Identification of synaptosomal proteins binding to monomeric and oligomeric α-synuclein.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25659148", "kind": "science-record", "revision": 7, "content_hash": "sha256:d625607a64fd40b29f49c974609f324d9a309801811618f635eaff39464063bc", "created_at": "2026-11-01T15:40:07Z", "updated_at": "2026-11-01T21:58:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of synaptosomal proteins binding to monomeric and oligomeric α-synuclein.", "doi": "10.1371/journal.pone.0116473", "pmid": "25659148", "authors": ["Cristine Betzer", "A James Movius", "Min Shi", "Wei-Ping Gai", "Jing Zhang", "Poul Henning Jensen"], "journal": "PloS one", "year": 2015, "abstract": "Monomeric α-synuclein (αSN) species are abundant in nerve terminals where they are hypothesized to play a physiological role related to synaptic vesicle turn-over. In Parkinson's disease (PD) and dementia with Lewy body (DLB), αSN accumulates as aggregated soluble oligomers in terminals, axons and the somatodendritic compartment and insoluble filaments in Lewy inclusions and Lewy neurites. The autosomal dominant heritability associated to mutations in the αSN gene suggest a gain of function associated to aggregated αSN. We have conducted a proteomic screen to identify the αSN interactome in brain synaptosomes. Porcine brain synaptosomes were fractionated, solubilized in non-denaturing detergent and subjected to co-immunoprecipitation using purified recombinant human αSN monomers or oligomers as bait. The isolated αSN binding proteins were identified with LC-LTQ-orbitrap tandem mass spectrometry and quantified by peak area using Windows client application, Skyline Targeted Proteomic Environment. Data are available via ProteomeXchange with identifier PXD001462. To quantify the preferential binding an average fold increase was calculated by comparing binding to monomer and oligomer. We identified 10 proteins preferentially binding monomer, and 76 binding preferentially to oligomer and a group of 92 proteins not displaying any preferred conformation of αSN. The proteomic data were validated by immunoprecipitation in both human and porcine brain extracts using antibodies against monomer αSN interactors: Abl interactor 1, and myelin proteolipid protein, and oligomer interactors: glutamate decarboxylase 2, synapsin 1, glial fibrillary acidic protein, and VAMP-2. We demonstrate the existence of αSN conformation selective ligands and present lists of proteins, whose identity and functions will be useful for modeling normal and pathological αSN dependent processes.", "claims": [{"id": "claim-method", "statement": "In order for a protein to be considered as either monomer or oligomer binding Student’s t-test was applied and conventional significance of 95% was accepted.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25659148", "locator": "sections[8] \"Semi-quantitative identification of proteins based on mass spectrometric peptide mapping\" paragraph 2", "quote": "In order for a protein to be considered as either monomer or oligomer binding Student’s t-test was applied and conventional significance of 95% was accepted."