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FasciMass SpectrometryChemical cross-linking coupled with mass spectrometry proteomicsNot availableHistone variant specific interactionsHistone interaction network – ptm interplayNuclear interactomeNuclear protein-protein interactionsCrosslinking mass spectrometryhttp://www.ebi.ac.uk/pride/archive/projects/PXD007513Intact nuclei were isolated from U2OS cells through gentle mechanical lysis and soft centrifugation. The crosslinking of the nuclei was performed with the MS-cleavable crosslinker DSSO. The labeled nuclei were separated with sequential detergent fractionation and then digested using sequentially Lys-C and Trypsin. Crosslinked peptides were enriched through strong cation exchange (SCX) chromatography. The late SCX fractions were analyzed by LC-MS/MS using Agilent 1290 Infinity System (Agilent Technologies) in combination with an Orbitrap Fusion (Thermo Scientific), and the crosslinked peptides acquired through sequential collision-induced dissociation (CID) and electron transfer dissociation (ETD) in MS/MS.PrideNot availableiodoacetamide derivatized residuemonohydroxylated residueProteome Discoverer 2.2 (beta, version 2.2.0.196) was used for data analysis with the XlinkX (beta, version 0.1.3) nodes integrated. The processing workflow was set up with the following nodes. The built-in nodes ‘Spectrum Files’ and ‘Spectrum Selector’ were used to extract the MS2 scans together with a precise precursor m/z and charge. To extract precursor intensity information we added the built-in node ‘Minora feature detection’. The following crosslinking workflow consists of the following nodes. The ‘XlinkX Detect’ node performs diagnostic peak detection specific for the used labile crosslinker DSSO. The following ‘XlinkX Filter’ nodes only filters out all MS2 scans for which no diagnostic peak set was detected. The remaining MS2 scans were identified with the dedicated crosslink peptide search engine ‘XlinkX Search’ node, for which the following settings were used: Uniprot human protein database from January 2016 containing 42150 proteins, protease Trypsin (Full), 2 allowed missed cleavages, precursor mass tolerance of 10 ppm, fragment mass tolerance of 20 ppm, carbamidomethyl on C as static modification, oxidation on M as variable modification, where appropriate acetylation or ubiquitination on K were also set as variable modification. The results from the search were FDR corrected to 1% using the ‘XlinkX Validator’ node, which utilizes a specific set of crosslink peptide spectral features and machine learning to define the cutoff as developed for peptide spectral matches in Percolator. Finally, in the ‘Crosslink Consensus’ node the individual crosslink spectral matches were grouped in those cases where they represent the same peptide sequence and modification state.ProteomicsAlbert J.R. HeckOrbitrap Fusion ETDUtrecht UniversityPARTIALHomo Sapiens (human)d.fasci@uu.nl30021884 Fasci D, van Ingen H, Scheltema RA, Heck AJR. Histone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nuclei. Mol Cell Proteomics. 2018 10.1074/mcp.ra118.000924BiologicalUtrecht UniversityNetherlandsCells organize their actions partly through tightly controlled protein-protein interactions-collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the protein-protein interactions in intact human nuclei. Overall, we identified ∼8,700 crosslinks, of which 2/3 represent links connecting distinct proteins. From these data, we gain insights on interactions involving histone proteins. We observed that core histones on the nucleosomes expose well-defined interaction hot spots. For several nucleosome-interacting proteins, such as USF3 and Ran GTPase, the data allowed us to build low-resolution models of their binding mode to the nucleosome. For HMGN2, the data guided the construction of a refined model of the interaction with the nucleosome, based on complementary NMR, XL-MS, and modeling. Excitingly, the analysis of crosslinks carrying posttranslational modifications allowed us to extract how specific modifications influence nucleosome interactions. Overall, our data depository will support future structural and functional analysis of cell nuclei, including the nucleoprotein assemblies they harbor.Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei.Fasci Domenico D, van Ingen Hugo H, Scheltema Richard A RA, Heck Albert J R AJRliquid chromatography tandem mass spectroscopy, l(4)17, Kation, l(4)13, ANT-C, Gli, U2OS, Bhlha41, Scx, SCX, SOFT, Cid[Mel], cation, Antp1, Ci[D], bHLHa48, DMANTPE1, Antp P1, combined T cell and B cell immunodeficiency, Antp P2, lysis, SCXB, body system, combined T and B cell immunodeficiency, CENP-A, SCXA, LC-MS-MS, CENP-C, peptide, CenpA, Polypeptides, l(4)102ABc, peptido, resilient, scx, Detergents, tough, Hu, LC-MSMS, AntP1, system, 3.4, Separated, Siah, CenH3[Cid], CG13329, CenH3[CID], strong, ANTC, antp, Divorced, anatomical systems, BcDNA:RE21270, LCMSMS, peptides, beta-Trypsin, DmelCG13329, Divorces, xscleraxis, CG1028, BG:DS07700.1, X-linked combined immunodeficiency, cations, CI, bHLHa41, Cenp-A, ANT-P, CG2125, peptidos, Cation, ETD, autolysin activity, necrosis, AntP, ANTP, Chromatographies, ETD., CiD, combined immunodeficiency, LC-MS2, Ce, Ci, Trypsin/K, detergent, Kationen, LC-MS/MS, late, cenH3, U-2 OS, DmAntp, Thermo Scientific, not genetically inherited, Cell, Peptide, collisionally activated dissociation, cationes, Aus, CID, ciD, Cid, polypeptide, LC/MS/MS, CAD, ci[D], Ci155, BB114693, bacteriocin activity, ci-D, PIX2, l(3)84Ba, connected anatomical system, WDR51A, cenpA, Separation, Ant, holin, DmelCG2125, ci155, CenH3, Ci/Gli, Ci/GLI, CenH3/CID, CENP-A/Cid, CENP-A/CID, CENPA, Separations, Tripcellim, beta Trypsin, organ system, congenital combined immunodeficiency, Trypure, Ns, lysin activity, DmelCG1028, liquid chromatography-tandem mass spectroscopy, Isolation of Nuclei TAgged in specific Cell Types, bacteriolytic toxin activity, U2-OS, liquid chromatography tandem mass spectrometry, Peptid, DRO15DC96Z, Polypeptide, CenpA/CID, Ci-155, Scl, CID/CENP-AMass Spectrum Analysis, Cell Nuclei, Spectroscopy, Nucleus, Mass Spectrum, Analyses, Isolation of Nuclei TAgged in specific Cell Types, Nuclei, Mass, Spectrometry, Cell., Analysis, Spectrum Analyses, Mass Spectrum Analyses, Spectrum Analysis, Mass Spectroscopy, CellIPP2A2, e(-), primitive node, DELTA AND GAMMA, FBN, Gene, electron, precursor, betaTub1, thomson, extracted material, PHAPII, mass-to-charge ratio, 5730420M11Rik, peptide, Polypeptides, B1t, Drug Tolerance, ClvPrd, peptido, B-spec, template-activating factor I, dorsal marginal zone, ECTOL1, betaspec, Gene Products, node, Analysis, Work Flow, Transfer, WMS, shield, SET, Search Engines, Transfer Learning, Ubiquitylation, betatub(56D), kus, beta1tub, peptides, CG9277, Analyses, TAF-I, nodus primitivus, MS2, Machine, Elektron, phosphatase 2A inhibitor I2PP2A, beta[[1]] tubulin, ipp2a2, E430039A18Rik, human protein, beta-Trypsin, beta1t, Acetylations, T, beta-particle, 2pp2a, Spemann's organizer, proteins, CG10574, CD156, anon-EST:fe1B3, DmelCG4299, OCTD, 1t, set, IGAAD, e, 2PP2A, e-, 10^[-6], beta1Tub, DmelCG10574, SPEC8, taf-ibeta, stem node, Hensen node, ppm, dSET, dSet, Hensen's node, peptidos, ubiquitination, CG5870, organizer, GPHYSD2, embryo organizer, drug tolerance, SGS, phapii, beta-tubulin56D, Spec-beta, Dmbeta1, BETA 56D, immune system tolerance, Proteins, acetylation, Learning, igaad, Tubulin, StF-IT-1, Th, Search, i168, embryonic organizer, Peptide, results, Engine, ACMICD, polypeptide, Workflows, l(1)G0108, Immune Tolerance, I-2PP2A, Dm I-2, Protein, I2PP2A, Spemann Mangold organizer, Immunologic Tolerance, sequence, betaSpec, Henson's node, FLOWERING TIME CONTROL PROTEIN FCA ALPHA, MFS1, b-Spec, tandem MS, Data Base, WMS2, parent ion, beta-tub, DmelCG5870, l(1)G0074, l(1)G0198, Beta <eudicots>, HLA-DR-associated protein II, negatron, DI-2, nodal stem, beta[[1]]-tubulin, MS/MS, I-2Dm, Tripcellim, b spectrin, FCAALL.331, beta1, CG4299, MASS, beta56D, inhibitor of granzyme A-activated DNase, DmelCG9277, CD156a, beta Trypsin, beta, beta1-tub, beta(-), DTB2, Tub, I-2PP1, Protein Gene Products, Gene Proteins, Trypure, beta-Tub, dSET/TAF-Ibeta, 2610030F17Rik, TAF-IBETA, Self Tolerance, precursor ion, Tolerance, beta-spec, Data, i6, DL4180C, SSKS, BETA, DMZ, embryonic shield, primary structure of sequence macromolecule., Peptid, TAF-Ibeta, Polypeptide, beta-Tub56D, AA407739, i2pp2a, Spec, Data Analyses, Work