{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/msmsScans.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/proteinGroups.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/evidence.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/summary.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/peptides.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/parameters.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/Phospho_STYSites.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/mzRange.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/allPeptides.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/msms.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/Oxidation_MSites.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/modificationSpecificPeptides.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_12.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_05.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_10.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_09.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_07.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_02.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_04.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_06.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_11.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD051483/CD_220112_Expl_08.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["yimon.aye@epfl.ch"],"submitter":["Dalu Chang"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"software":[""],"submitter_keywords":["Proteomic. localis-rex"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD051483"],"tissue":["Cell Culture"],"sample_protocol":["Samples 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."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Raw 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 candidates"],"omics_type":["Proteomics"],"labhead":["Yimon Aye"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["EPFL"],"species":["Mus Musculus (mouse)"],"publication":["10.1038/S41589-025-02135-4"],"submitter_mail":["dalu.chang@epfl.ch"],"submitter_affiliation":["EPFL"],"submitter_country":["Switzerland"],"additional_accession":[]},"is_claimable":false,"name":"Aye Lab Localis-REX hits (202201)","description":"target ID for localis-REX, in mouse cells, under different subcelluar locations, with spatial and temporal control","dates":{"publication":"2026-06-04","submission":"2024-04-16"},"accession":"PXD051483","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:3555","NEWT:241368","NEWT:2","NEWT:157546","NEWT:190802","NEWT:35554","NEWT:9778","NEWT:150475","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:5180","NEWT:256737","NEWT:2042546","NEWT:115104","NEWT:1081927","NEWT:67825","NEWT:185579","NEWT:43179","NEWT:13076","NEWT:1249668","NEWT:317","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:415540","NEWT:4081","NEWT:876138","NEWT:554","NEWT:98334","NEWT:426428","NEWT:237561","NEWT:6928","NEWT:10036","NEWT:7574","NEWT:1351","NEWT:7215","NEWT:29204","NEWT:272563","NEWT:507601","NCBITaxon:79857","NCBITaxon:6157","NEWT:95648","NEWT:3885","NEWT:746360","NEWT:6239","NEWT:3888","NEWT:1589","NEWT:470150","NEWT:135622","NEWT:216257","NEWT:6915","NEWT:9986","NEWT:101510","NEWT:4054","NEWT:3880","NEWT:3641","NEWT:383379","NEWT:8782","NEWT:1263854","NEWT:1000589","NEWT:1902","NEWT:85962","NEWT:160488","NEWT:28104","NEWT:317447","NEWT:7955","NCBITaxon:2","NEWT:985076","NEWT:7959","NEWT:2261","NEWT:4565","NEWT:1264690","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:216595","NEWT:243230","NEWT:8355","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:7029","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:334747","NEWT:61235","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:436486","NEWT:6287","NEWT:2242","NEWT:300641","NEWT:4784","NEWT:727","NEWT:9796","NEWT:725","NEWT:360106","NEWT:260707","NEWT:287","NEWT:10117","NEWT:10239","NCBITaxon:6191","NEWT:10116","NEWT:1280","NEWT:1836","NEWT:1735272","NEWT:83334","NEWT:185431","NEWT:83332","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:44685","NEWT:2697049","NEWT:1148","NEWT:11676","NEWT:55571","NEWT:100226","NCBITaxon:6073","NEWT:4530","NEWT:4896","NEWT:6279","NEWT:1123869","NEWT:7370","NEWT:75058","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:1094343","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:296543","NEWT:1773","NEWT:38783","NEWT:8727","NEWT:1895","NEWT:4006","NEWT:1182590","NEWT:8726","NEWT:6669","NEWT:10090","NEWT:935293","NEWT:64152","NEWT:749200","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:990346","NEWT:5334","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:230741","NEWT:284812","NCBITaxon:10359","NCBITaxon:1313","NEWT:43330","NEWT:242619","NEWT:44544","NEWT:632957","NEWT:373995","NEWT:5689","NEWT:645463","NEWT:544404","NEWT:3702","NEWT:129249","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:990119","NEWT:2758385","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:421932","NEWT:196627","NEWT:408172","NEWT:5691","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:627025","NEWT:400772","NEWT:1097677","NEWT:3708","NEWT:128161","NEWT:106592","NEWT:61674","NEWT:1117957","NEWT:9913","NEWT:1432138","NEWT:10312","NEWT:1424507","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:8030","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:180066","NEWT:67767","NEWT:46835","NEWT:135588","NEWT:1843183","NEWT:95486","NEWT:58002","NEWT:9103","NEWT:4577","NEWT:1416333","NEWT:5664","NEWT:2157","NEWT:146479","NEWT:10306","NCBITaxon:2759","NEWT:1911079","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:1480154","NEWT:1274414","NEWT:27606","NEWT:59202","NEWT:9975","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:884019","NEWT:169963","NEWT:36329","NEWT:1147787","NCBITaxon:3044782","NEWT:72407","NEWT:9606","NEWT:367830","NEWT:157295","NEWT:641501","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:915099","NEWT:74940","NEWT:9721","NEWT:1450511","NEWT:360094","NEWT:470","NEWT:1313","NEWT:84023","NEWT:9838","NCBITaxon:9615","NCBITaxon:5811","NEWT:58334","NEWT:1193501","NEWT:3055","NEWT:6326","NEWT:6689","NEWT:2762","NEWT:5476","NEWT:1174673","NEWT:562","NEWT:33952","NEWT:2094720","NEWT:1274432","NEWT:1274426","NEWT:1423","NEWT:4932","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:3603","NEWT:698936","NEWT:2759","NEWT:3847","NEWT:39946","NEWT:9823","NEWT:178876","NEWT:9940","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1274420","NEWT:7091","NEWT:578458"],"pubmed":[]}}