Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/raw_data_explained.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/20240710_145530_240710_FS_WithoutRNA_Paper_Report.csvftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_str_AMP_2_055.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_str_Beads_2_034.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_unst_AMP_3_028.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_unst_AMP_1_021.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_str_Beads_1_031.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_str_K57A_3_048.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_unst_Beads_1_002.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_unst_K57A_2_015.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_unst_Beads_2_005.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_str_K57A_2_044.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_unst_K57A_1_011.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_str_AMP_1_052.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_unst_Beads_3_008.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_unst_K57A_3_018.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_str_Beads_3_038.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_str_AMP_3_058.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_unst_AMP_2_024.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Q2305_FS_230428_NoRNA_str_K57A_1_041.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/uniprot_sprot_2022-01-07_HUMAN.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/Frankenfield2022_Universal_Contaminants.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/250820_Rlig1AffinityEnrichment_1.6.15_Paper.spsftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD067856/20240710_145530_240710_FS_WithoutRNA_Paper.sneprimaryOK200florian.stengel@uni-konstanz.deFlorian StumpfAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryData-independent acquisitionEnrichmentHumanOxidative stressHek293RibosomeAp-msDis3AmpylationClp1Rna ligaseRlig1Q-exactive hfExosomeAngel2Rna repairIn-solution digestDiahttps://www.ebi.ac.uk/pride/archive/projects/PXD067856Cell CultureCell pellet production For the cell pellets, 8 x 10^6 cells were seeded in 20 mL medium in 15 cm cell culture plates. After 48 h at approximately 90 % confluency, the cells were harvested. For stressed cells, the medium was removed and 10 mL new medium containing 40 µM menadione in EtOH (0.1 %) was added and incubated (1 h, 37°C). Afterwards the medium was removed and 5 mL ice-cold DPBS was added to the cells. For unstressed cells the incubation with menadione was omitted and 5 mL ice-cold DPBS was directly added after removing the medium. The cells were harvested with a cell scraper and centrifuged (10 min, 500 g, 4°C). The resulting pellets were resuspended in 400 µL ice-cold DPBS and the cells of four plates were combined and centrifuged (10 min, 500 g, 4°C). After removing the DPBS the cell pellet was stored frozen ( 80°C). Lysate preparation for affinity enrichment Directly before the experiment the frozen cell pellet was lysed by resuspending it in 750 µL ice-cold lysis buffer (25 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 % (v/v) NP40, 1 mM DTT, 0.1 M Pefabloc® SC, 1 µg/mL aproptinin/leupeptin) and incubation on ice for 20 min. After the incubation, the lysate was cleared by centrifugation in an Eppendorf 5430R centrifuge (22’000 g, 30 min, 4°C). The protein concentration of the supernatant was determined by BCA as described above and adjusted to 6.67 mg/mL with lysis buffer. Subsequently, RNase If (6000 U/mL in lysis buffer) was added to the cell lysate (end concentration 600 U/mL with 6 mg/mL protein concentration) and incubated in a thermomixer (15 min, 37°C, 850 rpm) to result in the RNA digested cell lysate. Affinity enrichment using Rlig1 as bait For the affinity enrichment of Rlig1, Strep-Tactin® Superflow® bead slurry (50 µL, IBA Lifesciences) was prepared in 500 µL low-binding reaction tubes. The beads were equilibrated (3 x 400 µL) with washing buffer (25 mM Tris pH 7.5, 50 mM NaCl, 1 mM DTT) and kept on ice. His6-Strep-AMP-Rlig1 or His6-Strep-K57A-Rlig1 (100 µL, 0.5 mg/mL in washing buffer) was added to the equilibrated beads (50 µL). Washing buffer (100 µL) was used as negative control. The bead suspension was incubated in an overhead shaker (60 min, 4°C). Washing buffer (400 µL) was added to the beads and the sample was transferred to Mobicol spin columns (MoBiTec). The reaction tube that contained the beads was rinsed one time with washing buffer (100 µL) and the bead containing solutions were combined. The beads were washed (4 x 500 µL, washing buffer) and the RNA digested cell lysate (250 µL, 6 mg/mL) was added to the prepared beads and incubated on an overhead shaker (20 h, 4°C). The beads were washed (5 x 500 µL, washing buffer) and the protein was eluted with elution buffer (50 mM NH4HCO3, 0.8 mM biotin) (4 x 100 µL, 10 min, 37°C, 800 rpm). The eluate was dried in a SpeedVac (2 h, vacuum, no heating) and stored at -20°C. The samples were subsequently in-solution digested and the resulting peptides were desalted and dried in preparation for the mass spectrometry Analysis. Affinity enrichment mass spectrometry For MS measurement the samples were redissolved (0.1 % FA, 15 µL). The desalted peptide samples were analyzed on an EASY-nLC 1200 UHPLC system (Thermo Scientific) coupled to a Q-Exactive HF mass spectrometer (Thermo Scientific) and separated on a C18 Acclaim PepMap RSLC column (50 µm x 15 cm, 2 µm, 100 Å, Thermo Scientific) with a flow rate of 300 nL/min over a 120 min gradient. After starting for 4 min with 94 % buffer A (0.1 % FA) and 6 % buffer B (80 % ACN + 0.1 % FA) the concentration of buffer B was increased to 44 % over 105 min, then set to 56 % over 5 min and finally increased to 100 % buffer B over 1 min, followed by washing and re-equilibration of the column for 5 min. The samples were measured in data independent acquisition (DIA) mode using a total of 22 isolation windows of variable window size. The isolation width and window positions were adapted from Bruderer et al.