}], "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 PXD001462. Additional relevant data are within the paper and its Supporting Information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25659148", "locator": "sections[16] \"Data Availability\" 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 PXD001462. Additional relevant data are within the paper and its Supporting Information files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used Student’s t-test with conventional 95% significance and a ≥2-fold average increase criterion to classify preferential αSN binding; the underlying mass-spectrometry data are available through ProteomeXchange/PRIDE under identifier PXD001462.", "kind": "quantitative", "target": {"value": 2.0, "unit": "fold change", "tolerance": null, "source": "The criteria of ≥ 2-fold increase in average fold increase has to be fulfilled in order to be considered as preferential binding protein, similar to the criteria set up in the phospho-peptide interaction study by McFarland et al. [35]."}, "evidence": [{"asset": "source:pmid:25659148", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We demonstrate the existence of αSN conformation selective ligands and present lists of proteins, whose identity and functions will be useful for modeling normal and pathological αSN dependent processes."}, {"asset": "source:pmid:25659148", "locator": "sections[8] \"Semi-quantitative identification of proteins based on mass spectrometric peptide mapping\" paragraph 2", "quote": "In order for a protein to be considered as either monomer or oligomer binding Student’s t-test was applied and conventional significance of 95% was accepted."}, {"asset": "source:pmid:25659148", "locator": "sections[8] \"Semi-quantitative identification of proteins based on mass spectrometric peptide mapping\" paragraph 2", "quote": "The criteria of ≥ 2-fold increase in average fold increase has to be fulfilled in order to be considered as preferential binding protein, similar to the criteria set up in the phospho-peptide interaction study by McFarland et al. [35]."}, {"asset": "source:pmid:25659148", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD001462."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The paper used Student’s t-test with conventional 95% significance and a ≥2-fold average increase criterion to classify preferential αSN binding; the underlying mass-spectrometry data are available through ProteomeXchange/PRIDE under identifier PXD001462.", "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:25659148"], "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. 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receptor-associated protein 1", "F1RK45_PIG", "LP1", "6", "0.02"], ["Tropomodulin-2", "F1RZB5_PIG", "LP2", "8", "0.01"], ["Vesicle"], ["V-type proton ATPase subunit F", "F1SMN6_PIG", "LP1", "9", "<0.01"]], "row_count": 15, "column_count": 5, "numeric_cells": 30, "header_rows": 1, "locator": "section[8]/table-wrap[1]#pone.0116473.t001"}}, {"id": "asset:table:pmid:25659148:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:de6903ca415e0c6f845341cc9ce30e36fca4845c9d3b632e22cc102c40a8a3a1", "bytes": 5276, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[2]#pone.0116473.t002", "version": null, "note": "αSN oligomer interacting proteins.", "structure": {"pmcid": "PMC4319895", "section_index": 8, "section_title": "Semi-quantitative identification of proteins based on mass spectrometric peptide mapping", "row_count": 48, "column_count": 10}, "table": {"label": "Table 2", "caption": "αSN oligomer interacting proteins.", "rows": [["Protein", "UniProt/ swiss-Prot", "Synapto-somal fraction", "Fold increase", "p-value", "Protein", "UniProt/ swiss-Prot", "Synapto-somal fraction", "Fold increase", "p-value"], ["Mitochondrial"], ["3-hydroxyacyl-CoA dehydrogenase type-2", "F1RUI1_PIG", "LP1", "6", "0.01", "2-oxoglutarate/malate carrier protein", "F1RFX9_PIG", "LP2", "4", "0.05"], ["ADP/ATP translocase 