RF", "SEC-purified", "Pooled fractions from SEC purification"]], "row_count": 17, "column_count": 6, "numeric_cells": 18, "header_rows": 1, "locator": "section[13]/table-wrap[1]#T0001"}}, {"id": "asset:table:pmid:31275533:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3873ead682e2269ff4575230ce874c37c93c82b9c0d95363fb28cef9fb25302c", "bytes": 633, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[2]#T0002", "version": null, "note": "Summary of spectra, peptides and proteins identified and quantified in two 8-plex iTRAQ experiments.", "structure": {"pmcid": "PMC6598517", "section_index": 13, "section_title": "Comparison of overall EV protein profile between UPEC and Nissle", "row_count": 3, "column_count": 7}, "table": {"label": "Table 2.", "caption": "Summary of spectra, peptides and proteins identified and quantified in two 8-plex iTRAQ experiments.", "rows": [["Bacteria", "Experiment", "Total spectra", "Identified spectra (99% confidence)", "Identified distinct peptides (99% confidence)", "Identified proteins after grouping (Unused ProtScore >2)", "Quantified proteins (Unused ProtScore >2; with both iTRAQ ratio and p values)"], ["UPEC", "iTRAQ#1", "10,992", "3,387", "2,266", "205", "166"], ["Nissle", "iTRAQ#2", "10,930", "3,067", "1,854", "189", "158"]], "row_count": 3, "column_count": 7, "numeric_cells": 16, "header_rows": 1, "locator": "section[13]/table-wrap[2]#T0002"}}, {"id": "asset:table:pmid:31275533:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:852df3542117253871a46f34650eceae7b3fb919df05e298a6ce40b8c394082c", "bytes": 4474, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T0003", "version": null, "note": "Key findings from iTRAQ#1 experiment on the UPEC EV proteins that compared three EV preparation methods (crude input for DGC or SEC purifications, DGC-purified and SEC-purified) in R (without iron) and RF (with iron) growth conditions. Comparison A) indicates a protein enriched by both DGC and SEC purification methods in iron-restricted condition. Comparison B) indicates proteins depleted by both DGC and SEC purification methods in iron-restricted condition. Comparison C) indicates a protein enriched by both DGC and SEC purification methods in iron-supplemented condition. Comparison D) shows a protein depleted by both DGC and SEC purification methods in iron-supplemented condition. Comparison E) indicates proteins enriched in iron-supplemented condition. Comparison F) indicates proteins enriched in iron-restricted condition. N is the rank of the specified protein relative to all other detected proteins (sorted by Unused ProtScore). The details shown below are based on the winner protein selected by the ProteinPilot software for the specific N.", "structure": {"pmcid": "PMC6598517", "section_index": 14, "section_title": "Effect of purification method on the proteome of UPEC EVs produced under different iron availability conditions", "row_count": 23, "column_count": 6}, "table": {"label": "Table 3.", "caption": "Key findings from iTRAQ#1 experiment on the UPEC EV proteins that compared three EV preparation methods (crude input for DGC or SEC purifications, DGC-purified and SEC-purified) in R (without iron) and RF (with iron) growth conditions. Comparison A) indicates a protein enriched by both DGC and SEC purification methods in iron-restricted condition. Comparison B) indicates proteins depleted by both DGC and SEC purification methods in iron-restricted condition. Comparison C) indicates a protein enriched by both DGC and SEC purification methods in iron-supplemented condition. Comparison D) shows a protein depleted by both DGC and SEC purification methods in iron-supplemented condition. Comparison E) indicates proteins enriched in iron-supplemented condition. Comparison F) indicates proteins enriched