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552/100723V1RS1_Kaja_sample1_frac_66.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/08/PXD000552/100715V1RS1_Kaja_sample1_frac_15.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/08/PXD000552/completesearchinput-peakpickingProteomeDiscoverer.mgfftp://ftp.pride.ebi.ac.uk/pride/data/archive/2014/08/PXD000552/identifiedandannotatedMSMSspectra.zipprimaryOK200024890schutzbier@imp.ac.atMichael SchutzbierMass SpectrometryBottom-up proteomicsNot availableSynapse proteome ageinghttps://www.ebi.ac.uk/pride/archive/projects/PXD000552Not availablePrideNot availableNot availableProteomicsMichael SchutzbierServicePARTIALMus Musculus (mouse)25157418 Moczulska KE, Pichler P, Schutzbier M, Schleiffer A, Rumpel S, Mechtler K. Deep and precise quantification of the mouse synaptosomal proteome reveals substantial remodeling during postnatal maturation. J Proteome Res. 2014 Aug 26schutzbier@imp.ac.atBiologicalServiceAustriaDuring postnatal murine maturation, behavioral patterns emerge and become shaped by experience-dependent adaptations. During the same period, the morphology of dendritic spines, the morphological correlates of excitatory synapses, is known to change, and there is evidence of concurrent alterations of the synaptosomal protein machinery. To obtain comprehensive and quantitative insights in the developmental regulation of the proteome of synapses, we prepared cortical synaptosomal fractions from a total of 16 individual juvenile and adult mouse brains (age 3 or 8 weeks, respectively). We then applied peptide-based iTRAQ labeling (four pools of 4 animals) and high-resolution two-dimensional peptide fractionation (99 SCX fractions and 3 h reversed-phase gradients) using a hybrid CID-HCD acquisition method on a Velos Orbitrap mass spectrometer to identify a comprehensive set of synaptic proteins and to quantify changes in protein expression. We obtained a data set tracking expression levels of 3500 proteins mapping to 3427 NCBI GeneIDs during development with complete quantification data available for 3422 GeneIDs, which, to the best of our knowledge, constitutes the deepest coverage of the synaptosome proteome to date. The inclusion of biological replicates in a single mass spectrometry analysis demonstrated both high reproducibility of our synaptosome preparation method as well as high precision of our quantitative data (correlation coefficient R = 0.87 for the biological replicates). To evaluate the validity of our data, the developmental regulation of eight proteins identified in our analysis was confirmed independently using western blotting. A gene ontology analysis confirmed the synaptosomal nature of a large fraction of identified proteins. Of note, the set of the most strongly regulated proteins revealed candidates involved in neurological processes in health and disease states. This highlights the fact that developmentally regulated proteins can play additional roles in neurological disease processes. All data have been deposited to the ProteomeXchange with identifier PXD000552.Deep and precise quantification of the mouse synaptosomal proteome reveals substantial remodeling during postnatal maturation.Moczulska Kaja Ewa KE, Pichler Peter P, Schutzbier Michael M, Schleiffer Alexander A, Rumpel Simon S, Mechtler Karl K2Not Available, Unavailable.Mus musculus, House, Mus, Laboratory, Swiss, mice, Proteomes., Mus domesticus, mouse, Mus musculus domesticus, Swiss Mouse, total expressed protein, Mouse, House Mice, Swiss Mice, house mouse, Mice, Laboratory Mouse, House Mouse, domesticus, Laboratory MiceNot Available, Unavailable.Regulations, Forms, big, 3.4.22.