{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/20250916_MaxQuant.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/LUMOS_LVA_20231101_PP_MS2.xlsx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/20251022_MaxQuant.xlsx"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20250912_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/LVA_OrbitrapLUMOS_20231101_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20251020_01.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/LVA_OrbitrapLUMOS_20231101_03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20251020_03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20251020_07.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20250912_11.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20251020_11.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20250911_03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20251020_05.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20251020_15.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20251020_13.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20250911_11.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20250911_09.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/LVA_OrbitrapLUMOS_20231101_07.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20250911_07.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20250912_07.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20251020_09.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/LVA_OrbitrapLUMOS_20231101_05.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/09/PXD071805/KP_ObitrapLUMOS_20250912_09.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["lvalbrec@uci.edu"],"submitter":["Clinton Yu"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD071805"],"sample_protocol":["Experiment 1HEK293T cells stably expressing 3xHA-tagged TMEM192-RFP were used to immunoprecipitated lysosomes, as previously described (cells were a generous gift from Dr. Roberto Zoncu). Cells were grown to 90% confluency in 10 cm dishes and pre-treated with 5 µM IWP-2 (MilliporeSigma, I0536) for 4 hours before treatment with Wnt3a ligands (PeproTech, 315-20) diluted 1:1000 in L cell (catalog no. CRL-2648) media for 20 min with one 10 cm dish per condition. Lysosome-inhibited samples were pre-treated with 400 nM Bafilomycin (Cayman Chemical, 11038) for 4 hours, which continued through treatments. Following treatments, cells were washed and scraped with PBS, clarified by centrifugation, and resuspended in KPBS buffer [136 mM KCl, 10 mM KH2PO4, 0.5 mM tris(2-carboxyethyl)phosphine (TCEP), and Opti-Prep protease inhibitor cocktail, (pH 7.25)] and lysed with 23G syringes followed by another round of centrifugation to remove nuclei. The post-nuclear supernatant (PNS) was incubated with PBS-equilibrated anti-HA beads (Thermo Fisher Scientific, 88836) and rotated at 4°C for 2 hours. The anti-HA beads were placed on magnetic racks and were washed in KBPS buffer five times for 5 min rotating at 4°C. Next, 0.1% NP-40 in PBS was added to the samples, which were then incubated at 30 °C for 30 minutes. The supernatant was collected after magnetic separation, and the elution was repeated two more times for a total of three rounds. Samples were reduced in 5 mM dithiothreitol (DTT) at room temperature for 30 min, alkylated in 20 mM iodoacetamide at room temperature for 30 min and centrifuged. Cell pellets were washed twice with 4 volumes of ice-cold methanol and centrifuged. After air-drying, the pellets were digested with 1% LysC in 8 M urea prepared in 50 mM ammonium bicarbonate for 4 hours at 37 °C. Peptides were further digested in 0.5 µg trypsin overnight at 37 °C. The following day, samples were acidified with 0.1% TFA and desalted using SepPak C18 cartridges (Waters, WAT054955). Columns were washed with 0.1% TFA followed by 0.5% acetic acid, and peptides were eluted with 50% acetonitrile. Eluates were dried by SpeedVac and subjected to mass spectrometry analysis.For LC-MS acquisition, HPLC separation was