{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_12.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_10.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_6.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_11.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_5.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_8.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_9.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD080872/Ex2_20241205_CJX_DSBSOKatharina_NPC_HPH_5uL_3h_3.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["fliu@fmp-berlin.de"],"submitter":["Nanako Yokoyama"],"technology_type":["Mass Spectrometry","Chemical cross-linking coupled with mass spectrometry proteomics"],"software":["Not available"],"submitter_keywords":["Human","Nuclear pore complexes"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD080872"],"tissue":["Cell Suspension Culture"],"sample_protocol":["We crosslinked isolated nuclei purified from HEK293-F cells. Cells were cultured and washed with PBS once, and stored at −80°C. For cellular lysis, the cell pellets were thawed in lysis buffer (25 mM HEPES pH 7.3, 150 mM NaCl, 0.1% IGEPAL CA-630, 0.5 mM DTT, 0.5 mM EDTA pH 8.0) supplemented with complete protease inhibitor EDTA-free cocktail, followed by passing through a G24 needle ten times and incubation on ice for 30 minutes. Nuclei were collected by centrifugation at 1,000xg at 4°C for 5 min. The nuclear pellet was washed twice by gentle resuspension in wash buffer (25 mM HEPES pH 7.3, 150 mM NaCl, 0.5 mM EDTA pH 8.0) supplemented with complete protease inhibitor EDTA-free cocktail and subsequent centrifugation. Then, the nuclear pellet was resuspended in wash buffer to an approximate protein concentration of 10 mg/ml. Crosslinking was performed using 4 mM Azide-A-DSBSO for 15 min at room temperature with constant mixing. The reaction was quenched with a final concentration of 20 mM Tris-HCl pH 8.0 for 30 min at room temperature with constant mixing. The crosslinking efficiency was monitored by SDS-PAGE. The nuclei were collected by centrifugation and resuspended in urea buffer (50 mM TEAB pH 8.55, 7.12 M Urea, 0.1% ProteaseMax). nuclear lysis and DNA shearing were performed by sonication on ice (UP50H Ultrasonic Processor, Hielscher Ultrasonics GmbH) at 0.7 cycles and 60% amplitude for 1 min ten times, with at least 30 seconds in between with constant mixing at room temperature. Nuclear lysis was completed by prolonged incubation at room temperature with constant mixing for one hour total. Nuclear lysis efficiency was evaluated by microscopy. The nuclear extract was cleared by centrifugation at room temperature at 16,000xg for 3 min. The supernatant was collected and protein concentration was determined using the BCA protein assay kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. After protein reduction (5 mM TCEP, 15 min RT) and alkylation (40 mM Chloroacetamide, 1 hour 37°C), proteins were digested in solution using LysC (Mass Spec Grade, Promega) at a ratio of 1:75 for 2.5 hours at RT. Subsequently, the samples were digested in 0.05% ProteaseMax and <2 M Urea/50 mM TEAB using Trypsin (Sequencing Grade Modified Trypsin, Promega) at a ratio of 1:75 for 22 hours at 37°C. After quenching with 1% formic acid (final concentration), peptides were desalted using C8 cartridges (Waters), quantified spectrophotometrically (DeNovix DS-11) and dried in vacuo.  The digested peptide mixtures were enriched by dibenzocyclooctyne (DBCO)-coupled sepharose beads. Briefly, peptides after digestion were added to the prewashed DBCO beads for incubation overnight at room temperature with constant mixing. After incubation, the beads were washed with water, followed by a washing step with 0.5% SDS at 37 °C for 15 min. Next, the beads were washed thrice with 0.5% SDS, thrice with 8 M urea in 50mM TEAB, thrice with 10% ACN and twice with water using ten bead volumes each. The crosslinked peptides were eluted with two bead volumes using 10 % (v/v) trifluoracetic acid (TFA) for 2 h at room temperature and then dried using a vacuum concentrator. Enriched crosslinks were further fractionated by size exclusion chromatography (SEC) followed by Hi-pH fractionation. SEC was performed using a SuperdexTM 30 Increase 3.2/300 column (GE Healthcare) on an Agilent 1260 Infinity II system and Hi-pH fractionation was performed using Phenomenex Gemini C18 column on an Agilent 1260 Infinity II UPLC system. Hi-pH fractions were subjected to LC-MS analysis.For the analysis of DSBSO-crosslinked peptides, collected fractions were analyzed by LC-MS using an UltiMate 3000 RSLC nano LC system coupled on-line to an Orbitrap Exploris 480 mass spectrometer (Thermo Fisher Scientific). Reversed phase separation was performed with an in-house packed C18 analytical column (Poroshell 120 EC-C18, 2.7µm, Agilent Technologies). Fractions were run with 3 h LC gradients. The following MS parameters were applied: MS resolution 120,000; MS2 resolution 60,000; charge state 4-8 enable for MS2; MS2 isolation window, 1.6 m/z; stepped normalized collision energy, 19-25-30%; FAIMS compensation voltages were set to −50, −60, and −75."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Search parameters: minimum peptide length 6; maximal peptide length 60; missed cleavages 3. Fixed modification was set as cysteine carbamidomethylation, and variable modifications were set as methionine oxidation and protein N-terminal acetylation. The DSBSO cross-linker mass was specified as 308.0388 Da (short arm: 54.0106 Da, long arm: 236.0177 Da). Precursor mass tolerance was set to 10 ppm, and fragment mass tolerance to 20 ppm."],"omics_type":["Proteomics"],"labhead":["Fan Liu"],"instrument_platform":[""],"labhead_affiliation":["Department of Structural Biology, Leibniz - Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117 Berlin, Germany"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["yokoyama@fmp-berlin.de"],"publication":["Not available"],"submitter_affiliation":["Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)"],"submitter_country":["Germany"],"additional_accession":[]},"is_claimable":false,"name":"Nuclei cross-linking mass spectrometry","description":"Cross-linking mass spectrometry performed on intact nuclei purified from HEK293T for structural interactome profiling of the nuclear pore 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