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HanMass SpectrometryShotgun proteomicsNot availableBrainQuantitative proteomicsMouseEaeTmthttp://www.ebi.ac.uk/pride/archive/projects/PXD011428BrainTissue samples were prepared with the FASP procedure described previously. Before TMT labeling, the protein concentration of each sample was measured with the tryptophan assay. TMT labeling was then performed with several modifications to the manufacturer’s protocol. Briefly, the TMT reagent (0.8 mg) was dissolved in acetonitrile, and 10 µl of the reagent was added to 30 µl of peptides along with ACN to give a final concentration of 30% v/v. The peptides were then pooled after incubating at room temperature for 2 hours. The pooled sample was dried almost completely and desalted with an in-house C18 stage-tip.Before TMT labeling, the protein concentration of each sample was measured with the tryptophan assay. TMT labeling was then performed with several modifications to the manufacturer’s protocol [22]. Briefly, the TMT reagent (0.8 mg) was dissolved in acetonitrile, and 10 µl of the reagent was added to 30 µl of peptides along with ACN to give a final concentration of 30% v/v. The peptides were then pooled after incubating at room temperature for 2 hours. The pooled sample was dried almost completely and desalted with an in-house C18 stage-tip.PrideTMTiodoacetamide derivatized residuemonohydroxylated residueAfter the MS analysis, all raw files were processed in Proteome Discoverer 2.1 software based on the SEQUEST-HT search engine against the Mouse Uniprot FASTA database.Parameters were as follows: enzyme, full-trypsin; precursor ion tolerance, 10 ppm; MS/MS ion tolerance, 20 ppm; fixed modifications, TMT tags (N-term and Lys, +229.163 Da) and carbamidomethylation (Cys, +57.021 Da); and variable modifications, oxidation (Met, +15.995 Da). The false discovery rate (FDR) for all peptide-spectrum match (PSM) were adjusted to a 1%, and protein assignments were performed by the Percolator software package. Only the PSMs that contained all six reporter ions. Protein quantitation values were exported for further analysis in Microsoft Excel. Each reporter ion channel was summed across all quantified proteins and normalized assuming equal protein loading of all six samples.ProteomicsDohyun HanQ ExactivePARTIALProteomics core facility, Biomedical Research Institute, Seoul National University HospitalMus Musculus (mouse)hdh03@snu.ac.kr30724464 Hasan M, Min H, Rahaman KA, Muresan AR, Kim H, Han D, Kwon OS. Quantitative Proteome Analysis of Brain Subregions and Spinal Cord from Experimental Autoimmune Encephalomyelitis Mice by TMT-Based Mass Spectrometry. Proteomics. 2019:e1800355 10.1002/pmic.201800355BiomedicalProteomics Core Facility, Biomedical Research Institute, Seoul National University HospitalKorea, Republic ofMultiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS); its cause is unknown. To understand the pathogenesis of MS, researchers often use the experimental autoimmune encephalomyelitis (EAE) mouse model. Here, the aim is to build a proteome map of the biological changes that occur during MS at the major onset sites-the brain and the spinal cord. Quantitative proteome profiling is performed in five specific brain regions and the spinal cord of EAE and healthy mice with high-resolution mass spectrometry based on tandem mass tags. On average, 7400 proteins per region are quantified, with the most differentially expressed proteins in the spinal cord (1691), hippocampus (104), frontal cortex (83), cerebellum (63), brainstem (50), and caudate nucleus (41). Moreover, region-specific and commonly expressed proteins in each region are identified and bioinformatics analysis is performed. Pathway analysis reveals that protein clusters resemble their functions in disease pathogenesis (i.e., by inducing inflammatory responses, immune activation, and cell-cell adhesion). In conclusion, the study provides an understanding of the pathogenesis of MS in the EAE animal model. It is expected that the comprehensive proteome map of the brain and spinal cord can be used to identify biomarkers for the pathogenesis of