-, IPP2A2, single-organism developmental process, young adult, Procedures, determination, Laboratory, adult stage, vif Gene, postnatal development, Mus domesticus, vif, Mbp1, Gene, mini-ICE, growth and development, CASP-14, protein, sor Gene, A Genes, Spectrum Analyses, protein-containing complex, Foundation, House Mouse, Social Controls, PHAPII, froggy, Gyltl1a, 5730420M11Rik, method, Techniques, large, House, Method, method used in an experiment, Gene Products, Mass, Studies, Mus musculus domesticus, Synapse, Analysis, protein aggregate, myd, juvenile, Mice, Formal Social Controls, Technique, adult, Mass Spectroscopy, Mass Spectrum Analysis, A, study, SET, Analyses, TAF-I, Swiss, sor Genes, MDDGB6, ipp2a2, Q, 2pp2a, Mbp-1, Swiss Mice, labeling, LARGE, CG10574, Social, DmelCG4299, Study, juvenile stage, BPFD#36, IGAAD, set, 2PP2A, Methodological Studies, DmelCG10574, taf-ibeta, great, heterogeneity, dSET, dSet, A Gene, phapii, Data Set, Formal Social Control, gyltl1b-b, protein complex, Arts, Proteins, igaad, CASP14, mouse, StF-IT-1, sor, Procedure, Spectrum Analysis, group, Spectroscopy, development, native protein, Social Control, I-2PP2A, Mus, MDDGA6, mKIAA0609, Dm I-2, Protein, Mini-ICE, chemical analysis, I2PP2A, Q Gene, KIAA0609, Adults, Mass Spectrum Analyses, child, fg, Mus musculus, Mass Spectrum, vif Genes, Q Genes, Industrial, Genes, gyltl1b, HLA-DR-associated protein II, Industrial Arts, Caspase-14 subunit p10, function., ensemble, DI-2, mice, I-2Dm, postnatal growth, Swiss Mouse, mdc1d, Control, Spectrometry, expanded, House Mice, Caspase-14 subunit p19, CG4299, Methodological, Controls, MICE, Methodological Study, Laboratory Mice, domesticus, I-2PP1, Protein Gene Products, plan specification, Gene Proteins, dSET/TAF-Ibeta, MDC1D, 2610030F17Rik, TAF-IBETA, enr, enlarged, regulation, TAF-Ibeta, Mouse, assay, AA407739, Regulation, growth, i2pp2a, Laboratory Mousel(4)17, l(4)13, Gli, dmBest1, PROSA-28.1, Bhlha41, Scx, SCX, Product, Laboratory, Cid[Mel], Ci[D], Western, bHLHa48, growth and development, House Mouse, heavy chain disease, CENP-A, DmelCG6264, Social Controls, CENP-C, 28.1Pros, 5730420M11Rik, Polypeptides, scx, Method, Biological, Blottings, Western Blotting, Biological Product, myd, adult, Animalia, Pros-Dm28.1, average, SET, BcDNA:RE21270, Biologic Drugs, nervous system disease or disorder, Western Blots, Mbp-1, Dendritic Spine, Social, DmelCG4299, D11Bhm180e, set, Cognitions, CI, Biological Medicine, MAP126, Functions, bHLHa41, Role Concepts, Medicine, Homo sapiens disease, Cortical Portion of Kidney, 3422, Biologic Drug, CiD, Ce, Spine, Ci, anatomical protrusion, Data Set, Biologic Products, CG3422, Normalcy, Insight, Procedure, collisionally activated dissociation, Cid, CID, ciD, PSA4_DROME, Role Concept, Playthings and Play, disorder of nervous system, mKIAA0609, Role, Mastrin, ci-D, Ontology Projects, TU15B, Western Immunoblotting, child, fg, Ontology, HLA-DR-associated protein II, Projects, CENP-A/Cid, CENP-A/CID, DI-2, Biological Medicines, CENPA, I-2Dm, Biological Drug, dbest1, Swiss Mouse, expanded, Biologics, Methodological, Controls, AGE, I-2PP1, MDC1D, TAF-IBETA, enr, Mouse, TAF-Ibeta, Ci-155, Regulations, big, Hybrids, Western Immunoblots, Immunoblotting, Biologic Pharmaceuticals, number, Mitotic spindle-associated protein p126, Antp P1, nervous system disease, Antp P2, protein-containing complex, animals, Normalcies, SCXB, Gene Ontology Project, Gene Ontology, SCXA, CenpA, morphology, large, neurological disease, Hu, Gene Products, Mus musculus domesticus, disease or disorder, 3.4, Siah, alpha4, Technique, KIDNEY, Biologicals, Toy, Normalities, FACT80, anatomy, hMAP126, Playthings, VMD2, MDDGB6, Dendritic, Blots, 2pp2a, BMD, CG1028, CG10574, Cognitive Functions, Study, juvenile stage, 2PP2A, Puppets, dSET, dSet, CG2125, peptidos, Biologic, Puppet, RP50, Pharmaceuticals, Products, Individual Health, suprarenal cortex, synaptosome, Biologic Medicines, Proteins, disorders, DmAntp, Concept, polypeptide, N-acetyl-D-glucosamine 2-epimerase, native protein, Social Control, ci[D], I-2PP2A, Dm I-2, chemical analysis, Biopharmaceutical, condition, S17, Ontology Project, Ant, DmelCG2125, CenH3, ci155, ensemble, best, Function, postnatal growth, House Mice, plan specification, multicellular animals, Gene Proteins, Ns, DmelCG1028, Immunoblot, T160, DRO15DC96Z, regulation, CenpA/CID, BEST, Cognitive Function, Astrin, IPP2A2, ANT-C, Gene Ontology Projects, single-organism developmental