Identification of Potential Interacting Proteins With the Extracellular Loops of the Neuronal Glycoprotein M6a by TMT/MS.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32848694", "kind": "science-record", "revision": 8, "content_hash": "sha256:b796a4c50dbcef96e8aaca07a3500102c9f6731331e64327979fa923e83fb300", "created_at": "2026-11-01T15:41:08Z", "updated_at": "2026-11-01T22:45:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Potential Interacting Proteins With the Extracellular Loops of the Neuronal Glycoprotein M6a by TMT/MS.", "doi": "10.3389/fnsyn.2020.00028", "pmid": "32848694", "authors": ["Gabriela I Aparicio", "Karina Formoso", "Antonella León", "Alberto C Frasch", "Camila Scorticati"], "journal": "Frontiers in synaptic neuroscience", "year": 2020, "abstract": "Nowadays, great efforts are made to gain insight into the molecular mechanisms that underlie structural neuronal plasticity. Moreover, the identification of signaling pathways involved in the development of psychiatric disorders aids the screening of possible therapeutic targets. Genetic variations or alterations in GPM6A expression are linked to neurological disorders such as schizophrenia, depression, and Alzheimer's disease. GPM6A encodes the neuronal surface glycoprotein M6a that promotes filopodia/spine, dendrite, and synapse formation by unknown mechanisms. A substantial body of evidence suggests that the extracellular loops of M6a command its function. However, the proteins that associate with them and that modulate neuronal plasticity have not been determined yet. To address this question, we generated a chimera protein that only contains the extracellular loops of M6a and performed a co-immunoprecipitation with rat hippocampus samples followed by TMT/MS. Here, we report 72 proteins, which are good candidates to interact with M6a's extracellular loops and modify its function. Gene ontology (GO) analysis showed that 63% of the potential M6a's interactor proteins belong to the category \"synapse,\" at both sides of the synaptic cleft, \"neuron projections\" (51%) and \"presynapse\" (49%). In this sense, we showed that endogenous M6a interacts with piccolo, synaptic vesicle protein 2B, and synapsin 1 in mature cultured hippocampal neurons. Interestingly, about 28% of the proteins left were related to the \"myelin sheath\" annotation, suggesting that M6a could interact with proteins at the surface of oligodendrocytes. Indeed, we demonstrated the (cis and trans) interaction between M6a and proteolipid protein (PLP) in neuroblastoma N2a cells. Finally, the 72 proteins were subjected to disease-associated genes and variants screening by DisGeNET. Apart from the diseases that have already been associated with M6a, most of the proteins are also involved in \"autistic disorder,\" \"epilepsy,\" and \"seizures\" increasing the spectrum of disorders in which M6a could play a role. Data are available via ProteomeXchange with identifier PXD017347.", "claims": [{"id": "claim-method", "statement": "For differential protein expression analysis between conditions, a t-test was used and applied with Linear Models for Microarray Data (Limma) package (Ritchie et al., 2015).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32848694", "locator": "sections[22] \"Statistical Analysis\" paragraph 2", "quote": "For differential protein expression analysis between conditions, a t-test was used and applied with Linear Models for Microarray Data (Limma) package (Ritchie et al., 2015)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (www.proteomexchange.org) via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD017347.