(27) MS1 scans were acquired between 300 and 1650 m/z with a resolution of 120’000 at 200 m/z. A maximum injection time of 60 ms and an AGC target of 3e6 was used. After one MS1 scan the mass spectrometer cycled once through all DIA windows. Isolated ions were fragmented via higher-energy collisional dissociation (HCD) with stepped normalized collision energies of 25.5, 27 and 30 eV and fragment ion spectra were acquired with automatic injection time at a resolution of 30’000 at 200 m/z and an AGC target of 3e6. Spectra were recorded with a fixed first mass of 200 m/z.PrideNot availableData analysis of affinity enrichment The raw data from the MS measurements were first analysed with Spectronaut V16. Here, identification and label-free quantification of proteins was performed in library-free directDIA mode. The default settings were used with a minimum peptide length of 5 AAs. “Uniprot_sprot_2022_01_07_HUMAN.fasta” (downloaded 07/01/2022) and “Frankenfield2022_Universal_Contaminants.fasta” were used as databases. The results were exported from Spectronaut and all further analyses of the raw LFQ data was performed with Perseus V1.6.15.0. Contaminants were filtered out using the contamination database and the LFQ intensities were log2(x) transformed. Only proteins that were consistently identified with a minimum of three precursor peptides in all three replicates of at least one condition were subjected to further evaluation. Missing values were imputed from a normal distribution (width = 0.3, shift = 1.8) and an ANOVA multiple sample test was conducted (S0 = 0.1, FDR = 0.01), followed by a Post hoc Tukey’s test (FDR = 0.01). Proteins enriched solely for the bead control according to the Post hoc test were filtered out before further processing. Intenstities were normalised by z-scoring and the mean average of the triplicate measurements for each bait/condition was calculated. Only proteins with a minimum Z-score of >0.5 for the AMP-Rlig1 bait and a Z-score <0 for the bead control after the ANOVA analysis were considered as enriched for AMP-Rlig1 and considered for further analysis.ProteomicsFlorian StengelDepartment of Biology, University of Konstanz, GermanyPARTIALHomo Sapiens (human)florian.stumpf@uni-konstanz.deNot availableUniversity of KonstanzGermanyfalseHuman RNA ligase 1 as a novel regulator of ribosome function and translation under oxidative stressHuman RNA ligase 1 (Rlig1) is a recently identified human 5’-3’ RNA ligase essential for maintaining 28S rRNA integrity and promoting cell survival under oxidative stress. Although the enzymatic activity of Rlig1 implies a role in RNA maintenance or repair, its broader molecular context remains insufficiently characterised. Here we identify cellular interactors of Rlig1 using affinity enrichment coupled to mass spectrometry in a HEK293 Rlig1-KO model. Our approach revealed several RNA and DNA surveillance, degradation and repair proteins as well as a diverse set of RNA binding and RNA processing enzymes as potential interactors. Notably, ribosomal proteins were highly enriched, suggesting a link between Rlig1 and the translational machinery.2026-05-252025-08-28PXD067856NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:10245NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:43186NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:5757NCBITaxon:4563NEWT:5755NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:1736231NEWT:5518NEWT:398007NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:145458NEWT:633149NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:2065263NEWT:1772NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:3702NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:2850NEWT:118691NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:9483NEWT:333760NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NCBITaxon:4932NEWT:109760NEWT:943274NEWT:644223NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:352472NEWT:1071661NEWT:1202532NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:1218097NCBITaxon:50557NEWT:39251NEWT:39491NCBITaxon:5811NEWT:29491NEWT:101841NEWT:2014887NEWT:33952NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NEWT:272634NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:9534NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:4084NEWT:63577NEWT:36185NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:114155NEWT:6494NEWT:6491NEWT:507601NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:162425NEWT:216257NEWT:102169NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:353152NEWT:8496NEWT:7165NEWT:27448NEWT:40674NEWT:1194669NEWT:243230NEWT:1080772NEWT:519NEWT:8479NEWT:8485NEWT:6063NEWT:49240NEWT:1328388NEWT:104395NEWT:9557NEWT:6289NEWT:6287NEWT:300641NEWT:727NEWT:9796NEWT:9554NEWT:118562NEWT:725NEWT:7137NEWT:469008NEWT:256318NEWT:9321NEWT:206411NCBITaxon:6191NEWT:596153NEWT:229533NEWT:1836NEWT:214053NEWT:80863NEWT:90675NEWT:105231NEWT:104385NEWT:74649NEWT:52638NEWT:57075NEWT:206672NEWT:4097NEWT:8697NEWT:8695NEWT:884204NEWT:9785NEWT:6279NEWT:1123869NEWT:9544NEWT:9545NEWT:7370NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:38783NEWT:4006NEWT:6426NCBITaxon:5476NEWT:6669NEWT:9935NEWT:89453NEWT:287889NEWT:1114301NEWT:51515NEWT:588596NEWT:51511NEWT:8845NEWT:92867NEWT:92866NEWT:419610NEWT:5334NEWT:51750NEWT:202950NEWT:382352NEWT:413071NCBITaxon:10239NCBITaxon:714NEWT:295027NCBITaxon:11320NEWT:632957NEWT:11051NEWT:9925NEWT:89462NCBITaxon:9606NEWT:452680NEWT:8839NEWT:90690NEWT:1436183NEWT:4232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