Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077093/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077093/junge_jo000024_20210119_17951_BioID_GFP1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077093/junge_jo000024_20210119_17951_BioID_FZD4_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077093/junge_jo000024_20210119_17951_BioID_FZD4_2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077093/junge_jo000024_20210119_17951_BioID_GFP2_pt2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/04/PXD077093/junge_jo000024_20210119_17951_BioID_LFQ_ANOVA.mzTabprimaryOK200junge@umn.eduKevin MurrayData-dependent acquisitionMass SpectrometryBottom-up proteomicshttps://www.ebi.ac.uk/pride/archive/projects/PXD077093Cell CultureEndothelial CellbEnd.3 cells were virally transduced with vectors encoding V5-FZD4-BioID or GFP-BioID as well as blasticidin resistance. After selection, the stable populations were used for a proximity biotinylation screen, for which GFP-BioID cells served as negative control. Four 150 cm2 dishes per sample were incubated for 24 hours with 50 µM biotin. Duplicate samples were generated. Cells were washed in PBS and directly lysed. Cells were lysed in 8 M urea 50 mM Tris, pH 7.4, buffer with protease inhibitor (87785; Thermo Fisher Scientific) and DTT under sonication, precleared with gelatin-sepharose beads (17095601; Cytiva), incubated with streptavidin-sepharose beads (17511301; Cytiva/GE Healthcare), washed in 8 M urea, 50 mM Tris, pH 7.4, and resuspended in 50 mM ammonium bicarbonate saturated with 1 mM biotin. Samples were reduce-alkylated in 8 M urea, 50 mM ammonium bicarbonate buffer with 10 mM tris(2-carboxyethyl)phosphine (TCEP) at 30 °C for 60 min and 30 mM iodoacetamide (IAA) in the dark at room temperature for 30 min. Samples were diluted to 1M urea and digested with mass spec grade Trypsin/LysC mix overnight (V5071; Promega). The peptide eluates were acidified with formic acid and purified via a C18 matrix (5190-6532; Agilent) using Agilent AssayMap BRAVO liquid handling system. Solvent was removed in a SpeedVac and subjected to LC-MS/MS. We reconstituted the dried peptide mixtures in 98:2:0.1,H2O:acetonitrile (ACN):formic acid (FA) and analyzed ~200 nanogram of each sample by capillary LC-MS on an Orbitrap Fusion mass spectrometer (Thermo Fisher Scientific, Inc., Waltham, MA) online with a Thermo UltiMate™ 3000 RSLCnano LC system. Peptides were separated on a 40 cm self-packed C18 capillary column with 100 um inner diameter, with Dr. Maisch GmbH ReproSil-PUR 12 Å C18-AQ, 1.9 um particle size; the column was maintained at 55°C with a column heater from Sonation (Biberach, Germany). Peptides were loaded directly on column at 325 nl/min with 98:2:0.1,H2O:ACN:FA. We performed elution of the peptides with the following gradient: 5 – 32% solvent B from 0 – 50 minutes, 32 – 45% solvent B from 50 – 55 minutes, 45 – 90% solvent B from 55 – 60 minutes 325 nl/minute, where solvent A was 0.1% formic acid in water and solvent B was 0.1% formic acid in ACN. We operated the mass spectrometer with the following parameters: ESI voltage 2.1kV, ion transfer tube 275 °C; Orbitrap MS1 scan 120k resolution in profile from 380 – 1580 m/z with 50 msec injection time and 120% normalized automatic gain control (AGC); MS2 triggered on precursors charge states 2 – 5 above 20000 counts; precursor isolation window 1.6 Da; MIPS (monoisotopic peak determination) set to Peptide; higher energy collisional dissociation (HCD) at 35% with MS2 Orbitrap detection at 50k resolution (at 200 m/z), 86 msec injection time, 100% (1000) AGC, dynamic exclusion duration 15 sec with +/- 10 ppm mass tolerance.PrideWe processed peptide tandem MS using SEQUEST (Thermo Scientific) in Proteome Discoverer 4.0. The mouse Universal Proteome database (UP000000589) was downloaded from UniProt on 11/19/2021 and merged with a common lab contaminant protein database (https://www.thegpm.org/crap/) (55,214 total protein sequences). We applied the precursor mass recalibration node with precursor mass tolerance 20 ppm, product ion tolerance 0.2 Da with fixed carbamidomethyl (CAM) modification of cysteine 57.0215 m/z. The SEQUEST (PMID: 24226387) database search parameters included enzyme trypsin full specificity, 2 missed cleave sites; precursor tolerance 15 ppm, fragment ion tolerance 0.05 Da and maximum 4 dynamic modifications per peptide. We specified CAM cysteine (+57.021 Da) as a fixed modification and the dynamic modifications were acetylation of protein N-terminus (+42.011 Da), oxidation of methionine (+15.995 Da), conversion of glutamine to pyroglutamic acid (-17.027 Da), methionine loss at the protein N-terminus (-131.040 Da), methionine loss + acetylation at the protein N-terminus (-89.030 Da), biotinylation of lysine (226.078 Da) and deamidation of asparagine or glutamine (+0.984 Da). We applied 1% protein and peptide False Discovery Rate (FDR) filters using the Percolator algorithm (https://doi.org/10.1038/nmeth1113) in PD. We used the label free quantification workflow in PD 2.4 that included steps for feature extraction, chromatographic alignment, peptide mapping to features, protein abundance calculation, normalization, protein relative abundance ratio calculation and hypothesis testing for significance of relative fold chance. We applied the Minora Feature Detector algorithm in PD 2.3 for the assignment of chromatographic features for isotopically related peaks within a 0.2 minute retention time range. After features were assigned, chromatographic alignment was performed; the file with the largest number of features was assigned as the reference to which features from each file were aligned within a 4 minute (RT) window tolerance and 12 ppm mass tolerance. Retention times were adjusted from a non-linear regression-based fit of the differences in retention time between reference and sample. Peptide were mapped to retention time-aligned consensus features across samples with the requirement that at least one sample contains a peptide spectral match. We applied total peptide summed normalization across samples. Protein abundance calculations were made from summed peptide abundances. We used the background t-test for hypothesis testing with the null hypothesis of equal protein abundance. Protein relative abundances between groups were reported with p-values adjusted with the Benjamini-Hochberg method for multiple testing corrections.ProteomicsHarald JungeCOMPLETEAssociate Professor and Research Director Department of Ophthalmology and Visual Neuroscience University of MinnesotaMus Musculus (mouse)Not availablemurra668@umn.eduCenter for Metabolomics and Proteomics - University of MinnesotaUnited States10.6019/PXD077093falseProximity interactions of Frizzled4 (FZD4) in the bEnd.3 mouse brain endothelial cell lineFrizzled4 (FZD4) is a pivotal molecule in the CNS vasculature and a target for therapeutic intervention. Little is known how FZD4 is regulated. A proximity biotinylation screen with FZD4 as bait in a mouse brain endothelial cell line was performed. The goal is to identify candidate regulators of 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