MS.Quantitative Proteome Analysis of Brain Subregions and Spinal Cord from Experimental Autoimmune Encephalomyelitis Mice by TMT-Based Mass Spectrometry.Hasan Mahbub M, Min Hophil H, Rahaman Khandoker Asiqur KA, Muresan Anca Raluca AR, Kim Hyeyoon H, Han Dohyun D, Kwon Oh-Seung OSNup32D, PLIP, MeCN, NCMe, developmental stage, ACINUS, PMS Tryptophan, ratio-Tryptophan, Tryptacin, L Tryptophan ratiopharm, Type 2A-interacting protein, ESA1, Intervention or Procedure, peptide, Polypeptides, method, ratio Tryptophan, peptido, BANF, dJ69E11.3, method used in an experiment, CH3-C#N, Arabidopsis NAC domain containing protein 91, B1, zk, Trofan, HTATIP, nup154, portion of tissue, l(2)10432, C79325, dermoid cyst with malignant transformation, reactivo, peptides, Acinus, interventionDescription, PMS-Tryptophan, 2610036I19Rik, Tissue, 2610510L13Rik, Interventional, labeling, L-Tryptophan, study assay, SURGICAL AND MEDICAL PROCEDURES, acinusL, fSAP152, DmelCG4579, ms(2)zk, cPLA2, acinusS, Ardeydorm, scientific observation, ACN, sample, Acn, D1, nup154., peptidos, stage, l(2)01501, TIP, thiol methyltransferase activity, reagents, PTHB1, Naturruhe, Intervention Strategies, measuring, L-Tryptophan-ratiopharm, 1-(14)C-labeled, 3H-labeled, ZC2HC5, BcDNA:LD21772, Tryptophan Metabolism Alterations, HTATIP1, Procedure, acetonitrile, tip, ANAC091, Peptide, mKIAA0670, polypeptide, any method, Putative MAPK-activating protein PM10, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Temperatures, C18, tissue portion, simple tissue, TIP60, L Tryptophan, reactif, ACETONITRILE, Tryptan, Ardeytropin, cyanomethane, teratoma with malignant transformation, Intervention, nup32D, Levotryptophan, Optimax, CG4579, pooled, reagent, ethanenitrile, study protocol, sample population, Lyphan, plan specification, concentration, TCV-interacting protein, Peptid, Polypeptide, methyl cyanide, SCH, tlp, TMT, TIP41the brain, 3.4.22.-, Coccygeal Cord, Terminalis, Medullari, determination, Laboratory, Mus domesticus, number, Allergic Encephalomyelitis, experimental autoimmune encephalomyelitis, mini-ICE, CASP-14, Spectrum Analyses, presence, House Mouse, EAE, House, Mass, Mus musculus domesticus, synganglion, Allergic encephalomyelitis, Analysis, Experimental allergic encephalomyelitis (disorder), cerebro-cerebellar fissure, Autoimmune, Mice, Mass Spectroscopy, spinal cord structure, Mass Spectrum Analysis, Thoracic Cord, Spinali, fissura cerebro-cerebellaris, dermoid cyst with malignant transformation, Analyses, Coccygeal, Swiss, Allergic, Autoimmune Experimental, Swiss Mice, Conus Medullaris, suprasegmental levels of nervous system, Myelons, Conus, Conus Terminali, Coccygeal Cords, SpC, Sacral, AUTOIMMUNE ENCEPH EXPER, EXPER ALLERGIC ENCEPH, thiol methyltransferase activity, Experimental Allergic Encephalomyelitis, Terminali, Spinal Cords, ENCEPH EXPER AUTOIMMUNE, suprasegmental structures, ALLERGIC ENCEPH, Experimental Allergic Encephalomyelitides, Autoimmune Encephalomyelitis, Sacral Cords, Cords, mouse, total expressed protein, Medullaris, ALLERGIC ENCEPH EXPER, medulla spinalis, fissura cerebrocerebellaris, encephalon, Spectrum Analysis, Cord, Spectroscopy, count in organism, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Experimental, Medulla, Conus Medullari, Mus, chemical analysis, Mini-ICE, Myelon, Experimental Autoimmune, Experimental Encephalomyelitis, Sacral Cord, cerebrocerebellar fissure, Mass Spectrum Analyses, teratoma with malignant transformation, EXPER AUTOIMMUNE ENCEPH, Mus musculus, Mass Spectrum, Encephalomyelitis, Experimental Allergic, Thoracic Cords, ENCEPH ALLERGIC, Caspase-14 subunit p10, mice, Encephalon, Swiss Mouse, Spectrometry, Spinalis, House Mice, Lumbar Cords, Caspase-14 subunit p19, Conus Terminalis, MICE, Allergic encephalomyelitis (disorder), Laboratory Mice, domesticus, spinal medulla, ENCEPH AUTOIMMUNE EXPER, Spinal, Mass., AUTOIMMUNE EXPER ENCEPH, Mouse, assay, quantitative, Medulla Spinalis, TMT, Proteomes, Lumbar, Thoracic, Lumbar Cord, Laboratory Mouse, Medulla Spinali, presence or absence in organism, Autoimmune Experimental EncephalomyelitisSH2-Bb, Bru, Raw, ion, Hgfr, determination, AI326280, Irip, 