← All .science files
pmid:32486122
Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis.
Jayaseelan Murugaiyan · Murat Eravci · Christoph Weise · Uwe Roesler · Lisa D Sprague · Heinrich Neubauer · Gamal Wareth
Biomolecules · 2020 doi:10.3390/biom10060836
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 · 7 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 · 7 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 · 6 items
[0] array · 4 items
[1] array · 3 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[3] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 4 items
[0] array · 2 items
[1] array · 6 items
[2] array · 7 items
[3] array · 7 items
[4] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 19 items
[0] array · 2 items
[1] array · 6 items
[2] array · 7 items
[3] array · 7 items
[4] array · 7 items
[5] array · 7 items
[6] array · 7 items
[7] array · 7 items
[8] array · 7 items
[9] array · 7 items
[10] array · 7 items
[11] array · 7 items
[12] array · 7 items
[13] array · 7 items
[14] array · 7 items
[15] array · 7 items
[16] array · 7 items
[17] array · 7 items
[18] array · 7 items
[5] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 9 items
[0] array · 5 items
[1] array · 5 items
[2] array · 3 items
[3] array · 3 items
[4] array · 5 items
[5] array · 5 items
[6] array · 5 items
[7] array · 5 items
[8] array · 2 items
[6] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 50 items
[0] array · 2 items
[1] array · 1 item
[2] array · 2 items
[3] array · 2 items
[4] array · 2 items
[5] array · 2 items
[6] array · 2 items
[7] array · 2 items
[8] array · 2 items
[9] array · 2 items
[10] array · 2 items
[11] array · 2 items
[12] array · 1 item
[13] array · 2 items
[14] array · 2 items
[15] array · 2 items
[16] array · 2 items
[17] array · 2 items
[18] array · 2 items
[19] array · 2 items
[20] array · 2 items
[21] array · 2 items
[22] array · 2 items
[23] array · 2 items
[24] array · 2 items
[25] array · 2 items
[26] array · 2 items
[27] array · 2 items
[28] array · 2 items
[29] array · 2 items
[30] array · 2 items
[31] array · 2 items
[32] array · 1 item
[33] array · 2 items
[34] array · 2 items
[35] array · 2 items
[36] array · 2 items
[37] array · 2 items
[38] array · 2 items
[39] array · 2 items
[40] array · 1 item
[41] array · 2 items
[42] array · 2 items
[43] array · 2 items
[44] array · 2 items
[45] array · 2 items
[46] array · 2 items
[47] array · 2 items
[48] array · 2 items
[49] array · 2 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 · 7 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 · 3 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 4 items
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[2] 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:32486122", "kind": "science-record", "revision": 7, "content_hash": "sha256:d608ed0c9f9e8b9edfa35480a50efcb8629c59c7e93b2d54c06dffb8b9c1dda3", "created_at": "2026-11-01T15:41:02Z", "updated_at": "2026-11-01T22:01:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Pan-Proteomic Analysis and Elucidation of Protein Abundance among the Closely Related Brucella Species, Brucella abortus and Brucella melitensis.", "doi": "10.3390/biom10060836", "pmid": "32486122", "authors": ["Jayaseelan Murugaiyan", "Murat Eravci", "Christoph Weise", "Uwe Roesler", "Lisa D Sprague", "Heinrich Neubauer", "Gamal Wareth"], "journal": "Biomolecules", "year": 2020, "abstract": "Brucellosis is a zoonotic infection caused by bacteria of the genus Brucella. The species, B. abortus and B. melitensis, major causative agents of human brucellosis, share remarkably similar genomes, but they differ in their natural hosts, phenotype, antigenic, immunogenic, proteomic and metabolomic properties. In the present study, label-free quantitative proteomic analysis was applied to investigate protein expression level differences. Type strains and field strains were each cultured six times, cells were harvested at a midlogarithmic growth phase and proteins were extracted. Following trypsin digestion, the peptides were desalted, separated by reverse-phase nanoLC, ionized using electrospray ionization and transferred into an linear trap quadrapole (LTQ) Orbitrap Velos mass spectrometer to record full scan MS spectra (m/z 300-1700) and tandem mass spectrometry (MS/MS) spectra of the 20 most intense ions. Database matching with the reference proteomes resulted in the identification of 826 proteins. The Cluster of Gene Ontologies of the identified proteins revealed differences in bimolecular transport and protein synthesis mechanisms between these two strains. Among several other proteins, antifreeze proteins, Omp10, superoxide dismutase and 30S ribosomal protein S14 were predicted as potential virulence factors among the proteins differentially expressed. All mass spectrometry data are available via ProteomeXchange with identifier PXD006348.", "claims": [{"id": "claim-method", "statement": "Statistical analysis was carried out using a two-way Student t-test, error correction (p < 0.05) and FDR correction of the alpha error was carried out by the method of Benjamini–Hochberg [43].