3", "ADT3_PIG", "LS1", "66", "<0.01", "Glutamate carrier 1", "F1RYY8_PIG", "LS1", "49", "<0.01"], ["ATP synthase subunit α", "F1RPS8_PIG", "LS1", "13", "<0.01", "Mitochondrial import inner membrane translocase subunin", "F1SA66_PIG", "LS2", "3", "0.01"], ["Ca2+-binding mitochondrial carrier protein Aralar2", "I3L614_PIG", "LS1", "17", "0.01", "Phosphatidate cytidylyl-transferase 2", "I3LAQ3_PIG", "LS1", "5", "<0.01"], ["Elongation factor Tu", "F1RFI1_PIG", "LP1", "22", "<0.01", "Pyruvate carboxylase", "F1RUV6_PIG", "LS1", "7", "0.01"], ["Heat shock 60 kDa protein 1", "F1SMZ7_PIG", "LS2", "22", "<0.01", "Heat shock 70kDa protein 9 (Mortalin)", "F1RGJ3_PIG", "LS1", "2", "<0.02"], ["LETM1 and EF-hand domain-containing protein 1", "F1S6V4_PIG", "LS2", "60", "<0.01", "Trifunctional enzyme α", "ECHA_PIG", "LS1", "7", "<0.01"], ["Endoplasmic reticulum"], ["78 kDa glucose-regulated protein", "F1RS36_PIG", "LP2, LS2", "3", "0.03", "Hypoxia up regulated protein 1", "F1SAI8_PIG", "LP2", "4", "0.04"], ["Endoplasmin", "ENPL_PIG", "LS1", "4", "0.01", "Reticulocalbin 2", "F1SJ93_PIG", "All", "15", "<0.01"], ["Plasma membrane"], ["Excitatory amino acidtransporter 1", "F1SNA0_PIG", "LS1, LP2", "4", "0.03", "Plasma membrane Ca2+ ATPase 4", "F1S6B3_PIG", "LS1", "6", "<0.01"], ["Excitatory amino acidtransporter 2", "F1SHF9_PIG", "LS1", "7", "<0.01", "Syntaxin-binding protein 1", "F1RS11_PIG", "LS1, LS2", "23", "0.05"], ["", "Transmembrane protein 33", "F1S4G6_PIG", "LS1", "399", "<0.01"], ["Cytoplasm"], ["40S ribosomal protein S3", "RS3_PIG", "LS2", "7", "<0.01", "Dynein 1, light intermediate chain 2", "I3LQU0_PIG", "LS2", "22", "<0.01"], ["40S ribosomal protein S5-like isoform 2", "F2Z5E6_PIG", "LP2", "5", "0.02", "Glial fibrillary acidic protein*", "F1RR02_PIG", "LS1", "3", "<0.01"], ["60S ribosomal protein L32", "RL32_PIG", "LS1", "19", "<0.01", "Glutamate decarboxylase 2*", "DCE2_PIG", "LS2", "38", "<0.01"], ["52 kDa Rho protein", "F1RHN8_PIG", "LS2", "2", "0.03", "Neuronal migration protein doublecortin", "I3L5C8_PIG", "LS1, LS2", "53", "<0.01"], ["α-crystallin B chain", "CRYAB_PIG", "LP2", "3", "0.01", "Rab GDP dissociation inhibitor α", "I3L893_PIG", "LS1", "8", "0.01"], ["Aminoacyl tRNA synthase complex-interacting multifunctional protein 2", "F1RFM7_PIG", "LP2", "10", "0.01", "Ribosomal protein, large, P2", "F1RYZ0_PIG", "LS1", "11", "<0.01"], ["ATP-citrate synthase", "F1S0N1_PIG", "LS2", "58", "0.02", "S100 Ca2+ binding protein A14", "F1SFV3_PIG", "LS1", "3", "0.01"], ["Ca2+-binding protein 1", "F1RJI3_PIG", "LP2", "10", "0.01", "Seryl-tRNA synthetase", "F1S5Z3_PIG", "LS2", "261", "<0.01"], ["cAMP-dependent protein kinase catalytic β", "KAPCB_PIG", "LP2", "5", "0.01", "T-complex protein 1 α", "F1SB63_PIG", "LS2", "373", "<0.01"], ["Chaperonin containing TCP1, subunit 2β", "D0G0C8_PIG", "LS2", "478", "<0.01", "T-complex protein 1 δ", "F1SQN1_PIG", "LS1", "11", "0.01"], ["Dynein 1 intermediate chain 2", "F1S087_PIG", "LS1", "10", "<0.01", "T-complex protein 1 η", "F1SLF6_PIG", "LS1", "133", "0.03"], ["FMR1-interacting protein 2", "F1RQE9_PIG", "LP2", "3", "0.02", "T-complex protein 1 γ", "F1RP17_PIG", "LS1, LS2", "204", "<0.01"], ["Dihydropyrimidinase 2", "I3LJE2_PIG", "LS1, LS2", "23", "<0.01", "14–3–3 protein ζ/δ", "F2Z558_PIG", "LP1", "2", "0.04"], ["Dynein heavy polypeptide", "F1S9Y5_PIG", "LS2, LP2", "802", "<0.01", "14–3–3 protein γ", "F2Z4Z1_PIG", "LP1", "9", "0.03"], ["Nucleus"], ["A-kinase anchor protein 5", "F1SA75_PIG", "LS1", "9", "0.01", "Signal recognition particle 54 kDa protein", "F2Z5M9_PIG", "LS2", "18", "<0.01"], ["Vesicle"], ["Amphiphysin", "I3L8X6_PIG", "LP2", "5", "0.03", "Synaptic