5730555F13Rik, protein, NAALAdase, peptide, Polypeptides, NAALADase I, FOLH, protein polypeptide chains, Drug Tolerance, Methionine, ClvPrd, peptido, HGFR, 2, C530001K22Rik, Software Engineering, 3.4.17.21, protein aggregate, Computer Program, Svc, SH2-B, somitogenic mesoderm, F, dermoid cyst with malignant transformation, peptides, Membrane glutamate carboxypeptidase, K, MUB3_18, M, Open, Computer Programs and Programming, epsilon-diaminocaproic acid, proteins, NAALAD1, MUB3.18, Folylpoly-gamma-glutamate carboxypeptidase, Lys, LYS, ppm, Lysin, house mouse, RG7MT1, Racemethionine, drug tolerance, Lzm, ratio, Lzp, proto-oncogene c-Met, PRO, unsegmented mesenchyme, immune system tolerance, mouse, 2-Amino-4-(methylthio)butyric acid, Search, 9130215G10Rik, SH2-B PH domain-containing signaling mediator 1, CYS, Source Softwares, Software Tools, Programs, Program, Computer Applications, S-adenosyl-L-methionine:thiol S-methyltransferase activity, Ionen, PSM, Psm, Computer Applications Software, 163, Computer Applications Softwares, lysine, Immunologic Tolerance, Methionin, Lzm-s1, methionine, Softwares, Hmet, presumptive somite mesoderm, Prostate-specific membrane antigen, fixed, and GLY protein 2, parent ion, HGF receptor, HGF/SF receptor, and GLY protein 1, Pteroylpoly-gamma-glutamate carboxypeptidase, Software Applications, Source Software, mice, FGCP, proportionality, rate, alpha, hCMT1c, c-Met, beta Trypsin, Pro-rich, Lysm, Applications, Self Tolerance, precursor ion, Tolerance, PSMA, Mouse, Polypeptide, TMT, Computer Software Applications, SH2 domain-containing protein 1B, 2-amino-4-(methylsulfanyl)butanoic acid, False, unsegmented paraxial mesoderm, Gene, Computer, precursor, protein-containing complex, somitomeric mesoderm, GCPII, HGF, polypeptide chain, Gene Products, N-acetylated-alpha-linked acidic dipeptidase I, F15E12.6, mKIAA1299, Del(8)44H, RCCP2, Application, Open Source Softwares, Search Engines, SH2B, F15E12_6, proportion, scatter factor receptor, Software Application, iones, beta-Trypsin, Open Source Software, mGCP, ions, AUTS9, Computer Software Application, 2-amino-4-(methylthio)butanoic acid, Tools, 10^[-6], peptidos, AI838057, metionina, thiol methyltransferase activity, Applications Software, Lyzs, Open Source, Computer Software, DL-Methionine, protein complex, Proteins, Peptide, Engine, Tool, GCP2, Glutamate carboxypeptidase II, polypeptide, Software Tool, Cell growth-inhibiting gene 27 protein, Immune Tolerance, native protein, natural protein, Mus, chemical analysis, Protein, segmental plate, Sh2bpsm1, Software, Data Base, ATCMPG1, MET, Met, teratoma with malignant transformation, ATCMPG2, PH and SH2 domain-containing signaling mediator, Col4a-1, Protein., tyrosine-protein kinase Met, Engineering, Tripcellim, Folate hydrolase 1, Protein Gene Products, Computer Programs, Trypure, Gene Proteins, Applications Softwares, Ion, AI425885, alpha-amino-gamma-methylmercaptobutyric acid, quotient, Peptid, assay, Par4, variable, 6-diaminohexanoic acid, 5730455C01Rik, SF receptor, Immunological Tolerancetype 2, insular sclerosis, Terminalis, Medullari, HSN1E, methionine aminopeptidase activity, Laboratory, Mus domesticus, Cerebrospinal Axis, positive regulation by symbiont of host non-apoptotic programmed cell death, experimental autoimmune encephalomyelitis, CASP-14, House Mouse, Central Nervous, "Multiple sclerosis" EXACT [SNOMEDCT_2005_07_31:155023009], Nervous Systems, autoimmune disease, hemolysis by symbiont of host RBCs, pathogenesis, 2, autoimmunity, synganglion, Allergic encephalomyelitis, Analysis, Experimental allergic encephalomyelitis (disorder), Autoimmune, WMS, peptidase M activity, spinal cord structure, adenomas, Mass Spectrum Analysis, rabGAPLP, Spinali, modification by symbiont of host biological process, L-methionine aminopeptidase activity, fissura cerebro-cerebellaris, stimulation by symbiont of host programmed cell death, Analyses, Coccygeal, activation inducer molecule, Allergic, RabGAP-5, Age of onset, Swiss Mice, Conus Medullaris, suprasegmental levels of nervous system, activation by organism of programmed cell death in other organism during symbiotic interaction, Conus, Conus