performed on an UltiMate 3000 UHPLC (Thermo Fisher Scientific) using an EasySpray 50cm x 75μm I.D. Acclaim® PepMap RSLC column heated at 45° C and coupled in-line to an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific). Peptides were separated using a 4-22% Buffer B gradient (Buffer A: 0.1% formic acid; Buffer B: 100% acetonitrile containing 0.1% formic acid) run over 57 minutes (1.5-hour method). Each full cycle of MS analysis consisted of an MS1 survey scan (375–1800 m/z, resolution of 120,000 at m/z 200, AGC target 4.0x 105, maximum injection time 50 ms) followed by data-dependent MS/MS acquired in the linear ion trap with HDC NCE30 on ions with +2-6 charge at top speed for 3 sec. Target ions already selected for MS/MS were dynamically excluded for 30 sec. MS2 scans were acquired using ‘Rapid’ mode with AGC target 2.0x 104 and maximum injection time of 35 ms. Experiments 2 & 3For proteomic analysis of PRMT3 MrTACs, HEK293 cells were seeded in 6-well plates with 8x105 cells per well and were transfected with 1 µg Halo-GSK3β as described above. The following day, cells were treated for 24 hours with either MrTAC-5 (0.1 µM) or DMSO control. Cell pellets were then snap frozen in liquid nitrogen and stored at -80°C before downstream processing. For proteomic analysis of PRMT5 MrTACs, HEK293 cells were seeded in 6-well plates with 8x105 cells per well and were treated for 24 hours with either MrTAC-8 (1 µM) or a combination of either warhead (Cmp 2 and JQ1, both 1 µM). Cell pellets were then snap frozen in liquid nitrogen and stored at -80°C before downstream processing.Cell pellets were suspended in RIPA buffer (Cell Signaling Technology) containing protease inhibitor cocktail (cOmplete™ Protease Inhibitor Cocktail, Roche). The suspension was sonicated at 4 °C for 10 min, followed by centrifugation at 16,000 g for 10 min at 4 °C. The supernatant was collected and digested by the filter-aided sample preparation (FASP) method. Briefly, the supernatant was transferred into a spin filter column (10 kDa cutoff). Proteins were reduced with 10 mM DTT for 1 hr at 56 °C, and alkylated with 20 mM iodoacetic acid for 30 min at room temperature in the dark. Next, the buffer was exchanged with 50 mM NH4HCO3 by washing the membrane three times. Free trypsin was added into the protein solution at a Trypsin to protein ratio of 1:50 and incubated overnight at 37 °C. The tryptic digests were recovered in the supernatant after centrifugation, and an additional wash with water. The combined supernatants were vacuum-dried and then adjusted to 200 μL with 0.5% acetic acid. The peptide mixture was then subjected to C18 solid-phase extraction (The Nest Group, Inc.) for desalting.Proteomics data were acquired via LC-MS/MS using an UltiMate 3000 UHPLC (Thermo Fisher Scientific), coupled in-line with an Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific) with an ESI nanospray source. Mobile phase A was composed of 0.1% formic acid (FA) in water, and Mobile phase B was composed of 0.1% formic acid (FA) in ACN. The total flow rate was 300 nL min-1, and peptides were separated over a 57 min gradient from 4% to 25% buffer B (total run time 90 min per sample) on an Acclaim PepMap RSLC column (50cm x 75 μm). Survey (MS) scans were acquired in Orbitrap (FT) with automated gain control (AGC) target 8E5, maximum injection time 50 msec, and dynamic exclusion of 30 sec across the scan range of 375-1800 m/z. MS/MS spectra were acquired in data-dependent acquisition mode at top speed for 3 sec per cycle; the AGC target was set to 1E4 with maximum injection time of 35 msec. Ions were subjected to stepped-energy higher-energy collision dissociation (seHCD) fragmentation at a normalized collision energy (NCE) of 20±5 %."