process, determination, adult stage, Mus domesticus, Antp1, postnatal development, pros28.1, metazoans, Synaptosome, Mbp1, histology, protein, peptide, Techniques, DmelCG3422, peptido, disease of nervous system, diseases, Roles, Cortical Portion of the Kidney, DEEPEST, AntP1, ARB, Project, Concepts, Synapse, diseases and disorders, CORTEX, protein aggregate, Cortex of adrenal gland, anatomy and histology, Formal Social Controls, CG13329, Western blot, human disease, peptides, TAF-I, Immunoblottings, Natural, FACT, PROS-Dm28.1, PROS-28.1, Swiss Mice, Biological Drugs, xscleraxis, alpha4_dm, BG:DS07700.1, IGAAD, Methodological Studies, DmelCG10574, Cenp-A, ANT-P, Western Blot, Medicines, house mouse, disease or disorder of nervous system, Alpha-4, phapii, CG6264, gyltl1b-b, mouse, StF-IT-1, Aus, neurological disorder, Menstruation, AI874642, HCD, Biopharmaceuticals, MDDGA6, RENBP, BB114693, Diseases, Plaything, Pros28, Biologic Product, spine., Prosalpha4, neurological problem, Individual, KIAA0609, Adults, cenpA, dBest1, Mus musculus, Gene Ontologies, Epistemology, gyltl1b, Ontologies, CenH3/CID, Ci/Gli, Ci/GLI, mice, mdc1d, Control, Toys, CG4299, Methodological Study, domesticus, disease, Health, enlarged, spine, Polypeptide, Regulation, i2pp2a, Proteomes, Western Blottings, other disease, Plays, young adult, Procedures, neurologic disorder, DMANTPE1, Gene, anon-WO0118547.380, presence, PHAPII, froggy, Gyltl1a, protrusion, l(4)102ABc, method, House, method used in an experiment, Studies, Animal, juvenile, Mice, cortex of suprarenal gland, CenH3[Cid], CenH3[CID], Drugs, ANTC, antp, Swiss, Cortical, Western Immunoblottings, ipp2a2, Natural Product, DmelCG13329, labeling, LARGE, Chimeras, non-neoplastic, X-linked combined immunodeficiency, BPFD#36, taf-ibeta, Spines, great, Immunoblots, Play, disorder, AntP, ANTP, Formal Social Control, protein complex, RnBP, igaad, total expressed protein, GlcNAc 2-epimerase, cenH3, medical condition, Peptide, group, development, Insights, count in organism, CAD, Hybrid, Period, Mus, Ci155, Protein, Metazoa, I2PP2A, l(3)84Ba, Deepest, Dbest, Normality, Blot, neurologic disease, cortex glandulae suprarenalis, Cognitive, Laboratory Mice, Protein Gene Products, Drug, dSET/TAF-Ibeta, 2610030F17Rik, renin-binding protein, Natural Products, Peptid, a4, assay, Western Immunoblot, AA407739, growth, Laboratory Mouse, nervous system disorder, Scl, CID/CENP-AMus musculus, House, Mus, Laboratory, Swiss, mice, Proteomes., Mus domesticus, mouse, Mus musculus domesticus, Swiss Mouse, total expressed protein, Mouse, House Mice, Swiss Mice, house mouse, Mice, Laboratory Mouse, House Mouse, domesticus, Laboratory Mice489falseDeep and precise quantification of the mouse synaptosomal proteome reveals substantial remodeling during postnatal maturationIn order to understand the molecular underpinnings of the functional and morphological heterogeneity of synapses and their regulation during development it is essential to identify the set of proteins that form these structures. Here, we prepared cortical synaptosomal fractions from juvenile and adult mice, processed them using a multidimentional protein identification technology approach, applied iTRAQ labelling and used mass spectroscopy to identify a comprehensive set of synaptic proteins and to quantitatively analyze changes in protein expression during development. We obtained a dataset tracking expression levels of 3424 proteins during development. The inclusion of biological replicates in a single mass spectrometry analysis demonstrated a high accuracy of our method. A gene ontology analysis confirmed the synaptic nature of a large fraction of identified proteins. Furthermore, developmental regulation of eight proteins identified in our analysis was confirmed independently using Western blotting. In summary, we provide a comprehensive dataset describing the developmental regulation of synaptosomal proteins, which serves as an essential foundation for the investigation of synaptic function and