{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_003_S601097_C7-bFGF_3_C7___bFGF.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_016_S601092_C7-bFGF_2_C7___bFGF.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_005_S601089_Control_2_Control.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_009_S601090_SFM_2_Serum-free_medium.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_013_S601094_Control_3_Control.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_014_S601095_SFM_3_Serum-free_medium.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_008_S601093_bFGF_2_bFGF.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_015_S601098_bFGF_3_bFGF.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_002_S601088_bFGF_1_bFGF.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_004_S601096_C7_3_C7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_006_S601091_C7_2_C7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_018_S601086_C7_1_C7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_017_S601084_Control_1_Control.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_012_S601085_SFM_1_Serum-free_medium.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/20231130_C33552_007_S601087_C7-bFGF_1_C7___bFGF.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/2406139.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD062524/C33552WU297243.zip"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["Martin.Baumgartner@kispi.uzh.ch"],"submitter":["Martin Baumgartner"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"disease":["Medulloblastoma"],"software":[""],"submitter_keywords":["Human","Medulloblastoma","Apex2","Frs2","Interactors"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD062524"],"tissue":["Brain"],"sample_protocol":["Lentiviral constructs were ordered from VectorBuilder (Santa Clara, CA, USA). A V5-tagged APEX2 or a mNeonGreen was fused to the C-terminus of human FRS2 using a flexible 3xGS linker. Using Western blot assays, we confirmed expression of the proteins and phosphorylation of Y436 upon stimulation with bFGF. Further, correct localization was confirmed by IFA. UW228 cells were starved overnight in serum-free medium (SFM before being treated with DMSO or C7 for 30 min at 37°C. Next, biotin phenol was added and incubated another 30 min at 37°C. For the last 3 min added 1 ml of SFM only or SFM + bFGF (final concentration 50 ng/ml) and immediately added 1 ml 6 mM H2O2 in PBS (final H2O2 concentration: 0.5 mM). Incubated 3 min at 37°C. Next, labeling activity was quenched and cells washed. Next, detached cells and collected cell pellets. Washed pellets with PBS and centrifuged before adding 2 ml lysis buffer (5 mM Trolox, 10 mM sodium ascorbate, 10 mM sodium azide, RIPA) containing protease and phosphatase inhibiotors. Incubated 30 min on ice before sonicating each sample twice and cleared by centrifugation . Performed acetone precipitation before resuspending the protein pellet in 2 ml RIPA buffer (incl. inhibitors). Residual pellet pieces were resolubilized by using a Douncer lyser. Samples were and cleared by centrifugation. Lysates were snap-frozen in liquid nitrogen and stored at –80°C. Technical triplicates were produced for each condition. After collection of all samples, lysates were thawed on ice and protein concentration measured by using Pierce BCA Protein Assay. 6 mg total protein was prepared for each sample in 1.8 ml RIPA buffer (incl. inhibitors). Per sample, 30 µl streptavidin-coated magnetic beads (Dynabeads™ MyOne™ Streptavidin T1, Invitrogen, #65601) were washed twice in RIPA before being incubated with lysates overnight at 4°C. Beads were washed twice with 1 ml RIPA, once with 1 ml RIPA high SDS (1% w/v SDS), once with 1 ml RIPA, and finally with 1 ml TBS. Tubes were kept on ice until further processing.For each sample, the washed beads were re-suspended in 45 µl digestion buffer (triethylammonium bicarbonate (TEAB), pH 8.2), reduced with 5 mM TCEP(tris(2-carboxyethyl)phosphine) and alkylated with 15 