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["Protein identification was carried out using Protein Prospector (6.3.4) 1002 against a randomly concatenated human proteome database obtained from SwissProt (20,424 entries; 1003 version from April 11, 2023). Parent mass tolerance was set at 15 ppm and results were exported at 1% 1004 FDR. Trypsin was selected for the protease with up to 2 missed cleavages; no nonspecific cleavage was 1005 allowed. Cysteine carbamidomethylation was set as a fixed modification, while methionine oxidation, 1006 arginine methylation, and N-terminal acetylation, methionine loss and pyroglutamate conversion were set 1007 as variable modifications, maximum of 2 per peptide.  The raw LC-MS/MS data files were analyzed using MaxQuant (version 2.6.3.0), with the spectra searched 1039 against the Uniprot mouse database (updated on May 21st, 2018). For identification of the peptides, the 1040 mass tolerances were 20 ppm for initial precursor ions, and 0.5 Da for fragment ions. Two missed cleavages 1041 in tryptic digests were allowed. Cysteine residues were set as static modifications. Oxidation of methionine 1042 was set as the variable modification. Filtering for the peptide identification was set at a 1% false discovery rate (FDR). GSK3B substrates were annotated based on Taelman et al. 201072 1043 . P-values calculated by 1044 Two-sided Unpaired T-test."],"omics_type":["Proteomics"],"labhead":["Lauren Veronica"],"instrument_platform":[""],"labhead_affiliation":["Developmental and Cell Biology University of California, Irvine Irvine, California, USA"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["42677305 Seabrook LJ, Karaj E, Sindi S, Brodie G, Livelo CR, Franco CN, Campos M, Leonard JT, Gao F, Skowronska-Krawczyk D, Griffin ME, Conway SJ, Choudhary A, Albrecht LV. Exploration of protein degradability enables fully endogenous MrTAC degraders. Chem. 2026 12(7):102998 10.1016/j.chempr.2026.102998"],"submitter_mail":["clinton.yu@uci.edu"],"submitter_affiliation":["University of California, Irvine"],"submitter_country":["United States"],"pubmed_abstract":["Small molecules can induce protein degradation by hijacking natural degrons, but most degraders rely on the same proteasome-targeting degron. Motivated by the need for chemically exploitable degrons, this study leverages the lysosome-targeting methylarginine degron for the development of methylarginine-targeting chimeras (MrTACs). First, lysosomal-capture proteomics identify substrates naturally modified by methylarginine degrons. Next, a tag-based protein library is used for understanding the characteristics that affect degradation by MrTACs, which induces methylarginine degrons by recruiting protein arginine methyltransferases (PRMTs). MrTACs degrade proteins regardless of their native proteolytic route, including targets that have eluded classic degrader modalities, across multiple PRMTs. We leverage this for endogenous MrTACs that recruit PRMTs with repurposed inhibitors, which can be transformed into silent recruiters via group-transfer chemistry. MrTACs drive <95% target degradation across disease-linked proteins at nanomolar doses. Overall, this study integrates native and chemically induced degradation to establish a platform for fully endogenous, therapeutically viable degraders."],"pubmed_title":["Exploration of protein degradability enables fully endogenous MrTAC degraders."],"pubmed_authors":["Seabrook Laurence J LJ, Karaj Endri E, Sindi Shaimaa S, Brodie Glen G, Livelo Catherine R CR, Franco Carolina N CN, Campos Melissa M, Leonard Jack T JT, Gao Fangyuan F, Skowronska-Krawczyk Dorota D, Griffin Matthew E ME, Conway Stuart J SJ, Choudhary Amit A, Albrecht Lauren V LV"],"additional_accession":[]},"is_claimable":false,"name":"Exploration of protein degradability enables fully endogenous MrTAC degraders","description":"Methylarginine degrons mark proteins for degradation in lysosomes. We leveraged the machinery responsible for methylarginine degron addition to create a chemically inducible degrader named a Methyl Arginine Targeting Chimera (MrTAC). First, we evaluated the contents of isolated lysosomes following activation of the native methylarginine degron pathway. Next, we evaluated global proteome abundance in human cell culture during treatment with different MrTACs