{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/File_Description_DPP9_Proxmity-Labeling_PRIDE.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq79766_QE2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq79765_QE2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq90397_88min_480Ex1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq90401_88min_480Ex1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq79421_QE2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq78915_QE2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq79422_QE2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq90398_88min_480Ex1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq90399_88min_480Ex1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/Seq78914_QE2.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/DPP9-ER-stress-Pride.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/2024-10-21-decoys-contam-reviewed-UP000005640_MiniTubro-dsRed.fas","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD067345/DPP9_Basal_Pride.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["okleifeld@technion.ac.il"],"submitter":["Oded Kleifeld"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Dpp9","Turboid","Proximity labeling"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD067345"],"sample_protocol":["HEK293 DPP9KO  and HA-mTB-DPP9-S (wt or S740A) sells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% tetracycline-free FBS, 2 mM L-glutamine, 100 U/mL penicillin, and 100  µg/mL streptomycin. Dox (10 ng/mL) was added for the indicated time periods to induce expression of HA-mTB-DPP9. Biotin (50 µM) was added to initiate proximity labeling for the indicated durations. Cells were harvested with cold PBS, centrifuged at 250 × g for 5 minutes at 4°C. Cell pellets were snap-frozen in liquid nitrogen and stored at -80°C. For each biological replicate, two 15 cm dishes were used.  Cell pellets were lysed in 5 mL of lysis buffer containing 50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.1% SDS, supplemented with protease inhibitor cocktail (1:1000; Sigma) and 250 U benzonase. Lysis was performed for 1 h at 4°C with constant rotation, followed by centrifugation at 16,000 × g for 30 minutes at 4°C. Supernatant were incubated with pre-washed streptavidin magnetic beads for 3 h at 4°C with rotation. Beads were washed three times with RIPA buffer (without protease inhibitors), and twice with 50 mM ammonium bicarbonate. Beads were transferred to fresh low-bind tubes and suspended in 200 µL of 50 mM ammonium bicarbonate (pH 8.0) containing 1 µg of sequencing-grade modified trypsin (Promega Cat# V5111). Digestion was carried out overnight at 37°C followed by the addition of an additional 0.5 µg trypsin for a 2 h incubation at 37°C. Peptides were recovered by transferring the supernatant to fresh tubes and washing the beads twice with 150 µL of 50 mM ammonium bicarbonate (ABC). All eluates, including the washes, were pooled. Samples were dried using a vacuum concentrator and resuspended in 20 µL of 0.1% formic acid (FA) in 2% acetonitrile (ACN). Peptides were desalted using C18 spin columns (PolyLC INC. Cat# TT200C1896) according to the manufacturer’s instructions. Eluted peptides were dried by SpeedVac and resuspended in 20 µL of 2% ACN with 1% FA.  Tryptic peptides were analyzed by LC-MS/MS using either a Q Exactive Plus mass spectrometer (Thermo Fisher Scientific) coupled to an Ultimate 3000 LC system (Thermo Fisher Scientific) via a nanospray ion source, or an Orbitrap Exploris 480 mass spectrometer (Thermo Fisher Scientific) coupled to an EvoSep One HPLC system (EvoSep Biosystems). Q-Exactive Plus–Ultimate 3000 Analysis: Desalted peptides were separated by reverse-phase chromatography on a homemade analytical column (30 cm length, 75 μm inner diameter) packed with ReproSil-Pur C18-AQ resin (1.9 μm, Dr. Maisch GmbH, Germany). Chromatographic separation was performed using a 60-minute linear gradient from 5% to 28% ACN in 0.1% FA, followed by a 15-minute increase to 95 % ACN, and a 10-minute wash at 95% ACN, at a flow rate of 0.15 μL/min. MS data were acquired in positive ion mode using data-dependent acquisition. Full MS scans were acquired over an m/z range of 300–1800 at a resolution of 120,000, with an AGC target of 3×10⁶ and a maximum injection time of 20 ms. The top 20 most intense precursor ions (charge states 2 – 7) were selected for higher-energy collisional dissociation (HCD) with a normalized collision energy (NCE) of 27. MS/MS scans were acquired at a resolution of 15,000, with an AGC target of 1×10⁵ and a maximum injection time of 30 ms. Dynamic exclusion was set to 20 seconds. Orbitrap Exploris 480–EvoSep One Analysis: Peptides were loaded onto EvoTips, washed twice with 20 μL of 0.1% formic acid, and kept moist with 150 μL of 0.1% FA until injection. Peptide separation was carried out on a 15 cm × 150 μm column packed with 1.9 μm C18 resin (EvoSep EV1106), using the manufacturer’s standard 88-minute method. Full MS scans were acquired from m/z 300 to 1500 at a resolution of 120,000, with an AGC target of 3×10⁶ and a maximum injection time of 25 ms. The top 20 most intense precursor ions were selected for HCD fragmentation and analyzed at a resolution of 17,500. Dynamic exclusion was set to 30 seconds."