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32486122", "locator": "sections[8] \"2.6. Data Analysis\" paragraph 2", "quote": "Statistical analysis was carried out using a two-way Student t-test, error correction (p < 0.05) and FDR correction of the alpha error was carried out by the method of Benjamini–Hochberg [43]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All mass spectrometry data are available via ProteomeXchange with identifier PXD006348.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32486122", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "All mass spectrometry data are available via ProteomeXchange with identifier PXD006348."}], "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:32486122"], "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:PXD006348"], "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:PXD006348"], "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:32486122", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/biom10060836", "sha256": "sha256:6a1346fefbab35aa099c0c3477397ed565b290d1db34e5345a84bc91f4932980", "bytes": 53881, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/biom10060836", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7355635", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD006348", "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=PXD006348", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD006348", "version": null, "note": "All mass spectrometry data are available via ProteomeXchange with identifier PXD006348.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All mass spectrometry data are available via ProteomeXchange with identifier PXD006348.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Label-free quantitative proteomic analysis of Brucella abortus and Brucella melitensis", "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:32486122:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:368b21a1d73611ba011ed16f002474bcd184caf4b5ea58f8a3729eb0957cd871", "bytes": 491, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#biomolecules-10-00836-t001", "version": null, "note": "Brucella strains used in this study.", "structure": {"pmcid": "PMC7355635", "section_index": 3, "section_title": "2.1. Brucella Culture", "row_count": 6, "column_count": 6}, "table": {"label": "Table 1", "caption": "Brucella strains used in this study.", "rows": [["Strain", "Designation/ID/Number", "Host", "Geographical Region"], ["FAO", "ATCC", "NCTC"], ["B. melitensis T", "16M", "23456", "10094", "Goat", "USA"], ["B. abortus T", "544", "23448", "10093", "Cattle", "UK"], ["B. melitensis", "C *", "", "", "Sheep", "China"], ["B. abortus", "T *", "", "", "Cattle", "Turkey"]], "row_count": 6, "column_count": 6, "numeric_cells": 6, "header_rows": 2, "locator": "section[3]/table-wrap[1]#biomolecules-10-00836-t001"}}, {"id": "asset:table:pmid:32486122:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:00b1d05c1e5fe2b537ac313c21b6af6ed33e74b4acd41e3408c8a2fef20069e5", "bytes": 422, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#biomolecules-10-00836-t002", "version": null, "note": "Number of regulated proteins among type and field strains.", "structure": {"pmcid": "PMC7355635", "section_index": 16, "section_title": "3.4. Comparative Proteomics of B. abortus and B. melitensis", "row_count": 4, "column_count": 7}, "table": {"label": "Table 2", "caption": "Number of regulated proteins among type and field strains.", "rows": [["Regulation", "Category"], ["IM vs. A", "IIM2 vs. A2", "IIIM2 vs. A", "IVM vs. A2", "VA2 vs. A", "VIM2 vs. M"], ["Down-", "173", "142", "166", "223", "83", "96"], ["Up-", "216", "199", "221", "248", "97", "129"]], "row_count": 4, "column_count": 7, "numeric_cells": 12, "header_rows": 2, "locator": "section[16]/table-wrap[1]#biomolecules-10-00836-t002"}}, {"id": "asset:table:pmid:32486122:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d9dc0269e2ec01d0c96b3b72baa36301f163ab4831960c01b44c9bbccfc932c2", "bytes": 1293, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#biomolecules-10-00836-t003", "version": null, "note": "KEGG pathways and the distribution of differentially expressed proteins.", "structure": {"pmcid": "PMC7355635", "section_index": 