Terminali, Coccygeal Cords, RUSC3, cytolysis by organism of host cells, house mouse, autoimmune disorder, GPHYSD2, SGS, Spinal Cords, Disseminated Sclerosis, ENCEPH EXPER AUTOIMMUNE, suprasegmental structures, Experimental Allergic Encephalomyelitides, Sacral Cords, mouse, MYH-associated polyposis, autosomal recessive familial adenomatous polyposis, Maps, ALLERGIC ENCEPH EXPER, Medullaris, fissura cerebrocerebellaris, positive regulation by symbiont of host programmed cell death, Spectrum Analysis, Central Nervous Systems, ACMICD, Spectroscopy, autoimmune, Experimental, enhancement of host programmed cell death, Medulla, Mini-ICE, Experimental Autoimmune, Myelon, modulation by symbiont of host system process, "Generalized multiple sclerosis (disorder)" EXACT [SNOMEDCT_2005_07_31:192928003], Sacral Cord, cerebrocerebellar fissure, haemolysis in host, autosomal recessive, EXPER AUTOIMMUNE ENCEPH, MUTYH-associated polyposis, early T-cell activation antigen p60, MUTYH-related AFAP, Mus musculus, ADCADN, RUTBC3, Encephalomyelitis, systema nervosum centrale, Caspase-14 subunit p10, mice, Encephalon, Swiss Mouse, perturbation by symbiont of host defense response, Spectrometry, "insular sclerosis" EXACT [CSP2005:2042-2324], Lumbar Cords, Caspase-14 subunit p19, MASS, MICE, Allergic encephalomyelitis (disorder), induction by organism of programmed cell death in other organism during symbiotic interaction, modification by symbiont of host morphology or physiology, RABGAP5, domesticus, Multiple, disease, regulation of cytolysis of host cells by symbiont, ENCEPH AUTOIMMUNE EXPER, induction by symbiont of host programmed cell death, hemolysis by symbiont of host red blood cells, activation by symbiont of host programmed cell death, multiple colorectal, Axi, MUTYH-related attenuated familial polyposis coli, Mouse, CD69, Proteomes, Autoimmune Experimental Encephalomyelitis, the brain, "multiple sclerosis" EXACT [NCI2004_11_17:C3243], 3.4.22.-, Coccygeal Cord, Sclerosis, regulation by symbiont of host system process, modulation by organism of defense response of other organism involved in symbiotic interaction, Multiple Sclerosis, number, Allergic Encephalomyelitis, FBN, EA1, mini-ICE, Spectrum Analyses, MLR-3, autoimmune hypersensitivity disease, presence, Cerebrospinal, AIM, EAE, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, House, ECTOL1, hypersensitivity reaction type II disease, Mass, Mus musculus domesticus, early activation antigen CD69, "Multiple sclerosis" EXACT [ICD9CM_2006:340], cerebro-cerebellar fissure, Mice, familial adenomatous polyposis, MAP, Mass Spectroscopy, upregulation by symbiont of host programmed cell death, "Multiple sclerosis (disorder)" EXACT [SNOMEDCT_2005_07_31:24700007], Thoracic Cord, "Multiple sclerosis NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:192930001], induction of non-apoptotic programmed cell death by other organism, Nervous System, CNS, Swiss, familial adenomatous polyposis 2, Autoimmune Experimental, Myelons, autosomal recessive multiple colorectal adenomas, OCTD, autoimmune disease or disorder, leukocyte surface antigen Leu-23, generalised multiple sclerosis, SpC, Sacral, C-type lectin domain family 2 member C, AUTOIMMUNE ENCEPH EXPER, EXPER ALLERGIC ENCEPH, generalized multiple sclerosis, Experimental Allergic Encephalomyelitis, Terminali, MUTYH-related attenuated familial adenomatous polyposis, neuraxis, disruption by symbiont of host cell, activation by organism of non-apoptotic programmed cell death in other organism, ALLERGIC ENCEPH, MUTYH-Associated Polyposis, Central, hemolysin activity, Autoimmune Encephalomyelitis, DNMT, Cords, total expressed protein, medulla spinalis, MS (Multiple Sclerosis), MCMT, encephalon, Cord, BL-AC/P26, count in organism, MS, Mus, Conus Medullari, MUTYH-related attenuated FAP, Systems, cerebrospinal axis, modulation by symbiont of host defense response, Experimental Encephalomyelitis, MFS1, induction by organism of programmed cell death in other organism involved in symbiotic interaction, mitigation by symbiont of host defense response, Mass Spectrum Analyses, WMS2, CXXC9, Mass Spectrum, Experimental Allergic, Thoracic