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32848694", "locator": "sections[30] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (www.proteomexchange.org) via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD017347."}], "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:32848694"], "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:PXD017347"], "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:PXD017347"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32848694", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnsyn.2020.00028", "sha256": 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(www.proteomexchange.org) via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD017347.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (www.proteomexchange.org) via the PRIDE (Vizcaíno et al., 2016) partner repository with the dataset identifier PXD017347.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "TMT spectrometry unveils key M6a interactorsTMT spectrometry unveils key M6a interactors", "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:32848694:1", "role": "table", "format": "jats-table", "media_type": 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3: 350 μg/each"], ["", "co-IP3 R1", "50 μl", "5 μg/Batch #1905424"], ["", "co-IP3 R2", "50 μl"]], "row_count": 11, "column_count": 6, "numeric_cells": 24, "header_rows": 2, "locator": "section[17]/table-wrap[1]#d38e574"}}, {"id": "asset:table:pmid:32848694:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:15608491cc724bdbce6fb512dc4ba89862758d90b765b764029f3b112fa02203", "bytes": 5396, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[1]#T1", "version": null, "note": "Gene ontology (GO) enrichment analysis of 72 potential M6a’s interactors.", "structure": {"pmcid": "PMC7396582", "section_index": 25, "section_title": "Proteomics Analysis", "row_count": 17, "column_count": 9}, "table": {"label": "Table 1", "caption": "Gene ontology (GO) enrichment analysis of 72 potential M6a’s interactors.", "rows": [["", "ID", "Annotation", "p-value", "FDR B&H", "FDR B&Y", "Bonferroni", "Genes from input (72)", "Protein symbol"], ["Molecular function", "GO:0022853", "active ion transmembrane transporter activity", "1.562E-20", "3.85E-18", "2.602E-17", "7.545E-18", "22 (31%)", "Atp6v1a, Atp6v1b2, Atp6v1c1, Atp6v1e1, Atp6v1g2, Atp6v1h, Atp6v0a1, Anxa5, Slc17a7, Atp1a1, Atp1a2, Atp1a3, Slc4a4, Atp1b1, Atp1b2, Atp2b1, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Slc3a2, Slc12a5"], ["", "GO:0005215", "transporter activity", "1.631E-20", "3.85E-18", "2.602E-17", "7.878E-18", "38 (53%)", "Gja1, Atp6v1a, Dpp6, Atp6v1b2, Atp6v1c1, Atp6v1e1, Cpne6, Stx1a, Atp6v1g2, Atp6v1h, Atp6v0a1, Nrxn3, Sv2b, Sv2a, Anxa5, Scn2a, Syngr3, Syn1, Slc17a7, Grin1, Ttyh3, Snap25, Atp1a1, Atp1a2, Atp1a3, App, Slc4a4, Atp1b1, Atp1b2, Aqp4, Atp2b1, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Slc1a3, Atp2b4, Slc3a2, Vdac1, Slc12a5"], ["", "GO:0019829", "ATPase-coupled cation transmembrane transporter activity", "2.391E-20", "3.85E-18", "2.602E-17", "1.155E-17", "16 (22%)", "Atp6v1a, Atp6v1b2, Atp6v1c1, Atp6v1e1, Atp6v1g2, Atp6v1h, Atp6v0a1, Anxa5, Atp1a1, Atp1a2, Atp1a3, Atp1b1, Atp1b2, Atp2b1, Atp2b2, Atp2b4"], ["", "GO:0042625", "ATPase-coupled ion transmembrane transporter activity", "5.2E-20", "6.279E-18", "4.244E-17", "2.512E-17", "16 (22%)", "Atp6v1a, Atp6v1b2, Atp6v1c1, Atp6v1e1, Atp6v1g2, Atp6v1h, Atp6v0a1, Anxa5, Atp1a1, Atp1a2, Atp1a3, Atp1b1, Atp1b2, Atp2b1, Atp2b2, Atp2b4"], ["", "GO:0022857", "transmembrane