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Merl-Pham"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Nscs","Map1b","Lc-ms/ms"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063724"],"tissue":["Brain"],"sample_protocol":["The subcellular fractionation and interactome were all digested using a modified FASP procedure as described before. For NSC’s subcellular protomics analysis, digested peptides of the cellular fractionation samples were measured on a TimsTOF HT mass spectrometer (Bruker) equipped with a CaptiveSpray 2 source online coupled to a Vanquish Neo HPLC (Thermo Scientific). A nano-trap column was used (300-µm inner diameter (ID) × 5 mm, packed with Acclaim PepMap100 C18, 5µm, 100 Å from LC Packings) before separation by reversed-phase chromatography (Aurora 75µm ID × 250 mm, 1.8µm from Ionoptics) at 40°C. Peptides were eluted from the column at 250 nl/min using a nonlinear 45 min acetonitrile gradient from 3 to 40% in 0.1% formic acid. The DIA-Pasef method covered a mass range from 300 to 1,250 m/z and a mobility range from 0.65 to 1.35 1/ko, with a ramp and accumulation time of each 100ms. Precursor peptides were isolated using 34 variable MS/MS windows and 17 MS/MS ramps, resulting in a cycle time of 1.91 sec. Collision energy for 0.6 1/ko was set to 20 and for 1.6 1/ko to 59. For MAP1B’s interactome, digested peptides were measured on a QExactive HF X mass spectrometer (Thermo Scientific) online coupled to an Ultimate 3000 nano-RSLC (Thermo Scientific) as described before. Samples were automatically loaded onto the C18 pre-column cartridge and after 5 min eluted and separated on the C18 analytical column (nanoEase MZ HSS T3, 100 Å, 1,8 µm, 75 µm x 250 mm; Waters) in a 95 min non-linear acetonitrile gradient from 5 to 40% at a flow rate of 250 nl/min. MS spectra were recorded at a resolution of 60,000 with an automatic gain control (AGC) target of 3e6 and a maximum injection time of 30 ms from 300 to 1500 m/z. From the MS scan, the 15 most abundant peptide ions were selected for fragmentation via HCD with a normalized collision energy of 28, an isolation window of 1.6 m/z, and a dynamic exclusion of 30 s. MS/MS spectra were recorded at a resolution of 15,000 with an AGC target of 1e5 and a maximum injection time of 50 ms. Unassigned charges and charges of +1 and > +8 were excluded from precursor selection."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Generated measurement files of fractionation samples were quantitatively analyzed in the Spectronaut 19.9 software (Biognosis) in directDIA using BGS settings, allowing for quantification on only proteotypic peptides and applying the QUANT2.0 label-free quantification method allowing for a mean TOP3 protein group quantity calculation. Searches were performed using the Swissprot Human (20432 sequences) or Swissprot Mouse (17061 sequences) databases. TOP3 protein group quantities were imported in Perseus 2.0.11 software15 (MPI Martinsried). Abundances were log2 transformed and the data was filtered for at least 3 valid values per protein in at least one sample group per dataset. Missing values were imputed from normal distribution using default settings. The average quantities per protein per group were calculated and used for ratio calculations. Groups were compared applying a Student’s t-test with (q) and without (p) Benjamini-Hochberg correction. Enriched proteins in each subcellular fraction were considered as those with an adjusted p-value<0.05, and a logFoldChange>2. Generated raw files for IP samples were quantitatively analyzed in the Proteome Discoverer 2.5 software (Thermo Scientific) for peptide and protein identification and quantification. Database search was performed using the Sequest HT search engine against the Swissprot Human database (20432 sequences, version 2020_02), considering full tryptic specificity, allowing for up to one missed cleavage, a precursor mass tolerance of 10 ppm and a fragment mass tolerance of 0.02 Da. Carbamidomethylation of cysteine was set as a static modification and deamidation of asparagine and glutamine, oxidation of methionine, and a combination of methionine loss with acetylation on protein N-terminus were allowed as dynamic modifications as well as phosphorylation of serine, threonine or tryptophane. The Percolator algorithm17 was used for validating peptide spectrum matches. Match-between runs for label-free quantification was performed in the Minora node with limitations to a retention time window of 1 minute and a mass shift of 0.5 ppm. Quantification of proteins was based on peptide intensities for the TOP3 unique peptides per protein with a XCorr score >1 and a peptide FDR < 1% without normalization. Resulting raw protein abundances were filtered for a protein FDR of 1% and exported for further analysis in Perseus 2.0.11 software15 (MPI Martinsried). Data was filtered for 3 valid values in the dataset, followed by log2 transformation of abundance values and low abundance imputation of missing values from normal distribution separately per column using default settings. The average abundances per group were used for calculation of IP enrichment values. All reported statistical tests correspond to Student’s t-tests with Benjamini-Hochberg FDR corrections for multiple testing. Enriched interactors were considered as those with an adjusted p-value<0.05, and a logFoldChange>3. Enriched interactions are reported separately for cytosolic and nuclear-enriched fractions. For proteins enriched in both fractions separately, gene-set enrichment analysis (GSEA) was conducted using the get_enrichment function in STRINGdb, using the whole human proteome as background. GSEA p-values were corrected for multiple testing using the Benjamini-Hochberg FDR method. Proteins with an adjusted p-value<0.05 were kept for further use. For GSEA-significant gene ontology term of interest, STRING networks including enriched peptides for each fraction were obtained and colored with the reported logFoldChange from fraction enrichment. For MAP1B, both unphosphorylated and phosphorylated peptides were identified, and their respective abundance values across individual samples were exported