Cords, enhancement of host programmed cell death by organism, ENCEPH ALLERGIC, Spinalis, House Mice, Conus Terminalis, MYH-Associated Polyposis, Age symptoms begin, Disseminated, Acute Fulminating, Axis, SSKS., Laboratory Mice, spinal medulla, activation by organism of host programmed cell death, GP32/28, Cerebrospinal Axi, Spinal, AUTOIMMUNE EXPER ENCEPH, MAP syndrome, quantitative, Medulla Spinalis, Lumbar, Thoracic, Lumbar Cord, Laboratory Mouse, CLEC2C, Medulla Spinali, FAP2, colorectal adenomatous polyposis, presence or absence in organismtype 2, insular sclerosis, Terminalis, Surrogate Endpoints, Laboratory, Cerebrospinal Axis, experimental autoimmune encephalomyelitis, House Mouse, Lobus Frontalis, protein polypeptide chains, "Multiple sclerosis" EXACT [SNOMEDCT_2005_07_31:155023009], Formations, Biological, lamina pallidi incompleta, 2, autoimmunity, Analysis, Frontal, WMS, adenomas, average, Nucleus, modification by symbiont of host biological process, L-methionine aminopeptidase activity, fissura cerebro-cerebellaris, stimulation by symbiont of host programmed cell death, Analyses, Allergic, Age of onset, Conus Medullaris, proteins, suprasegmental levels of nervous system, lobus frontalis, Conus, Parencephalon, Conus Terminali, infratentorial region, Coccygeal Cords, Homo sapiens disease, autoimmune disorder, SGS, Brodmann's, Spinal Cords, Disseminated Sclerosis, suprasegmental structures, Ammon, Viral, lamina medullaris accessoria, Experimental Allergic Encephalomyelitides, animalia, MYH-associated polyposis, ALLERGIC ENCEPH EXPER, Medullaris, fissura cerebrocerebellaris, Normalcy, Spectrum Analysis, Frontal Eye Fields, Cerebella, seahorse, ACMICD, autoimmune, Experimental, enhancement of host programmed cell death, Hippocampal, Marker, Experimental Autoimmune, single organismal cell-cell adhesion, Sacral Cord, Subiculum, cerebrocerebellar fissure, activation, haemolysis in host, EXPER AUTOIMMUNE ENCEPH, MUTYH-associated polyposis, early T-cell activation antigen p60, MUTYH-related AFAP, RUTBC3, Encephalomyelitis, frontal region, whole organism, Caspase-14 subunit p10, End Points, Swiss Mouse, perturbation by symbiont of host defense response, Spectrometry, "insular sclerosis" EXACT [CSP2005:2042-2324], Caspase-14 subunit p19, Immunologic, Laboratory Marker, Supplementary, Allergic encephalomyelitis (disorder), Multiple, regulation of cytolysis of host cells by symbiont, nucleus caudatus, Area 8, parencephalon, Cerebellums, induction by symbiont of host programmed cell death, Supplementary Eye Fields, hemolysis by symbiont of host red blood cells, activation by symbiont of host programmed cell death, multiple colorectal, Koerper, MUTYH-related attenuated familial polyposis coli, Mouse, cortex of frontal lobe, "multiple sclerosis" EXACT [NCI2004_11_17:C3243], 3.4.22.-, Lobe, multi-cellular organism, region or site annotation, Clinical Marker, Sclerosis, regulation by symbiont of host system process, modulation by organism of defense response of other organism involved in symbiotic interaction, Multiple Sclerosis, number, mini-ICE, protein-containing complex, AIM, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, lobi frontales, hypersensitivity reaction type II disease, Brodmann's Area 8, Gene Products, Mus musculus domesticus, disease or disorder, early activation antigen CD69, "Multiple sclerosis" EXACT [ICD9CM_2006:340], Cornu Ammonis, MAP, upregulation by symbiont of host programmed cell death, Hippocampus, Normalities, "Multiple sclerosis (disorder)" EXACT [SNOMEDCT_2005_07_31:24700007], Thoracic Cord, "Multiple sclerosis NOS (disorder)" EXACT [SNOMEDCT_2005_07_31:192930001], positional, Clinical, CNS, familial adenomatous polyposis 2, lamella pallidi incompleta, frontal cortex, Autoimmune Experimental, Frontal Eye Field, accessory medullary lamina of pallidum, hippocampus major, autoimmune disease or disorder, SpC, C-type lectin domain family 2 member C, EXPER ALLERGIC ENCEPH, Supplementary Eye Field, Biologic, Experimental Allergic Encephalomyelitis, Terminali, Horn, disruption by symbiont of host cell, hemolysin activity, Autoimmune Encephalomyelitis, body, Proper, Proteins, Serum