mM chloroacetamide. Proteins were on-bead digested using 500 ng of Sequencing Grade Trypsin (Promega). The digestion was carried out at 37°C overnight. The supernatants were transferred into new tubes and the beads were washed with 150 µl trifluoroacetic acid (TFA) -buffer (0.1% TFA, 50% acetonitrile) and combined with the first supernatant. The samples were dried to completeness and re-solubilized in 20 µL of MS sample buffer (3% acetonitrile, 0.1% formic acid). Peptide concentration was determined using the Lunatic UV/Vis polychromatic spectrophotometer (Unchained Labs). Mass spectrometry analysis was performed on an Orbitrap Exploris 480 mass spectrometer (Thermo Fisher Scientific) equipped with a Nanospray Flex Ion Source (Thermo Fisher Scientific) and coupled to an M-Class UPLC (Waters). MS solvent composition at the two channels was 0.1% formic acid for channel A and 0.1% formic acid, 99.9% acetonitrile for channel B. Column temperature was set to 50°C. For each sample, peptides corresponding to 0.2 absorbance measurement were loaded on a commercial nanoEase MZ Symmetry C18 Trap Column (100Å, 5 µm, 180 µm x 20 mm, Waters) in-line connected to a nanoEase MZ C18 HSS T3 Column (100Å, 1.8 µm, 75 µm x 250 mm, Waters). The peptides were eluted at a flow rate of 300 nL/min with a gradient from 5 to 22 % B in 40 min and 22 to 32% B in an additional 5 min. The column was cleaned after each run by increasing to 95 % B and prior to re-establishing loading condition for another 10 minutes. Pepides from proximity labeling experiments were analysed in data-dependent mode (DDA) with a maximum cycle time of 3 s, using Xcalibur (tune version 4.1 (DDA) or 4.3 (DIA)), with spray voltage set to 2.5 kV, funnel RF level at 40 %, heated capillary temperature at 275 °C, and Advanced Peak Determination (APD) on. Full-scan MS spectra (350−1’200 m/z) were acquired at a resolution of 120’000 at 200 m/z after accumulation to a target value of 3’000’000 or for a maximum injection time of 45 ms. Precursors with an intensity above 5’000 were selected for MS/MS. Ions were isolated using a quadrupole mass filter with 1.2 m/z isolation window and fragmented by higher-energy collisional dissociation (HCD) using a normalized collision energy of 30 %. HCD spectra were acquired at a resolution of 30’000 and maximum injection time was set to 119 ms. The automatic gain control (AGC) was set to 100’000 ions. Charge state screening was enabled such that singly, unassigned and charge states higher than seven were rejected. Precursor masses previously selected for MS/MS measurement were excluded from further selection for 20 s, and the exclusion window was set at 10 ppm."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["The acquired DIA data were processed for identification and quantification using DIA-NN 1.8.260.Spectra were searched against the Uniprot Homo sapiens reference proteome (UP000005640, downloaded 2023-08-24), concatenated to its reversed decoyed FASTA database and common protein contaminants. Carbamidomethylation of cysteine was set as a fixed and methionine oxidation set as variable modification. Enzyme specificity was set to trypsin/P, allowing a minimal peptide length of 7 amino acids and a maximum of one missed cleavage. Interactor scoring was done using the SAINTexpress algorithm applied to intensities as protein abundance estimates. In short, a set of R functions implemented in the R package prolfqua was used to convert the intensity protein abundances reported in the combined_protein.txt file into SAINTexpress-compatible format.  The mass spectrometry proteomics data were handled using the local laboratory information management system (LIMS). Obtained data sets were screened for significant hits by filtering enriched proteins with a log2FC ≥ 1 and FDR ≤ 0.05. Minimum FDR values were adjusted to 0.0001 to enable plotting of highly significant hits with and FDR of 0."],"omics_type":["Proteomics"],"labhead":["Martin Baumgartner"],"instrument_platform":[""],"labhead_affiliation":["University Children's Hospital Zurich"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["42169144 Kopp LL, Versamento D, Ciraulo B, Schönholzer MT, Hochuli D, Lin MS, Baumgartner M. Fibroblast growth factor receptor substrate 2 interactome mapping reveals novel candidate interactors associated with migration and invasion. Cell Commun Signal. 