maturation.2014-08-282013-10-30PXD000552NEWT:6945NEWT:184922NEWT:6703NEWT:3555NEWT:2NEWT:157546NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:544496NEWT:2102NEWT:2042546NEWT:45351NEWT:43179NEWT:4513NEWT:5722NEWT:376741NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:1351NEWT:1438992NEWT:2649997NEWT:272563NEWT:224326NCBITaxon:79857NEWT:1096976NEWT:95648NEWT:3885NEWT:3888NEWT:1589NEWT:135622NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:913645NEWT:1000589NEWT:85963NEWT:85962NEWT:317447NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:84645NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:197NEWT:1390363NEWT:288705NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:1270NEWT:374990NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:286NEWT:391619NEWT:287NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:1148NEWT:580240NEWT:294128NEWT:11676NEWT:55571NEWT:35500NEWT:100226NEWT:4530NEWT:4896NEWT:75058NEWT:13616NEWT:1390NEWT:1094343NEWT:172NEWT:296543NEWT:1773NEWT:1895NEWT:1182590NEWT:3712NEWT:105023NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:375146NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:243277NEWT:990119NEWT:408172NEWT:408170NEWT:493760NEWT:260710NEWT:257313NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:106592NEWT:536231NEWT:460519NEWT:1187947NEWT:1432138NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:9598NEWT:8030NEWT:9483NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:432359NEWT:46835NEWT:1182263NEWT:2711NEWT:376686NEWT:95486NEWT:9103NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:3635NEWT:5811NEWT:235443NEWT:108458NEWT:272623NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:169963NEWT:32644NEWT:225117NEWT:499175NEWT:109779NEWT:476272NEWT:3747NEWT:195051NEWT:367830NEWT:1255228NEWT:178616NEWT:410289NEWT:373153NEWT:352472NEWT:357NEWT:360094NEWT:470NEWT:1313NEWT:411469NEWT:84023NEWT:559292NEWT:39491NCBITaxon:5811NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:327159NEWT:178876NEWT:327160NEWT:573NEWT:9031NEWT:7091NEWT:108931NEWT:241368NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:5180NEWT:256737NEWT:9541NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1249668NEWT:7108NEWT:317NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:9644NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:554NEWT:27592NEWT:98334NEWT:426428NEWT:1276815NEWT:9639NEWT:7574NEWT:1715256NEWT:7215NEWT:575412NEWT:29204NEWT:2172103NEWT:7460NEWT:507601NEWT:643680NCBITaxon:6157NEWT:746360NEWT:6239NEWT:470150NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NEWT:13164NEWT:216129NCBITaxon:2NEWT:985076NEWT:1215323NEWT:52641NEWT:7038NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:1194669NEWT:51329NEWT:243230NEWT:8355NEWT:9685NEWT:7029NEWT:1080772NEWT:8479NEWT:1283300NEWT:6183NEWT:6063NEWT:630NEWT:334747NEWT:61235NEWT:15368NEWT:6289NEWT:436486NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:725NEWT:170187NEWT:469008NEWT:260707NEWT:256318NCBITaxon:6191NEWT:1836NEWT:185431NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:2697049NEWT:105231NEWT:1216981NEWT:4097NCBITaxon:6073NEWT:884204NEWT:6279NEWT:1123869NEWT:9544NEWT:7370NEWT:83906NEWT:607699NEWT:6282NEWT:208964NEWT:1134506NEWT:575584NEWT:38783NEWT:8727NEWT:4006NEWT:8726NEWT:6426NEWT:6669NEWT:10090NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:5334NEWT:37334NEWT:382352NCBITaxon:10359NEWT:242619NEWT:632957NEWT:34073NEWT:373995NEWT:5689NEWT:544404NEWT:9925NEWT:8839NEWT:4232NEWT:2758385NEWT:37349NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:714NEWT:36015NEWT:421932NEWT:196627NEWT:5691NEWT:48479NEWT:627025NEWT:1097677NEWT:61674NEWT:1117957NEWT:9913NEWT:8709NEWT:4100NEWT:2666255NEWT:1076NEWT:6763NEWT:803NEWT:29722NEWT:380394NEWT:1692259NEWT:180066NEWT:817NEWT:135588NEWT:1843183NEWT:58002NEWT:326423NEWT:36111NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:1678078NEWT:749906NEWT:418985NEWT:146479NEWT:749907NEWT:1911079NEWT:69373NEWT:264203NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:9612NEWT:38865NEWT:51953NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:112273NE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