in iron-restricted condition. N is the rank of the specified protein relative to all other detected proteins (sorted by Unused ProtScore). The details shown below are based on the winner protein selected by the ProteinPilot software for the specific N.", "rows": [["", "N", "Accession", "Protein Names", "Cellular component", "Biological function"], ["Comparison A)", "R: DGC-crude input < DGC-purified and SEC-crude input < SEC-purified", "", ""], ["", "60", "sp|P02925|RBSB_ECOLI", "Ribose import binding protein RbsB", "Outer membrane-bounded periplasmic space; inner membrane; integral component of membrane", "Monosaccharide transmembrane transporter activity; chemotaxis"], ["Comparison B)", "R: DGC-crude input > DGC-purified and SEC-crude input > SEC-purified", "", ""], ["", "c1", "sp|P09983|HLYAC_ECOLX", "Hemolysin, chromosomal", "Extracellular region; host cell plasma membrane; integral component of membrane", "Calcium ion binding; hemolysis in other organism; pathogenesis"], ["", "a8", "sp|Q0T9P8|CH60_ECOL5", "60 kDa chaperonin (GroEL protein, Protein Cpn60)", "Cytoplasm", "ATP binding; protein refolding"], ["", "12", "sp|P04949|FLIC_ECOLI", "Flagellin", "Extracellular region; bacterial inner membrane; flagellum filament", "Structural molecule activity; bacterial-type flagellum-dependent cell motility; toll-like receptor 5 signaling pathway"], ["", "c22", "sp|Q8XAS6|EFEO_ECO57", "Iron uptake system component EfeO", "Periplasmic space", "Iron-binding and/or electron-transfer component"], ["Comparison C)", "RF: DGC-crude input < DGC-purified and SEC-crude input < SEC-purified", "", ""], ["", "113", "sp|P76356|YOEA_ECOLI", "Putative uncharacterized protein YoeA", "Membrane", "Receptor activity; transport"], ["Comparison D)", "RF: DGC-crude input > DGC-purified and SEC-crude input > SEC-purified", "", ""], ["", "(Not identified)", "", ""], ["Comparison E)", "R < RF in at least 3 samples", "", "", ""], ["", "14", "sp|P09373|PFLB_ECOLI", "Formate acetyltransferase 1 (Pyruvate formate-lyase 1)", "Cytosol", "Formate C-acetyltransferase activity; glucose metabolic process; threonine catabolic process"], ["", "b28", "sp|P02931|OMPF_ECOLI", "Outer membrane protein F (Outer membrane protein 1A, Outer membrane protein B, Outer membrane protein IA, Porin OmpF)", "Cell outer membrane", "Colicin transmembrane transporter activity; drug transmembrane transporter activity; ion transmembrane transporter activity; porin activity"], ["", "39", "sp|P46130|YBHC_ECOLI", "Putative acyl-CoA thioester hydrolase YbhC", "Cell outer membrane", "Aspartyl esterase activity; pectinesterase activity; cell wall modification"], ["", "84", "sp|P37194|SLP_ECOLI", "Outer membrane protein slp", "Cell outer membrane", "Identical protein binding"], ["Comparison F)", "R > RF in 3 samples", "", "", ""], ["", "c1", "sp|P09983|HLYAC_ECOLX", "Hemolysin, chromosomal", "Extracellular region; host cell plasma membrane; integral component of membrane", "Calcium ion binding; hemolysis in other organism; pathogenesis"], ["", "2", "sp|P17315|CIRA_ECOLI", "Colicin I receptor", "Cell outer membrane; integral component of membrane", "Colicin transmembrane transporter activity; receptor activity; siderophore transmembrane transporter activity; iron assimilation"], ["", "21", "sp|P0CK95|ACFD_ECOLI", "Putative lipoprotein AcfD homolog", "Bacterial inner membrane", "(Not known)"], ["", "c,a22", "sp|Q8XAS6|EFEO_ECO57", "Iron uptake system component EfeO", "Periplasmic space", "Iron-binding and/or electron-transfer"], ["", "a27", "sp|Q8X9X2|YNCE_ECO57", "Uncharacterized protein YncE", "(Not known, predicted periplasmic protein)", "(Not known)"]], "row_count": 23, "column_count": 6, "numeric_cells": 33, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T0003"}}, {"id": "asset:table:pmid:31275533:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b17a0d06b02d7eae3d7e4d2e0fd3aad709f3b01c638a6fb415c5f83a712ed116", "bytes": 5410, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#T0004", "version": null, "note": "Key findings from iTRAQ#2 experiment on the Nissle EV proteins that compared 3 EV preparation methods (crude input for DGC or SEC purifications, DGC-purified and SEC-purified) in R (without iron) and RF (with iron) growth conditions. Comparison A) indicates a protein enriched by both DGC and SEC purification methods in iron-restricted condition. Comparison B) indicates proteins depleted by both DGC and SEC purification methods in iron-restricted condition. Comparison C) indicates a protein enriched by both DGC and SEC purification methods in iron-supplemented condition. Comparison D) shows a protein depleted by both DGC and SEC purification methods in iron-supplemented condition. Comparison E) indicates proteins enriched in iron-supplemented condition. Comparison F) indicates proteins enriched in iron-restricted condition. N is the rank of the specified protein relative to all other detected proteins (sorted by Unused ProtScore). The details shown below are based on the winner protein selected by the ProteinPilot software for the specific N.", "structure": {"pmcid": "PMC6598517", "section_index": 15, "section_title": "Effect of purification method on the proteome of Nissle EVs produced under different iron availability conditions", "row_count": 30, "column_count": 6}, "table": {"label": "Table 4.", "caption": "Key findings from iTRAQ#2 experiment on the Nissle EV proteins that compared 3 EV preparation methods (crude input for DGC or SEC purifications, DGC-purified and SEC-purified) in R (without iron) and RF (with iron) growth conditions. Comparison A) indicates a protein enriched by both DGC and SEC purification methods in iron-restricted condition. Comparison B) indicates proteins depleted by both DGC and SEC purification methods in iron-restricted condition. Comparison C) indicates a protein enriched by both DGC and SEC purification methods in iron-supplemented condition. Comparison D) shows a protein depleted by both DGC and SEC purification methods in iron-supplemented condition. Comparison E) indicates proteins enriched in iron-supplemented condition. Comparison F) indicates proteins enriched in iron-restricted condition. N is the rank of the specified protein relative to all other detected proteins (sorted by Unused ProtScore). The details shown below are based on the winner protein selected by the ProteinPilot software for the specific N.", "rows": [["", "N", "Accession", "Protein Names", "Cellular component", "Biological function"], ["Comparison A)", "R: DGC-crude input < DGC-purified and SEC-crude input < SEC-purified", "", ""], ["", "23", "sp|Q1RG12|BAMA_ECOUT", "Outer membrane protein assembly factor BamA", "Cell outer membrane; integral component of membrane", "Membrane assembly"], ["Comparison B)", "R: DGC-crude input > DGC-purified and SEC-crude input > SEC-purified", "", ""], ["", "a8", "sp|Q1R3B6|CH60_ECOUT", "60 kDa chaperonin (GroEL protein, Protein Cpn60)", "Cytoplasm", "ATP binding; protein refolding"], ["", "67", "sp|Q8FHC7|MAND_ECOL6", "D-galactonate dehydratase family member RspA", "(Not known)", "Magnesium ion binding; mannonate dehydratase activity; carbohydrate catabolic process; cellular amino acid catabolic process"], ["Comparison C)", "RF: DGC-crude input < DGC-purified and SEC-crude input < SEC-purified", "", ""], ["", "(Not identified)", "", ""], ["Comparison D)", "RF: DGC-crude input > DGC-purified and SEC-crude input > SEC-purified", "", ""], ["", "(Not identified)", "", ""], ["Comparison E)", "R < RF in at least 3 samples", "", "", ""], ["", "3", "sp|Q8FDA1|LPOA_ECOL6", "Penicillin-binding