2026 24(1):416 10.1186/s12964-026-02943-8"],"submitter_mail":["martin.baumgartner@kispi.uzh.ch"],"curator_keywords":["String"],"submitter_affiliation":["University Children's Hospital Zürich"],"submitter_country":["Switzerland"],"pubmed_abstract":["The scaffold protein FRS2 is central to FGFR signaling, linking receptor activation to MAPK/ERK and PI3K/AKT pathways. Elevated FRS2 expression correlates with aggressive tumor phenotypes and poor prognosis across multiple cancers, including the pediatric cerebellar tumor medulloblastoma (MB).Here, we characterized FRS2's subcellular localization and interactome in MB cells, employing live-cell imaging, phosphoproteomics, immunoprecipitation, and APEX2-based proximity labeling. We found that increased FRS2 expression is associated with increased motile and invasive behavior in MB tumor cells. We furthermore identified novel candidate FRS2-associated proteins involved in actin cytoskeleton remodeling, cell junction assembly, and translation initiation, which indicate a growth factor-dependent reorganization of the FRS2 signalosome. Our data additionally indicate a regulatory role of FRS2 in directing subcellular distribution of the cell junction and cell motility regulator TJP1.Our findings highlight the relevance of FRS2 as a mediator of cell motility and invasiveness and provide candidate proteins associated with FRS2 that are involved in cellular processes governing migration and invasion. This study thus provides a framework for exploring the FRS2 interactome as a possible target to attenuate FGFR-driven oncogenic processes with next-generation therapeutic strategies."],"pubmed_title":["Fibroblast growth factor receptor substrate 2 interactome mapping reveals novel candidate interactors associated with migration and invasion."],"pubmed_authors":["Kopp Levi Luca LL, Versamento Dejana D, Ciraulo Bernard B, Schönholzer Marc Thomas MT, Hochuli Dina D, Lin Meng-Syuan MS, Baumgartner Martin M"],"additional_accession":[]},"is_claimable":false,"name":"APEX2 proximity labelling of FRS2 interactors in UW228 cells","description":"The scaffold protein FRS2 is overexpressed in medulloblastoma (MB) and correlates with aggressive tumor phenotype and poor prognosis. Studies regarding FRS2's interactome have been limited to the assembly of the well described canonical FGFR signalosome. Here, we explored the proteomic proximity of FRS2 in MB cells exposed to serum-free medium conditions, stimulation with bFGF or treatment with the FRS2 small molecule ligand C7. Towards this aim, we expressed APEX2 fused to FRS2 in UW228 cells and stimulated labeling activity by co-incubation with biotinphenol and hydrogen peroxide. In the control setup, we expressed a FRS2-mNeonGreen fusion without a peroxidase enzymatic function. After labling and streptavidin purification of biotinylated proteins, we performed mass spectrometry and quantified relative abundances compared to control conditions.","dates":{"publication":"2026-09-07","submission":"2025-04-02"},"accession":"PXD062524","cross_references":{"TAXONOMY":["NEWT:68239","NEWT:108018","NEWT:377960","NEWT:1131","NEWT:2042546","NEWT:148942","NEWT:295546","NEWT:258594","NEWT:1126","NEWT:1129","NEWT:309807","NEWT:89184","NEWT:309800","NEWT:57577","NEWT:1323429","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:77173","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:10034","NEWT:661410","NEWT:224326","NEWT:376619","NEWT:3765","NEWT:3767","NEWT:433727","NEWT:135622","NEWT:672127","NEWT:656061","NEWT:37965","NEWT:656064","NEWT:3760","NEWT:36630","NEWT:381198","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:44250","NEWT:317447","NEWT:5537","