Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/msmsScans.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/proteinGroups.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/evidence.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/summary.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/peptides.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/parameters.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/Phospho_STYSites.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/mzRange.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/allPeptides.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/msms.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/Oxidation_MSites.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/modificationSpecificPeptides.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_01.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_03.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_12.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_05.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_10.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_09.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_07.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_02.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_04.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_06.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_11.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_08.rawprimaryOK200yimon.aye@epfl.chDalu ChangData-dependent acquisitionMass SpectrometryProteomic. localis-rexhttps://www.ebi.ac.uk/pride/archive/projects/PXD051483Cell CultureSamples were separated by SDS-PAGE on a 12% polyacrylamide gel and Coomassie blue stained. Each gel lane was entirely sliced and proteins were in-gel digested. The gel pieces were washed twice with 50% ethanol in 50 mM ammonium bicarbonate (AB, Sigma-Aldrich) for 20 min and dried by vacuum centrifugation. Proteins were reduced with 10 mM dithioerythritol (Merck-Millipore) for 1 h at 56°C followed by a washing-drying step as described above. Reduced proteins were alkylated with 55 mM iodoacetamide (Sigma-Aldrich) for 45 min at 37°C in the dark followed by a washing-drying step as described above. Proteins were digested overnight at 37°C using mass spectrometry grade Trypsin gold (Typsin Gold, Promega) at a concentration of 12.5 ng/µl in 50 mM AB supplemented with 10 mM CaCl2. Resulting peptides were extracted in 70% ethanol, 5% formic acid (FA, Merck-Millipore) twice for 20 min, dried by vacuum centrifugation. Resulting peptides were desalted on stagetips [doi:10.1038/nprot.2007.261] and dried under a vacuum concentrator. Samples were resuspended in 2% acetonitrile (Biosolve), 0.1% FA and nano-flow separations were performed on a Dionex Ultimate 3000 RSLC nano UPLC system (Thermo Fischer Scientific) on-line connected with an Exploris 480 Orbitrap Mass Spectrometer or a Lumos Orbitrap Mass Spectrometer (Thermo Fischer Scientific). A capillary precolumn (Acclaim Pepmap C18, 3 μm-100Å, 2 cm x 75μm ID) was used for sample trapping and cleaning. A 50cm long capillary column (75 μm ID; in-house packed using ReproSil-Pur C18-AQ 1.9 μm silica beads; Dr. Maisch) was then used for analytical separations at 250 nl/min over 150 min biphasic gradients. Acquisitions were performed through Top Speed Data-Dependent acquisition mode. The most intense parent ions were selected and fragmented by High energy Collision Dissociation (HCD) with a Normalized Collision Energy (NCE) of 30%. Selected ions were then excluded for the following 20 s.PrideNot availableRaw data were processed using MaxQuant 1.6.10.43 [doi: 10.1038/nbt.1511] against a database consisting of the Mus Musculus Reference proteome database (55341 protein sequences Release2021_02) and the Halo Protein sequence or the Homo Sapiens Reference proteome database (77027protein sequences Release2021_01). Carbamidomethylation was set as fixed modification, whereas oxidation (M), phosphorylation (S, T, Y), acetylation (Protein N-term) and glutamine to pyroglutamate were considered as variable modifications. A maximum of two missed cleavages were allowed and “Match between runs” option was enabled. A minimum of 2 peptides was required for protein identification and the false discovery rate (FDR) cutoff was set to 0.01 for both peptides and proteins. Label-free quantification