Markers, disorders, Hippocampus Propers, Hippocampal Formation, whole body, medulla spinalis, MS (Multiple Sclerosis), MCMT, encephalon, Immune Marker, BL-AC/P26, truncus encephali, MS, archipallium, Cortex, native protein, Conus Medullari, Surrogate End Point, MUTYH-related attenuated FAP, cerebrospinal axis, chemical analysis, condition, MFS1, Mass Spectrum Analyses, Hippocampus Proper, Biologic Markers, CXXC9, Experimental Allergic, Thoracic Cords, enhancement of host programmed cell death by organism, Surrogate, Endpoints, Spinalis, House Mice, CNS - Brain - Hippocampus (MMHCC), Conus Terminalis, Understanding, Disseminated, primary structure of sequence macromolecule, Gene Proteins, hippocampus, Eye Fields, activation by organism of host programmed cell death, Cerebrospinal Axi, MAP syndrome, quantitative, Lumbar, Lumbar Cord, CLEC2C, Immune Markers, Biological Markers, Viral Marker, corpus cerebelli, Nucleus Caudatus, Medullari, HSN1E, methionine aminopeptidase activity, determination, Ammon horn fields, Mus domesticus, epencephalon-1, positive regulation by symbiont of host non-apoptotic programmed cell death, Biochemical, Endpoint, CASP-14, protein, Serum, Central Nervous, Readability, Laboratory Markers, Tier, Nervous Systems, diseases, autoimmune disease, hemolysis by symbiont of host RBCs, pathogenesis, diseases and disorders, synganglion, Allergic encephalomyelitis, Experimental allergic encephalomyelitis (disorder), protein aggregate, animal, Autoimmune, peptidase M activity, spinal cord structure, Mass Spectrum Analysis, rabGAPLP, Spinali, human disease, Frontal Cortex, Coccygeal, activation inducer molecule, RabGAP-5, Swiss Mice, caudatus, activation by organism of programmed cell death in other organism during symbiotic interaction, Ammons Horn, Frontal Cortices, caudatum, Brodmann Area 8, Immune, Markers, Ammons horn, RUSC3, Viral Markers, cytolysis by organism of host cells, house mouse, GPHYSD2, ammon gyrus, ENCEPH EXPER AUTOIMMUNE, Surrogate Endpoint, formatio hippocampi, Sacral Cords, mouse, autosomal recessive familial adenomatous polyposis, Maps, Ammon Horn, hippocampus proper, Biochemical Markers, positive regulation by symbiont of host programmed cell death, Biologic Marker, Central Nervous Systems, regio frontalis, Spectroscopy, Subiculums, organism, Medulla, frontal lobe cortex, Mini-ICE, Myelon, Diseases, modulation by symbiont of host system process, "Generalized multiple sclerosis (disorder)" EXACT [SNOMEDCT_2005_07_31:192928003], major hippocampus, Ammon's Horn, brain stem, region, upregulation by symbiont of host programmed cell death., autosomal recessive, Mus musculus, ADCADN, Ammon's, Ammon's horn, Parencephalons, positional polypeptide feature, systema nervosum centrale, mice, Encephalon, Brodmanns Area 8, frontal neocortex, Lumbar Cords, MASS, MICE, induction by organism of programmed cell death in other organism during symbiotic interaction, modification by symbiont of host morphology or physiology, RABGAP5, domesticus, disease, ENCEPH AUTOIMMUNE EXPER, Health, primal cortex, Biochemical Marker, Axi, CD69, Proteomes, Autoimmune Experimental Encephalomyelitis, gray matter of frontal lobe, the brain, other disease, Coccygeal Cord, Clinical Markers, ammon horn, Allergic Encephalomyelitis, FBN, EA1, Gene, Spectrum Analyses, MLR-3, autoimmune hypersensitivity disease, presence, Cerebrospinal, lamina medullaris incompleta pallidi, Surrogate End Points, Surrogate Markers, EAE, polypeptide chain, House, ECTOL1, Mass, cerebro-cerebellar fissure, Mice, familial adenomatous polyposis, Mass Spectroscopy, study, Biomarker, induction of non-apoptotic programmed cell death by other organism, Nervous System, Swiss, hippocampus (Crosby), Biological Marker, metazoa, Eye Field, Myelons, autosomal recessive multiple colorectal adenomas, OCTD, non-neoplastic, leukocyte surface antigen Leu-23, Immunologic Markers, generalised multiple sclerosis, Sacral, AUTOIMMUNE ENCEPH EXPER, site, disorder, generalized multiple sclerosis, Immunologic Marker, Caudate, MUTYH-related attenuated familial adenomatous polyposis, Cornu ammonis, neuraxis, activation by organism of non-apoptotic programmed