relative to control treatments.","dates":{"publication":"2026-09-14","submission":"2025-12-10"},"accession":"PXD071805","cross_references":{"TAXONOMY":["NEWT:68239","NEWT:108018","NEWT:377960","NEWT:1131","NEWT:190486","NEWT:2737160","NEWT:2042546","NEWT:148942","NEWT:295546","NEWT:258594","NEWT:1126","NEWT:1129","NEWT:89187","NEWT:309807","NEWT:89184","NEWT:309800","NEWT:57577","NEWT:156563","NEWT:1323429","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:44270","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:77173","NEWT:93217","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:10034","NEWT:661410","NEWT:488003","NEWT:224326","NEWT:376619","NEWT:3765","NEWT:2433","NEWT:3767","NEWT:433727","NEWT:135622","NEWT:672127","NEWT:656061","NEWT:37965","NEWT:656064","NEWT:3760","NEWT:36630","NEWT:381198","NEWT:1176302","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:44250","NEWT:77151","NEWT:317447","NEWT:5537","NEWT:698761","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:1177","NEWT:11308","NEWT:12637","NEWT:2164133","NEWT:1180","NEWT:2767846","NEWT:1343074","NEWT:314344","NEWT:108061","NEWT:224308","NEWT:3134131","NEWT:49928","NEWT:160621","NEWT:110368","NEWT:1916073","NEWT:1310161","NEWT:1230383","NEWT:77133","NCBITaxon:5207","NEWT:160620","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:1410384","NEWT:1310173","NEWT:37919","NEWT:1072569","NEWT:1072568","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:135666","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:65121","NEWT:3716","NEWT:3715","NEWT:2065263","NEWT:1549675","NEWT:177437","NEWT:9014","NEWT:10891","NEWT:118221","NEWT:34869","NEWT:226126","NEWT:1616117","NEWT:34865","NEWT:28174","NEWT:550537","NEWT:284812","NEWT:284811","NEWT:980415","NEWT:2902907","NEWT:3701","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:1246791","NEWT:34875","NEWT:1431297","NEWT:9005","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:1883426","NEWT:657321","NEWT:1423687","NEWT:657322","NEWT:34878","NEWT:10886","NEWT:3708","NEWT:536231","NEWT:219813","NEWT:1301262","NEWT:319224","NEWT:2305479","NEWT:215451","NEWT:460519","NEWT:272843","NEWT:272844","NEWT:1348799","NEWT:55784","NEWT:485","NEWT:2709072","NEWT:2499525","NEWT:467144","NEWT:142786","NEWT:28196","NEWT:2853422","NEWT:487","NEWT:1679718","NEWT:387344","NEWT:657318","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:272831","NEWT:987059","NEWT:491","NEWT:422203","NEWT:460523","NEWT:2423","NEWT:133894","NEWT:85694","NEWT:85692","NEWT:911045","NEWT:3750","NEWT:123606","NEWT:85698","NEWT:291146","NEWT:29466","NEWT:233271","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:278161","NEWT:415978","NEWT:410289","NEWT:191701","NEWT:9054","NEWT:472","NEWT:29459","NEWT:34839","NEWT:476","NEWT:1380096","NEWT:28128","NEWT:470","NEWT:41122","NEWT:1328300","NEWT:748693","NCBITaxon:50557","NEWT:63363","NEWT:3735","NEWT:29491","NEWT:911022","NEWT:446","NEWT:153481","NEWT:714485","NEWT:445","NEWT:2003758","NEWT:29486","NEWT:63366","NEWT:64697","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:3726","NEWT:30455","NEWT:28141","NEWT:9030","NEWT:9031","NEWT:3728","NEWT:108931","NEWT:219799","NEWT:1325292","NEWT:219798","NEWT:548","NEWT:150475","NEWT:546","NEWT:1431340","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:40686","NEWT:1225786","NEWT:771870","NEWT:8665","NEWT:51338","NEWT:377142","NEWT:9995","NEWT:28112","NEWT:49012","NEWT:28110","NEWT:10832","NEWT:311339","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:536","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:51315","NEWT:52641","NEWT:353152","NEWT:116597","NEWT:353153","NEWT:116598","NEWT:227377","NEWT:1774284","NEWT:27689","NEWT:207769","NEWT:40674","NEWT:51329","NCBITaxon:1763","NEWT:443906","NEWT:6055","NEWT:13037","NEWT:519","NEWT:941638","NEWT:511","NEWT:7394","NEWT:6063","NEWT:404330","NEWT:1328388","NEWT:13064","NEWT:529120","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:6039","NEWT:37003","NEWT:510516","NE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