and normalisation was performed by Maxquant using the MaxLFQ algorithm, with the standard settings [doi: 10.1074/mcp.M113.031591]. The statistical analyses of the label-free data were performed using Perseus version 1.6.15.0 [doi: 10.1038/nmeth.3901.] from the MaxQuant tool suite. Reverse proteins, potential contaminants and proteins only identified by sites were filtered out. Protein groups containing at least X% of valid values in at least one group were conserved for further analysis. Empty values were imputed with random numbers from a normal distribution. A two-sample t-test with permutation-based FDR statistics was performed to determine significant differentially abundant candidatesProteomicsYimon AyePARTIALEPFLMus Musculus (mouse)10.1038/S41589-025-02135-4dalu.chang@epfl.chEPFLSwitzerlandfalseAye Lab Localis-REX hits (202201)target ID for localis-REX, in mouse cells, under different subcelluar locations, with spatial and temporal control2026-06-042024-04-16PXD051483NEWT:6945NEWT:3555NEWT:241368NEWT:2NEWT:157546NEWT:190802NEWT:35554NEWT:9778NEWT:150475NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:307972NEWT:32046NEWT:544496NEWT:5180NEWT:256737NEWT:2042546NEWT:115104NEWT:1081927NEWT:67825NEWT:185579NEWT:43179NEWT:13076NEWT:1249668NEWT:317NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:7227NEWT:7469NEWT:885318NEWT:415540NEWT:4081NEWT:876138NEWT:554NEWT:98334NEWT:426428NEWT:237561NEWT:6928NEWT:10036NEWT:7574NEWT:1351NEWT:7215NEWT:29204NEWT:272563NEWT:507601NCBITaxon:79857NCBITaxon:6157NEWT:95648NEWT:3885NEWT:746360NEWT:6239NEWT:3888NEWT:1589NEWT:470150NEWT:135622NEWT:216257NEWT:6915NEWT:9986NEWT:101510NEWT:4054NEWT:3880NEWT:3641NEWT:383379NEWT:8782NEWT:1263854NEWT:1000589NEWT:1902NEWT:85962NEWT:160488NEWT:28104NEWT:317447NEWT:7955NCBITaxon:2NEWT:985076NEWT:7959NEWT:2261NEWT:4565NEWT:1264690NEWT:6192NEWT:28532NCBITaxon:38727NEWT:34305NEWT:59729NCBITaxon:183674NEWT:224308NEWT:626528NEWT:139927NEWT:4558NEWT:209285NEWT:216595NEWT:243230NEWT:8355NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:7029NEWT:1283300NEWT:6183NEWT:6063NEWT:334747NEWT:61235NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:3218NEWT:5759NEWT:1736231NEWT:436486NEWT:6287NEWT:2242NEWT:300641NEWT:4784NEWT:727NEWT:9796NEWT:725NEWT:360106NEWT:260707NEWT:287NEWT:10117NEWT:10239NCBITaxon:6191NEWT:10116NEWT:1280NEWT:1836NEWT:1735272NEWT:83334NEWT:185431NEWT:83332NEWT:29760NEWT:260704NEWT:703612NEWT:260705NEWT:80863NEWT:44685NEWT:2697049NEWT:1148NEWT:11676NEWT:55571NEWT:100226NCBITaxon:6073NEWT:4530NEWT:4896NEWT:6279NEWT:1123869NEWT:7370NEWT:75058NEWT:83906NEWT:607699NEWT:6282NEWT:1094343NEWT:208964NEWT:1134506NEWT:575584NEWT:296543NEWT:1773NEWT:38783NEWT:8727NEWT:1895NEWT:4006NEWT:1182590NEWT:8726NEWT:6669NEWT:10090NEWT:935293NEWT:64152NEWT:749200NEWT:4120NEWT:51515NEWT:5693NEWT:8724NEWT:51511NEWT:92867NEWT:8723NEWT:990346NEWT:5334NEWT:145953NEWT:257309NEWT:100816NEWT:230741NEWT:284812NCBITaxon:10359NCBITaxon:1313NEWT:43330NEWT:242619NEWT:44544NEWT:632957NEWT:373995NEWT:5689NEWT:645463NEWT:544404NEWT:3702NEWT:129249NEWT:9925NEWT:8839NEWT:4232NEWT:990119NEWT:2758385NEWT:4113NEWT:837NEWT:11298NEWT:171101NEWT:421932NEWT:196627NEWT:408172NEWT:5691NEWT:408170NEWT:493760NEWT:260710NEWT:627025NEWT:400772NEWT:1097677NEWT:3708NEWT:128161NEWT:106592NEWT:61674NEWT:1117957NEWT:9913NEWT:1432138NEWT:10312NEWT:1424507NEWT:4100NEWT:1076NEWT:6763NEWT:803NEWT:8030NEWT:29722NEWT:380394NEWT:1692259NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:180066NEWT:67767NEWT:46835NEWT:135588NEWT:1843183NEWT:95486NEWT:58002NEWT:9103NEWT:4577NEWT:1416333NEWT:5664NEWT:2157NEWT:146479NEWT:10306NCBITaxon:2759NEWT:1911079NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:3635NEWT:5811NEWT:235443NEWT:1480154NEWT:1274414NEWT:27606NEWT:59202NEWT:9975NEWT:3197NEWT:9615NEWT:10299NEWT:860688NEWT:884019NEWT:169963NEWT:36329NEWT:1147787NCBITaxon:3044782NEWT:72407NEWT:9606NEWT:367830NEWT:157295NEWT:641501NEWT:178616NEWT:410289NEWT:373153NEWT:915099NEWT:74940NEWT:9721NEWT:1450511NEWT:360094NEWT:470NEWT:1313NEWT:84023NEWT:9838NCBITaxon:9615NCBITaxon:5811NEWT:58334NEWT:1193501NEWT:3055NEWT:6326NEWT:6689NEWT:2762NEWT:5476NEWT:1174673NEWT:562NEWT:33952NEWT:2094720NEWT:1274432NEWT:1274426NEWT:1423NEWT:4932NEWT:70448NEWT:9825NEWT:1274423NEWT:3603NEWT:698936NEWT:2759NEWT:3847NEWT:39946NEWT:9823NEWT:178876NEWT:9940NEWT:327160NEWT:573NEWT:9031NEWT:1274420NEWT:7091NEWT:578458