transporter activity", "7.159E-19", "6.916E-17", "4.674E-16", "3.458E-16", "35 (49%)", "Gja1, Atp6v1a, Dpp6, Atp6v1b2 Atp6v1c1, Atp6v1e1, Stx1a, Atp6v1g2, Atp6v1h, Atp6v0a1, Nrxn3, Sv2b, Sv2a, Anxa5, Scn2a, Slc17a7, Grin1, Ttyh3, Snap25, Atp1a1, Atp1a2, Atp1a3, App, Slc4a4, Atp1b1, Atp1b2, Aqp4, Atp2b1, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Slc3a2, Vdac1, Slc12a5"], ["Biological Process", "GO:0098916", "anterograde trans-synaptic signaling", "2.463E-20", "2.819E-17", "2.373E-16", "6.274E-17", "31 (43%)", "Dpp6, Nptn, Cpne6, Stx1a, Nrxn3, Stxbp1, Synj1, Cadps, Sv2b, Sv2a, Pclo, Scn2a, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, App, Bsn, Grm1, Plp1, Slc1a2, Atp2b2, Slc1a3, Cnp, Vdac1, Slc12a5"], ["", "GO:0007268", "chemical synaptic transmission", "2.463E-20", "2.819E-17", "2.373E-16", "6.274E-17", "31 (43%)", "Dpp6, Nptn, Cpne6, Stx1a, Nrxn3, Stxbp1, Synj1, Cadps, Sv2b, Sv2a, Pclo, Scn2a, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, App, Bsn, Grm1, Plp1, Slc1a2, Atp2b2, Slc1a3, Cnp, Vdac1, Slc12a5"], ["", "GO:0099537", "trans-synaptic signaling", "3.319E-20", "2.819E-17", "2.373E-16", "8.456E-17", "31 (43%)", "Dpp6, Nptn, Cpne6, Stx1a, Nrxn3, Stxbp1, Synj1, Cadps, Sv2b, Sv2a, Pclo, Scn2a, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, App, Bsn, Grm1, Plp1, Slc1a2, Atp2b2, Slc1a3, Cnp, Vdac1, Slc12a5"], ["", "GO:0099536", "synaptic signaling", "5.078E-20", "3.235E-17", "2.724E-16", "1.294E-16", "31 (43%)", "Dpp6, Nptn, Cpne6, Stx1a, Nrxn3, Stxbp1, Synj1, Cadps, Sv2b, Sv2a, Pclo, Scn2a, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, App, Bsn, Grm1, Plp1, Slc1a2, Atp2b2, Slc1a3, Cnp, Vdac1, Slc12a5"], ["", "GO:0030001", "metal ion transport", "1.414E-18", "7.204E-16", "6.067E-15", "3.602E-15", "31 (43%)", "Gja1, Atp6v1a, Dpp6, Atp6v1b2, Atp6v1c1, Atp6v1e1, Stx1a, Atp6v1g2, Atp6v1h, Atp6v0a1, Thy1, Anxa5, Scn2a, Slc17a7, Grin1, Snap25, Atp1a1, Atp1a2, Atp1a3, Slc4a4, Atp1b1, Atp1b2, Atp2b1, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Epb41, Cntn1, Slc3a2, Vdac1, Slc12a5"], ["Celular Component", "GO:0045202", "synapse", "1.406E-30", "5.552E-28", "3.641E-27", "5.552E-28", "45 (63%)", "Nptn, Dpysl2, Dpysl3, Stx1a, Atp6v1g2, Atp6v0a1, Nrxn3, Stxbp1, Nckap1, Synj1, Scamp5, Cadps, Sv2b, Sv2a, Anxa5, Pclo, Scn2a, Ncan, Syngr3, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Bcan, Grin1, Snap25, Atp1a1, Atp1a2, Atp1a3, App, Bsn, Grm1, Epb41l3, Atp2b1, Eno2, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Epb41, Cntn1, Slc3a2, Vdac1"], ["", "GO:0098793", "presynapse", "2.191E-29", "4.328E-27", "2.838E-26", "8.656E-27", "35 (49%)", "Nptn, Dpysl2, Stx1a, Atp6v1g2, Atp6v0a1, Nrxn3, Stxbp1, Synj1, Scamp5, Cadps, Sv2b, Sv2a, Anxa5, Pclo, Scn2a, Syngr3, Cntnap1, Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a2, Atp1a3, App, Bsn, Grm1, Atp2b1, Slc1a2, Atp2b2, Atp2b4, Cntn1, Vdac1"], ["", "GO:0043209", "myelin sheath", "1.714E-20", "2.257E-18", "1.48E-17", "6.772E-18", "21 (28%)", "Atp6v1a, Atp6v1b2, Dpysl2, Stxbp1, Thy1, Cntnap1, Syn1, Syn2, Snap25, Atp1a1, Atp1a3, Atp1b1, Ppia, Eno2, Plp1, Omg, Cnp, Mog, Cntn1, Hsp90, Vdac1"], ["", "GO:0030054", "cell junction", "1.073E-19", "1.052E-17", "6.89E-17", "4.208E-17", "35 (63%)", "Vapa, Gja1, Stx1a, Thy1, Nckap1, Scamp5, Cadps, Sv2b, Tnc, Sv2a, Anxa5, Pclo, Scn2a, Syngr3, Cntnap1, Lrp1,"], ["", "", "", "", "", "", "", "", "Syn1, Slc17a7, Syn2, Syp, Syt1, Grin1, Snap25, Atp1a1, Atp1a2, App, Bsn, Epb41l3, Atp1b1, Ppia, Aqp4, Atp2b1, Atp2b2, Epb41, Epb41l2"], ["", "GO:0043005", "neuron