cell death in other organism, ALLERGIC ENCEPH, MUTYH-Associated Polyposis, Central, protein complex, DNMT, Cords, total expressed protein, End Point, medical condition, brainstem, Cord, Caudatus, count in organism, natural protein, Mus, Brodmann, Systems, Protein, modulation by symbiont of host defense response, Experimental Encephalomyelitis, sequence, induction by organism of programmed cell death in other organism involved in symbiotic interaction, mitigation by symbiont of host defense response, grey matter of frontal lobe, truncus encephalicus, WMS2, Mass Spectrum, cornu ammonis, hippocampus proprius, Serum Marker, Propers, ENCEPH ALLERGIC, Normality, Corpus Cerebelli, MYH-Associated Polyposis, Age symptoms begin, Surrogate Marker, Acute Fulminating, Axis, Laboratory Mice, Protein Gene Products, spinal medulla, GP32/28, SSKS, Spinal, AUTOIMMUNE EXPER ENCEPH, assay, Medulla Spinalis, Thoracic, Laboratory Mouse, Hippocampal Formations, Frontal Lobes, Medulla Spinali, FAP2, Formation, colorectal adenomatous polyposis, presence or absence in organismthe brain, Experimental Allergic Encephalomyelitis, MUTYH-related attenuated familial adenomatous polyposis, type 2, ENCEPH EXPER AUTOIMMUNE, suprasegmental structures, ALLERGIC ENCEPH, MUTYH-Associated Polyposis, Experimental Allergic Encephalomyelitides, methionine aminopeptidase activity, Autoimmune Encephalomyelitis, mouse, MYH-associated polyposis, autosomal recessive familial adenomatous polyposis, Allergic Encephalomyelitis, total expressed protein, Maps, experimental autoimmune encephalomyelitis, ALLERGIC ENCEPH EXPER, encephalon, Experimental, EAE, Mus, MUTYH-related attenuated FAP, Experimental Autoimmune, Experimental Encephalomyelitis, 2, synganglion, Allergic encephalomyelitis, Experimental allergic encephalomyelitis (disorder), Autoimmune, familial adenomatous polyposis, MAP, peptidase M activity, autosomal recessive, EXPER AUTOIMMUNE ENCEPH, adenomas, MUTYH-associated polyposis, mice., MUTYH-related AFAP, RUTBC3, rabGAPLP, Encephalomyelitis, Experimental Allergic, L-methionine aminopeptidase activity, ENCEPH ALLERGIC, mice, familial adenomatous polyposis 2, Allergic, Encephalon, Autoimmune Experimental, RabGAP-5, suprasegmental levels of nervous system, MYH-Associated Polyposis, Allergic encephalomyelitis (disorder), RABGAP5, autosomal recessive multiple colorectal adenomas, ENCEPH AUTOIMMUNE EXPER, RUSC3, multiple colorectal, AUTOIMMUNE ENCEPH EXPER, AUTOIMMUNE EXPER ENCEPH, MAP syndrome, MUTYH-related attenuated familial polyposis coli, EXPER ALLERGIC ENCEPH, Mouse, house mouse, Proteomes, FAP2, colorectal adenomatous polyposis, Autoimmune Experimental EncephalomyelitistrueMouse brain proteome map of Experimental autoimmune encephalomyelitis (EAE) mouse modelMultiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS); its cause is unknown. To understand the pathogenesis of MS, researchers often use the experimental autoimmune encephalomyelitis (EAE) mouse model. Here, our aim was to build a proteome map of the biological changes that occur during MS at the major onset sites—the brain and the spinal cord. We performed quantitative proteome profiling in five specific brain regions and the spinal cord of EAE and healthy mice with high-resolution mass spectrometry based on tandem mass tags.2019-02-252018-10-19PXD0114282806551646099180498295358511145284218809058113633363515242602758385NCBITaxon:128068888111430118726355557114526236493461327467073853883641135461582158236889511232944222911809923233654583334607925193659143205971293865581914932637371250232NCBITaxon:12721119577481866584345135867221755437408169180454266834453058611498225058149636745855452811320810039237514636942049433208964208963445974137979128384400667935293216599404832165972165954550131528221659116968332183217292042779447623764543172030949801975255569781439843948840479NCBITaxon:21575515343989903712285772059687623588845587077918178081736309431794571698936160488409859NCBITaxon:37162104782150590710613204913816936303555432046632633456545351217459216129410026420369456941016763410210761277351131658239254727933428146135843017463345774449167547604675684030191726518130194111929439367110411310