for further analysis. To visualize peptide coverage along the MAP1B sequence, the start and end positions of all detected peptides were mapped onto an array corresponding to the length of the canonical MAP1B sequence. This approach allowed us to pinpoint areas of high or low peptide representation across the protein. To account for variability in sample coverage, peptide abundance values were normalized by the total peptide count per sample, ensuring comparability across samples regardless of total coverage. Additionally, to facilitate more direct comparisons of peptide abundance across samples, each peptide’s abundance was scaled relative to its maximum value observed across samples, highlighting relative abundance variations within each peptide profile."],"omics_type":["Proteomics"],"labhead":["Magdalena Götz"],"instrument_platform":[""],"labhead_affiliation":["Division of Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität, Planegg-Martinsried, Germany. Institute of Stem Cell Research, Helmholtz Center Munich, Planegg-Martinsried, Germany."],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["10.1016/J.CELL.2026.05.019"],"submitter_mail":["juliane.merl@helmholtz-muenchen.de"],"submitter_affiliation":["Metabolomics and Proteomics Core, Helmholtz Munich"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"MAP1B as nuclear neural stem cell fate determinant involved in disease","description":"Cellular differentiation and morphogenesis rely on both cytoskeletal remodeling and transcriptional programs to drive cell fate decisions. Their coordination is critical for proper lineage progression, yet if and how cytoskeletal elements can regulate fate in the nucleus is largely unknown. To explore this comprehensively, we profiled the nuclear proteome of human and murine neural stem cells (NSCs). Cytoskeletal proteins were enriched among the most abundant nuclear components, with a predominance of microtubule (MT)-interacting proteins, including the MT-associated protein MAP1B. MAP1B mutations have been identified in patients with periventricular heterotopia (PH), linked to neuron migration deficits. We found that MAP1B translocates to the nucleus in NSCs, where it interacts with the BAF chromatin remodeling complex to regulate NSC identity and differentiation. Perturbing MAP1B cytoplasmic-to-nuclear balance in NSCs leads to the generation of ectopic neurons in the mouse cerebral cortex, as found in PH patients harboring MAP1B mutations. Patient iPSC-derived brain organoids show nuclear enrichment of mutant MAP1B resulting in enhanced BAF chromatin binding along with neuronal heterotopia. Thus, MAP1B acts as a novel nuclear regulator of NSC fate, highlighting the key role of cytoskeletal elements in the nucleus for fate specification, and how disruption of this process can lead to disease.","dates":{"publication":"2026-06-08","submission":"2025-05-07"},"accession":"PXD063724","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:259447","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NEWT:1129","NEWT:55153","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:10036","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:383379","NEWT:10029","NEWT:913645","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:4442","NEWT:192875","NEWT:59729","NEWT:2164133","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:658457","NEWT:77133","NEWT:145481","NCBITaxon:79824","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:5759","NEWT:1736231","NEWT:1392","NEWT:498217","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:5507","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:1143","NEWT:4896","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:935293","NEWT:375146","NEWT:263","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:7067","NEWT:2850","NEWT:408172","NEWT:408170","NEWT:3708","NEWT:332648","NEWT:536231","NEWT:1436733","NEWT:460519","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:9483","NEWT:1513458","NCBITaxon:40559","NEWT:84588","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:983964","NEWT:118499","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:571256","NEWT:40483","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:9778","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:7108","NEWT:40479","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:1268063","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:407821","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:28532","NEWT:353152","NEWT:27448","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:1080772","NEWT:519","NEWT:8479","NEWT:6063","NEWT:49240","NEWT:104395","NEWT:6289","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:469008","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:596153","NEWT:1836","NEWT:80863","NEWT:105231","NEWT:52638","NEWT:4097","NEWT:884204","NEWT:9785","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NCBITaxon:780","NCBITaxon:1502","NEWT:6282","NEWT:1134506","NEWT:38783","NEWT:4006","NEWT:6426","NCBITaxon:5476","NEWT:6669","NEWT:9935","NEWT:89453","NEWT:51515","NEWT:51511","NEWT:8845","NEWT:92867","NEWT:92866","NEWT:5334","NEWT:51750","NEWT:202950","NEWT:382352","NEWT:413071","NEWT:632957","NEWT:9925","NEWT:89462","NEWT:8839","NEWT:4232","NEWT:2758385","NEWT:11298","NEWT:171101","NEWT:714","NEWT:421932","NEWT:312017","NEWT:196627","NEWT:870435","NEWT:284593","NEWT:100392","NEWT:5315","NEWT:9913","NEWT:265872","NEWT:105841","NEWT:337330","NEWT:2666255","NEWT:2285","NCBITaxon:5693","NEWT:1392998","NEWT:380394","NEWT:981087","NEWT:180066","NEWT:226900","NEWT:430615","NEWT:326423","NEWT:452467","NEWT:36111","NEWT:326424","NEWT:1416333","NEWT:1678078","NEWT:749906","NEWT:418985","NEWT:749907","NEWT:145263","NEWT:694569","NEWT:27606","NEWT:9739","NEWT:59202","NEWT:9975","NEWT:51953","NEWT:3197","NEWT:860688","NEWT:13443","NEWT:36329","NEWT:62615","NCBITaxon:3044782","NEWT:160235","NEWT:72407","NEWT:349741","NEWT:157295","NEWT:2096","NEWT:9721","NEWT:137221","NEWT:9963","NEWT:1617910","NEWT:565050","NEWT:2785785","NEWT:411901","NEWT:105884","NCBITaxon:9615","NEWT:58334","NEWT:1193501","NEWT:58331",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