18, "section_title": "3.6. Bioinformatics Annotation of Differentially Expressed Proteins", "row_count": 19, "column_count": 7}, "table": {"label": "Table 3", "caption": "KEGG pathways and the distribution of differentially expressed proteins.", "rows": [["KEGG Pathways", "Category"], ["I", "II", "III", "IV", "V", "VI"], ["Metabolic pathways", "", "34 ↑", "", "", "", ""], ["Carbon metabolism", "", "", "6 ↑", "", "", ""], ["Glycolysis/gluconeogenesis", "", "", "", "7 ↓", "", ""], ["Pentose and glucuronate interconversions", "", "", "", "", "3 ↓", ""], ["Pyruvate metabolism", "", "", "4 ↑", "", "", ""], ["2-Oxocarboxylic acid metabolism", "4 ↓", "", "", "", "", ""], ["Microbial metabolism in diverse environments", "", "14 ↑", "10 ↑", "", "", ""], ["Biosynthesis of amino acids", "11 ↓", "", "", "14 ↓", "", ""], ["Histidine metabolism", "5 ↓", "5 ↓", "5 ↓", "6 ↓", "", ""], ["Valine, leucine and isoleucine biosynthesis", "", "", "", "4 ↓", "", ""], ["Purine metabolism", "", "7 ↑", "", "", "", ""], ["Pyrimidine metabolism", "5 ↑", "6 ↑", "", "7 ↑", "", ""], ["Biosynthesis of secondary metabolites", "19 ↓", "", "", "25 ↓", "", ""], ["RNA polymerase", "", "", "", "3 ↑", "", ""], ["Ribosome", "17 ↑", "18 ↓", "14 ↓", "19 ↑", "", "22 ↓"], ["Bacterial secretion system", "", "5 ↑", "5 ↑", "", "4 ↑", "5 ↑"], ["ABC transporters", "", "", "14 ↑", "", "", ""]], "row_count": 19, "column_count": 7, "numeric_cells": 33, "header_rows": 2, "locator": "section[18]/table-wrap[1]#biomolecules-10-00836-t003"}}, {"id": "asset:table:pmid:32486122:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3732a225385743c37f1a989fc205af924d22584c8a3432bdc417bb89439f3178", "bytes": 1001, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#biomolecules-10-00836-t004", "version": null, "note": "Differentially expressed proteins predicted as potentially virulence-associated.", "structure": {"pmcid": "PMC7355635", "section_index": 19, "section_title": "3.7. Predicted Virulence-Associated Proteins", "row_count": 9, "column_count": 5}, "table": {"label": "Table 4", "caption": "Differentially expressed proteins predicted as potentially virulence-associated.", "rows": [["Acc.", "Protein Description", "Reg", "Significance", "Reference"], ["D0B8I3*", "Antifreeze protein", "(+)", "Associated with MucR, a transcriptional regulator linked to Brucella virulence", "[63]"], ["Q8YIA9", "Antifreeze protein", "(-)"], ["Q2YM39", "Antifreeze protein type I", "(-)"], ["D0B248 *", "LipA family protein", "(-)", "", ""], ["Q2YIP8", "Lipoprotein Omp10", "(-)", "Reduced virulence in B. abortus with gene deletion and used in diagnostics", "[64,65,66]"], ["Q2YKV9", "Superoxide dismutase [Cu-Zn]", "(-)", "intracellular survival and used as antigens for subunit vaccines", "[19,67]"], ["Q2YRA8", "30S ribosomal protein S14", "(-)", "role in cellular adhesion and virulence in Candida albicans", "[68]"], ["ribosomal protein L7/L12 based subunit vaccines", "[69,70]"]], "row_count": 9, "column_count": 5, "numeric_cells": 10, "header_rows": 1, "locator": "section[19]/table-wrap[1]#biomolecules-10-00836-t004"}}, {"id": "asset:table:pmid:32486122:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:322bb30e21cdbf2551e23cd52ae80ca0390d56e5b939caed49e3fe573c380819", "bytes": 2600, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[20]/table-wrap[1]#biomolecules-10-00836-t005", "version": null, "note": "Differentially expressed proteins among the field isolates in comparison to that of the respective type strains.", "structure": {"pmcid": "PMC7355635", "section_index": 20, "section_title": "3.8. Field Strains and Host Adaptability", "row_count": 50, "column_count": 2}, "table": {"label": "Table 5", "caption": "Differentially expressed proteins among the field isolates in comparison to that of the respective type strains.", "rows": [["UniProt ID", "Protein"], ["Downregulated in Field Isolates"], ["Q8YBH7", "Bacterial extracellular solute-binding protein family 1"], ["Q8YIX9", "Glyceraldehyde-3-phosphate dehydrogenase"], ["Q2YMI0", "Phosphatidylserine decarboxylase proenzyme"], ["Q2YLU2", "Peptidylprolyl isomerase"], ["Q2YLF8", "Leu/Ile/Val-binding protein homolog 1"], ["Q2YLG0", "Leu/Ile/Val-binding protein homolog 2"], ["Q2YJA9", "Leu/Ile/Val-binding protein homolog 5"], ["Q2YQQ6", "Glutelin:Lipoprotein YaeC family:NLPA lipoprotein"], ["Q2YRP7", "Ribosome-recycling factor"], ["Q2YR20", "Uncharacterized protein"], ["Upregulated in Field Isolates"], ["Q2YJ78", "Type IV secretion system protein virB8"], ["Q2YJ79", "Type IV secretion system protein virB9"], ["Q2YJ81", "Type IV secretion system protein virB10"], ["Q2YJ83", "Type IV secretion system-outer membrane lipoprotein"], ["Q2YJ77", "Type