239320255598632582788396593474951652998355256631758543102431024598087574175551832019644714526804579619083233115611415542193255521123598755529NCBITaxon:47515476113615741465477180066556484337677299767982510216998238976411557444474153NCBITaxon:5055789969844100036465349334147548019467512991143597412764731370863265478765698353221599838192011985247946409860995867668599191572951372211711011076878349741986014884063342492359859886559746499870392021110729433117215987419085037117082835024145113919027463604614737593925325664890507945265919722119151774208588596NCBITaxon:6157505210283079895110517237505957613172000263419610264940772275689964975157244NCBITaxon:22023717NCBITaxon:1703612857050617476792745062724915961538400524643213686150596866629417347515363291018194301086731018557303963558633149286287132161865368595105135260710185687294110091416333NCBITaxon:619184023210007348824187878645159553470951451225786260704260705260707658457561007133705654195NCBITaxon:3055504457913998781681928752829126806315327341478281055524NCBITaxon:9606469008150251930283672859300852NCBITaxon:5693826883064017946991510151548242838111370475927237082816772850351581990119519532673863702492405360888175626158355833376057267119350199808611935021678793711371272407371457125627457903113335503728142433747924910078711082NCBITaxon:961559463318586260799141262200298492670NCBITaxon:12637192812528303856838569591110065812375612750454266625515197883750360094129349735247214012576499085151514389923745374744544641524323592887051580595536157932716029385114978633892894535936479437NCBITaxon:685441275422511715901090134167387158955210129661030612967158515845158493765327159100226376733889423451287689146479293652803421641332803828035369091089176894621812141080348179392287889295027113117493468192273218903821076012471904007271143114020641198108713554771424507229533796981291632180334708714537209164573315754699287770202060328114319338293550833291292211487252649997727550717629970767892683704152140532941281607839563924227377596205516936053307972551811354915974953502611595561432138406072334919496340161433471046603815184547448500356709747751240607699468810376201488728909316435649408941442423277422140921157781154756929793244704749906604162103591905158749907312989913112273170187103589915NCBITaxon:372961036098334113079813367953164071034015786303337330130641399253064236547881033729940445862073401153571119529652611114716113131663430531201799351299385057316317642619794011513458445772678728623862116079139222798351681196125522811676175731210807721348799861814084341033519963218496139248820963304393758626NCBITaxon:269704933986243694110312195883205092029061099758644864324995252972463438942786378942625673786391233435514149317998686554055343529148654514712454661042986357124679151641358884019373345087718238039129529719748693102868899951337310548771251632138985076255470119380625631886571303443516558658862238NCBITaxon:44664946454636493NCBITaxon:1107114280062883564918458810874391459438543311167810778543143933495346939773821899318226900351281459533996686959541869420030895448697244366206656395456233551804264308692200302284812426428150475149910510299386262903512089557117008930621864419306157558413101653823525577223994636010636010439947544404237610212790568813116229629817677187093128110502318557966946543186320519744173941245012885318388919885319111379103716473516601261557NCBITaxon:101142845031631198573859523343237956026087121346395984275295952664373343232235443142752422430814336195931334565943274169963112223360520121697952528386972864368012187073347474081882976038181249885340188439733127441416395888582955464803834369122432640817212419355955212816140559204254655194582288609183827127442340817019332982972127442012744269432841399616601876254829647187624748011991509564818822914801541204551384738481882945190695116633603648498505693101510693735294529722258594109767781231006191107927943447256848479387033384991722617561094616143512032581205136521850523525944732054937347446644991755825803880433301206781122026049910806124619624619732063752299186705150906812193879118794739800718680157230746835741258117571508476918388580329031388869152167786721273997844597247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