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:12637","NEWT:2164133","NEWT:2767846","NEWT:314344","NEWT:108061","NEWT:224308","NEWT:49928","NEWT:160621","NEWT:110368","NEWT:1916073","NEWT:1310161","NEWT:1230383","NEWT:77133","NEWT:1310165","NEWT:114727","NEWT:5516","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:33554","NEWT:1310173","NEWT:37919","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:419481","NEWT:5507","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:709964","NEWT:3712","NEWT:3711","NEWT:3714","NEWT:3715","NEWT:2065263","NEWT:1549675","NEWT:177437","NEWT:9014","NEWT:10891","NEWT:226126","NEWT:1616117","NEWT:34865","NEWT:28174","NEWT:550537","NEWT:284812","NEWT:980415","NEWT:3701","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:1246791","NEWT:9005","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:1883426","NEWT:657321","NEWT:34878","NEWT:10886","NEWT:3708","NEWT:536231","NEWT:219813","NEWT:215451","NEWT:460519","NEWT:272844","NEWT:1348799","NEWT:55784","NEWT:485","NEWT:2709072","NEWT:2499525","NEWT:142786","NEWT:2853422","NEWT:487","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:216778","NEWT:376686","NEWT:237610","EFO:0001352","NEWT:1385720","NEWT:219809","NEWT:219808","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:141469","NEWT:987059","NEWT:491","NEWT:460523","NEWT:133894","NEWT:85694","NEWT:85692","NEWT:3750","NEWT:291146","NEWT:29466","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:278161","NEWT:415978","NEWT:410289","NEWT:191701","NEWT:9054","NEWT:472","NEWT:29459","NEWT:1380096","NEWT:28128","NEWT:470","NEWT:41122","NEWT:1328300","NEWT:748693","NCBITaxon:50557","NEWT:3735","NEWT:29491","NEWT:911022","NEWT:446","NEWT:153481","NEWT:445","NEWT:2003758","NEWT:63366","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:3726","NEWT:30455","NEWT:28141","NEWT:9030","NEWT:9031","NEWT:3728","NEWT:108931","NEWT:219799","NEWT:219798","NEWT:548","NEWT:150475","NEWT:256737","NEWT:51350","NEWT:8694","NEWT:8692","NEWT:542","NEWT:394503","NEWT:13076","NEWT:219785","NEWT:451515","NEWT:8673","NEWT:550","NEWT:10804","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:1225786","NEWT:771870","NEWT:8665","NEWT:51338","NEWT:9995","NEWT:28112","NEWT:49012","NEWT:28110","NEWT:10832","NEWT:507601","NEWT:520","NEWT:64657","NEWT:186441","NEWT:2585209","NEWT:643680","NEWT:214092","NEWT:40697","NEWT:13095","NEWT:162425","NEWT:242124","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:595495","NEWT:80833","NEWT:479096","NEWT:28108","NEWT:28104","NEWT:1114957","NEWT:568703","NEWT:568708","NEWT:52641","NEWT:353152","NEWT:353153","NEWT:227377","NEWT:1774284","NEWT:27689","NEWT:207769","NEWT:40674","NEWT:51329","NCBITaxon:1763","NEWT:443906","NEWT:13037","NEWT:519","NEWT:7394","NEWT:6063","NEWT:404330","NEWT:1328388","NEWT:7375","NEWT:300641","NEWT:39655","NEWT:38323","NEWT:206411","NEWT:80869","NEWT:214053","NEWT:80863","NEWT:665890","NEWT:52639","NEWT:52638","NEWT:367774","NEWT:8697","NEWT:861109","NEWT:8695","NEWT:1196866","NEWT:510516","NEWT:1045775","NEWT:1123869","NCBITaxon:1335626","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:27697","NEWT:86185","NEWT:9935","NEWT:287889","NEWT:1028307","NEWT:52603","NEWT:92867","NEWT:92866","NEWT:1344414","NEWT:202950","NEWT:741158","NEWT:1293091","NEWT:202956","NEWT:315750","NEWT:99490","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:1436183","NEWT:4232","NEWT:9922","NEWT:416348","NEWT:105812","NEWT:11298","NEWT:4236","NEWT:398031","NEWT:196627","NEWT:523840","NEWT:1076878","NEWT:200308","NEWT:200302","NEWT:9917","NEWT:95912","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:1170227","NEWT:2666255","NEWT:999810","NEWT:28995","NEWT:1392998","NEWT:1392997","NEWT:114796","NEWT:1150621","NEWT:1085791","NEWT:745531","NEWT:226900","NEWT:231490","NEWT:590651","NEWT:449239","NEWT:244704","NEWT:9909","NEWT:9902","NEWT:430615","NEWT:563041","NEWT:36599","NEWT:41949","NEWT:9900","NEWT:326423","NEWT:326424","NEWT:13013","NEWT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