vesicle glycoprotein 2A", "F1SDF9_PIG", "LS1", "9", "<0.01"], ["Nipsnap homolog 1", "F1RFF5_PIG", "LP1", "3", "0.03", "Tripeptidyl-peptidase 1", "I3L812_PIG", "LS2", "45", "<0.01"], ["Sorting nexin 6", "F1SHH3_PIG", "LS2", "181", "<0.01", "Vacuolar protein sorting-associated protein 53", "F1RHI3_PIG", "LP2", "31", "<0.01"], ["Synapsin 1*", "B7TY10_PIG", "LS1, LS2, LP2", "9", "0.01", "V-type proton ATPase subunit d 1", "F2Z5H6_PIG", "LP2", "2", "0.03"], ["Cytoskeleton"], ["α-centractin", "F2Z5G5_PIG", "LS2", "20", "0.02", "Spectrin α chain", "F1RR78_PIG", "LS1", "3", "<0.01"], ["α-internexin", "F1S847_PIG", "LS1", "3", "0.02", "Tubulin α-4A chain", "F2Z5S8_PIG", "LS1", "6", "0.01"], ["Dynamin-2", "F1S593_PIG", "LS2", "64", "<0.01", "Tubulin β-3 chain", "F1S6M7_PIG", "LS1, LS2", "15", "0.01"], ["Microtubule-associated protein 6", "F1SUM1_PIG", "LS1, LS2", "28", "<0.01", "Tubulin β-4 chain", "F2Z5K5_PIG", "LS1, LS2, LP2", "9", "0.01"], ["Neurofilament heavy polypeptide", "F1RFH3_PIG", "LP1", "4", "0.02", "Tubulin polymerization-promoting protein", "I3LB30_PIG", "LP1", "3", "0.04"], ["Sirtuin 2", "I3L8A1_PIG", "LS1", "66", "0.01", "", "", "", ""], ["Secreted"], ["Complement C4 precursor", "F1RQW2_PIG", "LS1", "2", "0.01", "C-type natriuretic peptide", "F1S0P3_PIG", "LS1, LP2", "7", "0.05"], ["Complement C5 precursor", "F1SME1_PIG", "LS2", "19", "<0.01", "Tenascin-R", "F1S706_PIG", "LS2", "8", "0.01"]], "row_count": 48, "column_count": 10, "numeric_cells": 222, "header_rows": 1, "locator": "section[8]/table-wrap[2]#pone.0116473.t002"}}, {"id": "asset:table:pmid:25659148:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:efb837ec1432c5db4f0290979c317c992e295610dfd9f5e3d10de9e48adfb000", "bytes": 5665, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[3]#pone.0116473.t003", "version": null, "note": "Non-conformation specific αSN interacting proteins.", "structure": {"pmcid": "PMC4319895", "section_index": 8, "section_title": "Semi-quantitative identification of proteins based on mass spectrometric peptide mapping", "row_count": 57, "column_count": 6}, "table": {"label": "Table 3", "caption": "Non-conformation specific αSN interacting proteins.", "rows": [["Protein", "UniProt/ swiss-Prot", "Synaptosomal", "Protein", "UniProt/ swiss-Prot", "Synaptosomal"], ["Mitochondrial"], ["2-oxoglutarate dehydrogenase", "F1SSH8_PIG", "LP2", "Mitochondrial carrier homolog 2", "F1SIE0_PIG", "LP1"], ["39S ribosomal protein L12", "I3LSY1_PIG", "LP2", "Mitochondrial import inner membrane translocase subunit", "F1RK50_PIG", "LP1"], ["Adenine nucleotide translocator 2", "F2Z565_PIG", "LS1, LP1", "NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10-like", "I3LDC3_PIG", "LP1"], ["ATP synthase subunit beta", "F1SLA0_PIG", "LP2", "NADH dehydrogenase [ubiquinone] flavoprotein 1", "F1RVN1_PIG", "LP2"], ["Cytochrome b-c1 complex subunit 8-like isoform 2", "F1RI18_PIG", "LP2", "NADP-dependent malic enzyme", "F1STS4_PIG", "LP1"], ["Cytochrome c oxidase subunit 1", "COX1_PIG", "LP2", "Pentatricopeptide repeat domain 3", "F1SVC4_PIG", "LP2"], ["Chymodenin", "F1RLH7_PIG", "LP2", "Prohibitin 2", "I3LQN4_PIG", "LP1, LP2"], ["Dihydrolipoyllysine-residue acetyltransferase component of pyruvate", "F1SMB2_PIG", "LP1, LP2", "Pyruvate dehydrogenase: subunit beta", "F1SGH5_PIG", "LP2"], ["Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex", "ODO2_PIG", "LP1, LP2", "Short-chain specific acyl-CoA dehydrogenase", "F1RJH2_PIG", "LP1"], ["Glutamate dehydrogenase 1", "DHE3_PIG", "LP1", "Thioredoxin-dependent