Flows, betaTub, Specbeta, beta1-Tubulin, Immunological ToleranceControlling, data, human being, determination, Nucleoprotein., CT28175, protein complex, Nuclei, Proteins, ran10A, Gene, dran, protein, Spectrum Analyses, protein-containing complex, Spectrum Analysis, extracted material, Cell, gsp1, ara24, ran, CG1404, xran, Fe-containing alcohol dehydrogenase, RanGAP, Cell Nuclei, Spectroscopy, Hmg17, protein polypeptide chains, TC4, tc4, Polynucleosome, ranGap, ranGAP, Nucleosome, Sd-RanGAP, Sd-RanGap, native protein, natural protein, polypeptide chain, DmelCG1404, HOT, Protein, chemical analysis, Mass, Gene Products, Polynucleosomes, Carrying, Analysis, AAF30287, protein aggregate, Mass Spectrum Analyses, Mass Spectroscopy, Mass Spectrum Analysis, Dinucleosome, DmelCG9999, Nucleus, Mass Spectrum, rangap, l(1)G0075, ADHFe1, ARA24, reference sample, Charts, distinct, Analyses, 1.1.99.24, HMG-17, hot, ADH8, RanGap1, ligand, nuclear nucleosome, cytoplasmic nucleosome, SD, Spectrometry, proteins, man, human, Dinucleosomes, Alcohol dehydrogenase iron-containing protein 1, dRanGAP, Protein Gene Products, Gene Proteins, Isolation of Nuclei TAgged in specific Cell Types, high temperature, Gsp1, Sd, CG9999, assay, ran-1, Scl, Controlled, Ranhuman being, determination, Nucleoprotein., nucleocapsid, Gene, dran, protein, Spectrum Analyses, protein-containing complex, extracted material, ara24, ran, RanGAP, Histone H2b, protein polypeptide chains, Histone H2a, Polynucleosome, ranGap, ranGAP, Sd-RanGAP, Sd-RanGap, polypeptide chain, DmelCG1404, HOT, Mass, Gene Products, Low, Carrying, Analysis, AAF30287, protein aggregate, Mass Spectroscopy, Histone H3.3, Mass Spectrum Analysis, DmelCG9999, Nucleus, rangap, me75, ADHFe1, reference sample, Charts, Analyses, 1.1.99.24, hot, ADH8, ligand, nuclear nucleosome, SD, proteins, man, D17Mit170, T1, Histone H5, Histone H4, Sd, Histone H7, ran-1, Histone H1, Controlled, Histone H3, Controlling, data, cou, CT28175, protein complex, Nuclei, Proteins, ran10A, Tl3, Tl2, Spectrum Analysis, Histone, Cell, gsp1, CG1404, xran, Fe-containing alcohol dehydrogenase, Cell Nuclei, Spectroscopy, Hmg17, TC4, tc4, Nucleosome, Lr, native protein, natural protein, Protein, chemical analysis, core, Polynucleosomes, Mass Spectrum Analyses, Dinucleosome, Mass Spectrum, l(1)G0075, ARA24, distinct, HMG-17, RanGap1, cytoplasmic nucleosome, Spectrometry, Histone H1(s), human, Dinucleosomes, Alcohol dehydrogenase iron-containing protein 1, dRanGAP, Protein Gene Products, Gene Proteins, Isolation of Nuclei TAgged in specific Cell Types, high temperature, Gsp1, Bra, CG9999, assay, Scl, RanMass Spectrum Analysis, Cell Nuclei, Spectroscopy, Nucleus, Mass Spectrum, Analyses, Isolation of Nuclei TAgged in specific Cell Types, Nuclei, Mass, Spectrometry, Cell., Analysis, Spectrum Analyses, Mass Spectrum Analyses, Spectrum Analysis, Mass Spectroscopy, Cell4270trueHistone interaction landscapes visualized by crosslinking mass spectrometry in intact cell nucleiCells organize their actions partly through tightly controlled protein-protein interactions – collectively termed the interactome. Here we use crosslinking mass spectrometry (XL-MS) to chart the interactome of intact human nuclei. We overall identified ~8700 crosslinks, of which 2/3 represent links connecting distinct proteins. From this data we constructed an overview of the nuclear interactome. We observed that the histone proteins on the nucleosomes expose well-defined crosslinking hot-spots. For several nucleosome-interacting proteins, such as USF3 and Ran GTPase, the data allowed us to build models of their binding mode to the nucleosome. For HMGN2 the data guided the construction of a refined model of the interaction with the nucleosome, based on complementary NMR, XL-MS and modeling. Excitingly, several isoform-specific interactors seem to exist for distinct histone H1 variants and the analysis of crosslinks carrying post-translational modifications allowed us to extract how specific modifications influence the nucleosome interactome. Overall, our data depository will support future structural and functional analysis of cell nuclei, including the nucleoprotein assemblies they 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