IV secretion system putative lipoprotein virB7"], ["Q8YB25", "Alpha-methylacyl-CoA racemase"], ["Q2YIG7", "NADH:flavin oxidoreductase/NADH oxidase"], ["Q2YKS6", "Aminotransferase class IV"], ["Q8YCZ2", "N-acetylglucosamine-6-phosphate deacetylase"], ["Q8YI04", "ATP-dependent DNA ligase"], ["Q2YK32", "Catalase"], ["Q2YLX9", "Lipoprotein putative"], ["Q2YN45", "Probable cytosol aminopeptidase"], ["Q2YRJ0", "ATP/GTP-binding site motif A (P-loop)"], ["Q2YRN7", "Uncharacterized protein"], ["Q8YBU9", "Putative uroporphyrin-iii c-methyltransferase"], ["Q2YKY2", "Uncharacterized protein"], ["Q2YL40", "Uncharacterized protein"], ["Q2YLM7", "Uncharacterized protein"], ["Downregulated in B. abortus and Upregulated in B. melitensis"], ["Q2YME1", "Threonylcarbamoyl-AMP synthase"], ["Q2YNW9", "Dihydroxy-acid dehydratase"], ["Q8YHA5", "Glutaryl-CoA dehydrogenase"], ["Q2YP66", "Zinc-containing alcohol dehydrogenase"], ["Q2YQE3", "Periplasmic binding protein"], ["Q2YMW1", "Uncharacterized protein"], ["Q2YPK6", "Uncharacterized protein"], ["Upregulated in B. abortus and Downregulated in B. melitensis"], ["Q2YQV7", "50S ribosomal protein L20"], ["Q2YR56", "50S ribosomal protein L28"], ["Q2YRY0", "ABC-type glycine betaine transport system"], ["Q8YBF5", "Maltose-binding periplasmic protein (Sugar ABC transporter)"], ["Q8YCD1", "Cystine-binding periplasmic protein"], ["Q8YGE8", "Cationic amino acid ABC transporter"], ["Q2YKN7", "Uncharacterized protein"], ["Q2YKN9", "Uncharacterized protein"], ["Q2YQM2", "Uncharacterized protein"]], "row_count": 50, "column_count": 2, "numeric_cells": 22, "header_rows": 1, "locator": "section[20]/table-wrap[1]#biomolecules-10-00836-t005"}}], "gaps": ["asset:data:geo:PXD006348 not downloaded", "asset:data:geo:PXD006348 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": "Statistical analysis was carried out using a two-way Student t-test, error correction (p < 0.05) and FDR correction of the alpha error was carried out by the method of Benjamini–Hochberg [43]."}}], "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": ["PXD006348"], "resolved_accessions": ["PXD006348"], "statements": ["All mass spectrometry data are available via ProteomeXchange with identifier PXD006348."], "basis": "The paper names PXD006348 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:32486122", "data:geo:PXD006348", "asset:table:pmid:32486122:1", "asset:table:pmid:32486122:2", "asset:table:pmid:32486122:3", "asset:table:pmid:32486122:4", "asset:table:pmid:32486122:5"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD006348"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 45673, "completion_tokens": 1362, "cached_tokens": 793}}, "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:32486122", "type": "paper", "label": "pmid:32486122"}, {"id": "source:pmid:32486122", "type": "manuscript", "label": "PMID 32486122 full text"}, {"id": "data:geo:PXD006348", "type": "dataset", "label": "GEO PXD006348"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32486122", "type": "paper", "label": "pmid:32486122"}, {"id": "source:pmid:32486122", "type": "manuscript", "label": "PMID 32486122 full text"}, {"id": "data:geo:PXD006348", "type": "dataset", "label": "GEO PXD006348"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32486122", "type": "extraction", "used": ["source:pmid:32486122"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD006348", "type": "accession_resolution", "used": ["data:geo:PXD006348"], "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:32486122", "parent_hash": "sha256:59b151c65e00a95b8bac02ed09da4aef7cc546c1addbe8cfa812048d50f0ff31", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD006348 licence not read", "asset:data:geo:PXD006348 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": ["Pan-Proteomic Analysis and Elucidation of Protein Abundanc", "al hosts, phenotype, antigenic, immunogenic, proteomic and metabolomic properties. In the present s", "n the present study, label-free quantitative proteomic analysis was applied to investigate protein", "ll scan MS spectra (m/z 300-1700) and tandem mass spectrometry (MS/MS) spectra of the 20 most intense ions."], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["es. Type strains and field strains were each cultured six times, cells were harvested at a midloga"], "order_basis": "paper_text_order:585", "id": "assay:2"}, {"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": ["Statistical analysis was carried out using a two-way Student t-test, error correction (p < 0.05) and FDR correction of the alpha error was carried out by the method of Benjamini–Hochberg [43]."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}