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["MS data analysis was conducted using FragPipe v.22.0 (https://fragpipe.nesvilab.org/) in DDA+ mode (Yu et al, 2025) using the LFQ-MBR workflow with default parameters, except where noted. MSFragger v.4.2 was used for database searching against the Homo sapiens UniProt reference proteome (January 2024 release; 20,425 entries), supplemented with common contaminant sequences. The search enzyme was set to trypsin, allowing up to two missed cleavages. Carbamidomethylation of cysteine was set as a fixed modification, while methionine oxidation and protein N-terminal acetylation were included as variable modifications. Peptide-spectrum matches (PSMs) were rescored using MSBooster and validated with Percolator, applying a false discovery rate (FDR) threshold of 1% at both the peptide and protein levels. Label-free quantification (LFQ) was performed using IonQuant. The match-between-runs option was disabled for the analysis under basal conditions, but enabled for the ER stress condition, with the \"top runs\" parameter set to 2. Protein intensities were computed using the MaxLFQ algorithm. Label-free quantification data were imported into Perseus v2.1.30 (Tyanova & Cox, 2018)  where log₂ transformation and all statistical analyses were performed. Proteins were retained only if they had valid label-free quantification (LFQ) intensity values in all replicates of at least one experimental group. Missing values were imputed from a normal distribution (width = 0.3, downshift = 1.8). Differential abundance between groups was assessed using 1-sided-sample Student’s t-test."],"omics_type":["Proteomics"],"labhead":["Oded Kleifeld"],"instrument_platform":[""],"labhead_affiliation":["Faculty of Biology Technion- Israel Institute of Technology Technion City, Haifa, Israel"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["41636814 Wirtgen VE, Saied L, Zolg S, Alonso MC, Mayer B, Donzelli L, Maurer U, Timmers HTM, Knobeloch KP, Kleifeld O, Geiss-Friedlander R. Proximity labeling reveals non-catalytic interactions between DPP9 and ubiquitin signaling complexes. Cell Mol Life Sci. 2026 83(1):93 10.1007/s00018-025-06021-z"],"submitter_mail":["okleifeld@technion.ac.il"],"submitter_affiliation":["Technion"],"submitter_country":["Israel"],"pubmed_abstract":["Dipeptidyl peptidase 9 (DPP9) is an amino-peptidase with roles in immunity, DNA-repair, cell signaling, memory and neonatal survival; its dysregulation is linked to cancer and immune-related disorders. While many studies focus on its catalytic activity, scaffolding functions of DPP9 are emerging. Here, we mapped the DPP9 interactome using TurboID-based proximity labeling in DPP9 knock-out HEK293 cells reconstituted with doxycycline-inducible miniTurboID-DPP9, allowing fine-tuned expression that approximates physiological levels. Besides known partners, proteins involved in autophagy, mRNA decay and ubiquitin signaling along with DPP8, were strongly enriched among the identified DPP9 binding partners. Notably, we validated DPP8, the E3 ligase CBL, the deubiquitinase complex CYLD-SPATA2 and the BRISC complex components BRCC36/BRCC3 and ABRO1/ABRAXAS2 as novel DPP9 interactors. Furthermore, NanoBRET assays in living cells demonstrated that DPP9 disrupts the binding between BRCC36/BRCC3 and ABRO1/ABRAXAS2, and the interaction of CYLD with SPATA2, thereby compromising these protein-protein interactions. Mechanistically, these findings reveal physical and potentially regulatory interactions between DPP9 and components of the ubiquitin system and provide a basis for dissecting the non-catalytic functions of DPP9."],"pubmed_title":["Proximity labeling reveals non-catalytic interactions between DPP9 and ubiquitin signaling complexes."],"pubmed_authors":["Wirtgen Valentina Elena VE, Saied Layla L, Zolg Samuel S, Alonso Marta Campos MC, Mayer Bettina B, Donzelli Laura L, Maurer Ulrich U, Timmers H T Marc HTM, Knobeloch Klaus-Peter KP, Kleifeld Oded O, Geiss-Friedlander Ruth R"],"additional_accession":[]},"is_claimable":false,"name":"Mapping the DPP9 Interactome by Proximity Labeling","description":"Dipeptidyl peptidase 9 (DPP9) is an amino peptidase with the unusual ability to cleave a peptide bond post-proline. Its function affects immunity, DNA-repair, cell signaling, memory and neonatal survival; its dysregulation is linked to cancer and immune-related disorders. While most studies focus on its canonical catalytic function, scaffolding functions of DPP9 are just beginning to emerge. To define the interactome of DPP9, we used TurboID-based proximity labeling in DPP9 HEK293 knock-out cells reconstituted with doxycycline-inducible miniTurboID–DPP9.","dates":{"publication":"2026-08-31","submission":"2025-08-14"},"accession":"PXD067345","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:57577","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:111205","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:1596","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:1584","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:29064","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:273791","NEWT:3347","NEWT:49928","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:55350","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:33554","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:171719","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NCBITaxon:37162","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10891","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:66440","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:34878","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2499525","NEWT:2853422","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:1509","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1579","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:1640278","NEWT:472","NEWT:940825","NEWT:29459","NEWT:529507","NEWT:1071661","NEWT:28128","NEWT:470","NEWT:5911","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:11723","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:1290454","NEWT:906914","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:548","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:2126348","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:207340","NEWT:172271","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:33941","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:42410","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:771870","NEWT:51338","NEWT:9995","NEWT:575412","NEWT:28112","NEWT:49012","NEWT:6493","NEWT:10832","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:595495","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:1613","NEWT:986","NEWT:52641","NEWT:28532",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