projection", "2.962E-19", "2.925E-17", "1.918E-16", "1.17E-16", "37 (51%)", "Nptn, Dpysl2, Dpysl3, Cpne6, Stx1a, Stxbp1, Thy1, Rnpep, Synj1, Sv2b, Sv2a, Anxa5, Pclo, Scn2a, Cntnap1, Lrp1, Syn1, Slc17a7, Syp, Syt1, Bcan, Grin1, Snap25, Atp1a2, Atp1a3, App, Bsn, Grm1, Epb41l3, Atp2b1, Eno2, Slc1a2, Atp2b2, Slc1a3, Atp2b4, Hsp90, Slc12a5"]], "row_count": 17, "column_count": 9, "numeric_cells": 104, "header_rows": 1, "locator": "section[25]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32848694:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3494d1b42d429ff4af5ebf13857cce2a55f4c53eaa78c4565071829180e0f1c9", "bytes": 2368, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[2]#T2", "version": null, "note": "Disease-associated gene analysis of the 72 potential M6a’s interactors.", "structure": {"pmcid": "PMC7396582", "section_index": 25, "section_title": "Proteomics Analysis", "row_count": 11, "column_count": 9}, "table": {"label": "Table 2", "caption": "Disease-associated gene analysis of the 72 potential M6a’s interactors.", "rows": [["", "ID", "Annotation", "p-value", "FDR B&H", "FDR B&Y", "Bonferroni", "Genes from input (72)", "Protein symbol"], ["Disease", "C0004352", "Autistic Disorder", "1.84E-10", "3.041E-07", "2.43E-06", "3.041E-07", "20 (27%)", "Gja1, Dpysl2, Stx1a, Nrxn3, Stxbp1, Thy1, Scamp5, Tnc, Pclo, Scn2a, Cntnap1, Syn1, Syn2, Snap25, App, Aqp4, Plp1, Slc1a2, Atp2b2, Slc1a3"], ["", "C0014544", "Epilepsy", "1.05E-09", "8.625E-07", "6.89E-06", "1.73E-06", "19 (26%)", "Gja1, Dpysl3, Stx1a, Stxbp1, Sv2a, Scn2a, Syn1, Slc17a7, Syn2, Grin1, Atp1a2, Atp1a3, App, Grm1, Aqp4, Slc1a2, Slc1a3, Vdac1, Slc12a5"], ["", "C0036341", "Schizophrenia", "2.40E-09", "1.32E-06", "1.05E-05", "3.96E-06", "28 (38%)", "Nptn, Dpysl2, Stx1a, Nrxn3, Stxbp1, Sv2a, Pclo, Scn2a, Ncan, Lrp1, Syn1, Slc17a7, Syn2, Syp, Bcan, Grin1, Snap25, App, Grm1, Ppia, Aqp4, Eno2, Plp1, Slc1a2, Slc1a3, Cnp, Mog, Slc12a5"], ["", "C0002395", "Alzheimer’s Disease", "2.10E-05", "6.93E-03", "0.055", "0.035", "26 (34%)", "Gja1, Dpysl2, Dpysl3, Thy1, Synj1, Sv2a, Anxa5, Lrp1, Syn1, Slc17a7, Syn2, Syp, Syt1, Bcan, Grin1, Snap25, App, Ppia, Aqp4, Eno2, Slc1a2, Slc1a3, Cnp, Mog, Hsp90, Vdac1"], ["", "C0086237", "Epilepsy, Cryptogenic", "5.30E-06", "2.19E-03", "0.017", "0.009", "7 (9, 7%)", "Gja1, Scn2a, Grm1, Slc1a2, Slc1a3, Vdac1, Slc12a5"], ["", "C0005586", "Bipolar Disorder", "2.61E-05", "7.18E-03", "0.057", "0.043", "16 (22%)", "Vapa, Dpysl2, Synj1, Pclo, Ncan, Slc17a7, Syn2, Syp, Grin1, Snap25, Atp1a1, Atp1a2, Atp1a3, App, Slc1a2, Slc1a3"], ["", "C0036572", "Seizures", "4.81E-05", "0.010", "0.081", "0.079", "14 (19%)", "Gja1, Stxbp1, Synj1, Sv2a, Scn2a, Slc17a7, Syn2, Grin1, Atp1a2, App, Aqp4, Slc1a2, Slc1a3, Slc12a5"], ["", "C0011570", "Mental Depression", "4.92E-05", "0.010", "0.081", "0.081", "14 (19%)", "Gja1, Dpysl2, Pclo, Syn1, Syp, Grin1, Snap25, Atp1a3, App, Grm1, Aqp4, Slc1a2, Cnp, Hsp90"], ["", "C1269683", "Major Depressive Disorder", "1.27E-04", "2.11E-02", "1.70E-01", "2.19E-01", "13 (19%)", "Gja1, Pclo, Ncan, Lrp1, Slc17a7, Snap25, App, Plp1, Slc1a2, Slc1a3, Cnp, Mog, Hsp90"], ["", "C0011581", "Depressive disorder", "1.28E-04", "0.022", "0.176", "0.211", "14 (19%)", "Gja1, Dpysl2, Pclo, Syn1, Syp, Grin1, Snap25, Atp1a3, App, Grm1, Aqp4, Slc1a2, Cnp, Hsp90"]], "row_count": 11, "column_count": 9, "numeric_cells": 71, "header_rows": 1, "locator": "section[25]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:PXD017347 not downloaded", "asset:data:geo:PXD017347 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, 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