protein activator LpoA", "Cell outer membrane; periplasmic space", "Hydrolase activity, hydrolyzing O-glycosyl compounds; peptidoglycan biosynthetic process; regulation of cell shape"], ["", "b 5", "sp|Q8CVW1|OMPC_ECOL6", "Outer membrane protein C (Outer membrane protein 1B, Porin OmpC)", "Cell outer membrane", "Pore complex; porin activity; ion transport"], ["", "11", "sp|Q8FDW4|SAT_ECOL6", "Serine protease sat autotransporter", "Cell outer membrane; cell surface; extracellular region; integral component of membrane; periplasmic space", "Serine-type endopeptidase activity; pathogenesis"], ["", "14", "sp|P62606|FIM1C_ECOL6", "Type-1 fimbrial protein, C chain (Type-1C pilin)", "Pilus", "Cell adhesion"], ["", "b 21", "sp|P10100|RLPA_ECOLI", "Endolytic peptidoglycan transglycosylase RlpA (Rare lipoprotein A)", "Cell outer membrane; bacterial inner membrane", "Lyase activity; peptidoglycan binding; cell wall organization"], ["", "42", "sp|Q8FJM0|DPS_ECOL6", "DNA protection during starvation protein", "Cytoplasm; nucleoid", "DNA binding; ferric iron binding; oxidoreductase activity, oxidizing metal ions; cellular iron ion homeostasis; chromosome condensation; response to stress"], ["", "b 51", "sp|P21420|NMPC_ECOLI", "Putative outer membrane porin protein NmpC", "Cell outer membrane", "Pore complex; porin activity; ion transport; transport"], ["", "58", "sp|P29744|FLGL_ECOLI", "Flagellar hook-associated protein 3", "Bacterial-type flagellum hook; extracellular region", "Structural molecule activity; bacterial-type flagellum-dependent cell motility"], ["", "76", "sp|P0A913|PAL_ECO57", "Peptidoglycan-associated lipoprotein", "Cell outer membrane; integral component of membrane", "Thought to play a role in bacterial envelope integrity"], ["", "90", "sp|Q8CVU7|FADL_ECOL6", "Long-chain fatty acid transport protein (Outer membrane FadL protein)", "Cell outer membrane; integral component of membrane", "Lipid transport"], ["Comparison F)", "R > RF in at least 3 samples", "", "", ""], ["", "2", "sp|Q1R5Y2|EFTU1_ECOUT", "Elongation factor Tu 1", "Cytoplasm", "GTP binding; GTPase activity; translation elongation factor activity"], ["", "b4", "sp|P23847|DPPA_ECOLI", "Periplasmic dipeptide transport protein", "Periplasmic space", "Chaperone-mediated protein folding; chemotaxis; dipeptide transport; protein transport"], ["", "a,b 10", "sp|Q8X9X2|YNCE_ECO57", "Uncharacterized protein YncE", "(Not known, predicted periplasmic protein)", "(Not known)"], ["", "a 12", "sp|Q8FJ35|EFEO_ECOL6", "Iron uptake system component EfeO", "Periplasmic space", "Iron-binding and/or electron-transfer"], ["", "38", "sp|P65765|FKBA_ECO57", "FKBP-type peptidyl-prolyl cis-trans isomerase FkpA (Rotamase)", "Periplasmic space", "Peptidyl-prolyl cis-trans isomerase activity; protein folding"], ["", "57", "sp|P77717|YBAY_ECOLI", "Uncharacterized lipoprotein YbaY", "Bacterial inner membrane", "(Not known)"], ["", "63", "sp|P0A864|TPX_ECO57", "Thiol peroxidase (Scavengase P20)", "Periplasmic space", "Thioredoxin peroxidase activity; cell redox homeostasis"], ["", "70", "sp|P0A906|SLYB_ECO57", "Outer membrane lipoprotein SlyB", "Cell outer membrane", "(Not known)"]], "row_count": 30, "column_count": 6, "numeric_cells": 41, "header_rows": 1, "locator": "section[15]/table-wrap[1]#T0004"}}], "gaps": ["asset:data:geo:PXD011345 not downloaded", "asset:data:geo:PXD011345 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Bonferroni correction", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For the GO analysis, categories with Bonferroni-corrected p value <0.05 were selected."}}], "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 (Bonferroni correction), 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. 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