peroxide reductase", "F1S418_PIG", "LS1"], ["Hexokinase 1", "F1SUF2_PIG", "LP2", "Translocase of outer mitochondrial membrane", "F2Z4X6_PIG", "LP1"], ["Long-chain 3-ketoacyl-CoA thiolase", "F1SDN2_PIG", "LP1", "Voltage-dependent anion-selective channel 1", "VDAC1_PIG", "LP1, LP2"], ["Endoplasmic reticulum"], ["B-cell receptor-associated protein 31", "F1S2A8_PIG", "LP2", "Phospholipase D3", "I3L5D6_PIG", "LP2"], ["Ca2+/calmodulin-dependent protein kinase II γ-B", "Q7JFN4_PIG", "LP2", "Protein disulfide-isomerase A6", "E1CAJ6_PIG", "LP2"], ["NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15 kDa (NADH-coenzyme Q reductase)", "F1SV23_PIG", "LP1, LP2", "Stromal interaction molecule 1 precursor", "F1SUZ4_PIG", "LP2"], ["Plasma membrane"], ["Adaptor-related protein complex 2, mu 1 subunit", "I3LL07_PIG", "LP2", "Immunoglobulin superfamily member 8", "F1RJW5_PIG", "LP2"], ["AP-2 complex subunit β", "I3L6Y6_PIG", "LP2", "Neural cell adhesion molecule 1", "F1SM72_PIG", "LP1, LP2"], ["BPI fold-containing family B member 1", "I3LAK0_PIG", "LP2", "Neurotrimin", "F1S6D0_PIG", "LP2"], ["Brain acid soluble protein 1 isoform 1", "F1SRL9_PIG", "LP1", "Oligodendrocyte-myelin glycoprotein", "F1RJ55_PIG", "LP2"], ["Ca2+/calmodulin-dependent protein kinase II α", "F1RL74_PIG", "LP2", "Paralemmin-1", "PALM_PIG", "LP2"], ["Ca2+ modulating ligand", "F1RHC6_PIG", "LP2", "Plasma membrane Ca2+ ATPase 2", "I3LIE6_PIG", "LP2"], ["Cell adhesion molecule 2", "F1SK66_PIG", "LP2", "Prohibitin", "F2Z543_PIG", "LP2"], ["Cell cycle exit and neuronal differentiation protein 1", "CEND_PIG", "LP1", "Protein RER1", "I3LJC8_PIG", "LP2"], ["Cytolytic trigger molecule G7", "FCGR3_PIG", "LP1", "Protein transport protein Sec61 subunit α2", "F2Z5D0_PIG", "LP2"], ["EH domain-containing protein 3", "F1RQR4_PIG", "LP2", "Thy-1 membrane glycoprotein precursor", "B9ZSM8_PIG", "LP2"], ["Cytoplasm"], ["40S ribosomal protein S3a", "F2Z5C7_PIG", "LP2", "Elongation factor 1-α", "Q0PY11_PIG", "LP2"], ["60S ribosomal protein L6", "RL6_PIG", "LP2", "Elongation factor 1-β", "F1SHD6_PIG", "LP2"], ["60S ribosomal protein L12", "Q6QAS5_PIG", "LP2", "Glutathione transferase ζ 1", "F1S2N0_PIG", "LP1"], ["60S ribosomal protein L22", "RL22_PIG", "LP2", "Heterogeneous nuclear ribonucleoprotein K", "I3LQS0_PIG", "LP2"], ["60S acidic ribosomal protein P1", "F1SIT7_PIG", "LP2", "Proteasome subunit α type-2", "I3LAB6_PIG", "LP2"], ["ABI gene family member 3 isoform 2", "I3LB01_PIG", "LP2", "protein-arginine deiminase type-2", "I3LNE4_PIG", "LP2"], ["AP-1 complex subunit sigma-1A", "Q06AS6_PIG", "LP2", "Ribosomal phosphoprotein large PO subunit", "RLA0_PIG", "LP2"], ["cAMP-dependent protein kinase type II-α regulatory subunit", "KAP2_PIG", "LP1", "Protein kinase C ε type", "F1S5K7_PIG", "LP2"], ["Creatine kinase", "I3LPB5_PIG", "LP1, LP2", "S100 Ca2+ binding protein A16", "F2Z5M4_PIG", "LP2"], ["Cytoplasmic dynein 1 heavy chain 1", "F1S9Y5_PIG", "LS2, LP2", ""], ["Nucleus"], ["Barrier-to-autointegration factor-like isoform 1", "F1RU33_PIG", "LP1", "Nucleosome assembly protein 1", "F1SGD7_PIG", "LP2"], ["Dynein light chain Tctex-type 3", "I3LUI9_PIG", "LP2", "WD repeat-containing protein 61", "F1RKU4_PIG", "LP2"], ["Homeobox prox 1", "F1SFF4_PIG", "LP2", "", "", ""], ["Vesicle"], ["Membrane-associated progesterone receptor component 1", "PGRC1_PIG", "LP2", "Syntaxin-1A", "F1RJM9_PIG", "LP2"], ["Synaptic vesicle glycoprotein 2B", "F1SCI2_PIG", "LP2", "Vacuolar protein sorting-associated protein 45", "F1SDG5_PIG", "LP2"], ["Synaptotagmin-1", "F1RYK1_PIG", "LP2", "V-type proton ATPase subunit D", "F1SA40_PIG", "LP2"], ["", "Vesicle-associated membrane protein-associated protein B", "VAPB_PIG", "LP2"], ["Cytoskeleton"], ["Actin related protein 2/3 complex, subunit 4", "F1SQE6_PIG", "LP2", "Dynamin-1", "F1RRW8_PIG", "LP2"], ["Actin-related protein 2/3 complex subunit 5", "B5APV0_PIG", "LP2", "Erythrocyte membrane protein band 4.1", "F1SM86_PIG", "LP2"], ["Actin-related protein 3", "F2Z5D2_PIG", "LP2", "Microtubule-associated protein 1B", "F1SK12_PIG", "LP1"], ["Adenylyl cyclase-associated protein 1", "I3LVT1_PIG", "LP2", "Microtubule-associated protein 2 isoform 2", "F1SSS6_PIG", "LS1, LP1"], ["Cytoskeleton-associated protein 4", "F1SPP8_PIG", "LP2", "Septin 2", "F1SIP0_PIG", "LS1"], ["Secreted"], ["Granulin", "F1RQZ0_PIG", "LP1, LS2", "", "", ""]], "row_count": 57, "column_count": 6, "numeric_cells": 84, "header_rows": 1, "locator": "section[8]/table-wrap[3]#pone.0116473.t003"}}], "gaps": ["asset:data:geo:PXD001462 not downloaded", "asset:data:geo:PXD001462 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": 0.8, "band": "high", "quote": "Students t-test"}}, {"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": "In order for a protein to be considered as either monomer or oligomer binding Student’s t-test was applied and conventional significance of 95% was accepted."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "student_t", "expected_value": 2.0, "unit": "fold change", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-per-cent", "claim_id": "claim-target-result", "operation": "student_t", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD001462"], "resolved_accessions": ["PXD001462"], "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 PXD001462. Additional relevant data are within the paper and its Supporting Information files."], "basis": "The paper names PXD001462 in PRIDE partner repository via the ProteomeXchange Consortium and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:25659148", "data:geo:PXD001462", "asset:table:pmid:25659148:1", "asset:table:pmid:25659148:2", "asset:table:pmid:25659148:3"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001462"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:23:30Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 140533, "completion_tokens": 3027, "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:25659148", "type": "paper", "label": "pmid:25659148"}, {"id": "source:pmid:25659148", "type": "manuscript", "label": "PMID 25659148 full text"}, {"id": "data:geo:PXD001462", "type": "dataset", "label": "GEO PXD001462"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25659148", "type": "paper", "label": "pmid:25659148"}, {"id": "source:pmid:25659148", "type": "manuscript", "label": "PMID 25659148 full text"}, {"id": "data:geo:PXD001462", "type": "dataset", "label": "GEO PXD001462"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25659148", "type": "extraction", "used": ["source:pmid:25659148"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001462", "type": "accession_resolution", "used": ["data:geo:PXD001462"], "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:25659148", "parent_hash": "sha256:9112a3bf5de821520cf9ecdf5b4f1314dca69d9680a635048bcd82bcdce3c446", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:PXD001462 licence not read", "asset:data:geo:PXD001462 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": ["were identified with LC-LTQ-orbitrap tandem mass spectrometry and quantified by peak area using Windows cl", "iated to aggregated αSN. 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