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Pinto-FernandezMass SpectrometryBottom-up proteomicsCervix CarcinomaNot availableHumanImmunologyUbiquitomicsUsp24Innate immunityIsg15https://www.ebi.ac.uk/pride/archive/projects/PXD055843Epithelial CellCell CultureTotal proteome analysis Cells were lysed using lysis buffer (50 mM Tris-HCl, pH 7.4, 0.5% NP-40, 150 mM NaCl, 20 mM MgCl2) containing protease and phosphatase inhibitors. Protein amounts were measured using the BCA assay. 90 µg of protein was taken for total proteome analysis. Samples were reduced using a final concentration of 10 mM DTT per sample. Alkylation of the disulfides was done using Iodoacetamide (IAA) at a final concentration of 20 mM. Following this, the sample was acidified using phosphoric acid (final pH of sample ≤ 1). To the samples was added 620 µL of binding/wash buffer (90% Methanol, 100 mM TEAB, pH 7.55). Samples were next loaded onto S-trap columns and centrifuged at 4000 g for 30 sec in order to allow the proteins to bind to the column. The columns were washed with 400 µL of the same buffer for 4 times. Finally, the filters were transferred to new 2 mL collection tubes, and 125 µL of Trypsin (1:10 wt:wt ratio) was added to the filter. Tubes were kept at room temperature without shaking for overnight digestion. Peptides were eluted from the S-trap columns using 50 mM TEAB in water, pH 8.5, 0.2% formic acid in water, and 50% acetonitrile in water, successively. Eluted proteins were dried using a vacuum evaporator. Dried samples were stored at -80 °C and resuspended prior MS analysis in mass spectrometry grade 98% water + 2% acetonitrile + 0.1% TFA to a total volume of 15 µL. ISG15 interactome Cells were lysed using lysis buffer (50 mM Tris-HCl, pH 7.4, 0.5% NP-40, 150 mM NaCl, 20 mM MgCl2) containing protease and phosphatase inhibitors. 3 mg of protein was subjected to immunoprecipitation using ISG15 antibody. Lysates were incubated for 1 hr with the antibody on a rotor at 4 °C. Finally, 35 µL of Protein G agarose beads was added to the samples for immunoprecipitation. Samples were kept on the rotor overnight at 4 °C for efficient pull-down. Beads were washed with the lysis buffer 3-4 times and eluted using 2x Gel Loading buffer with 25 mM DTT. Samples were reduced, alkylated, digested and cleaned as in the previous section using S-Trap columns. GG-peptidomics using di-Gly antibodies Cell pellets were dissolved in 1 mL of 6 M urea diluted with 5 mL MilliQ water followed by reduction with DTT and alkylation with IAA. Protein digestion was done overnight at room temperature with trypsin and 1% final concentration of TFA was added to quench the digestion. Sep-Pak C18 columns were used to purify the peptides. Purified peptides were dried using vacuum centrifugation. Peptides were later enriched using di-Gly antibody immunoprecipitation using the PTMScan Ubiquitin Remnant Motif (K- ε-GG) Kit, catalog# 5562, eluted and dried by vacuum centrifugation. Refining of the ISGylome Cells were lysed using lysis buffer (50 mM Tris-HCl, pH 7.4, 0.5% NP-40, 150 mM NaCl, 20 mM MgCl2, 3 mM TCEP) containing protease and phosphatase inhibitors. 1 µM of USP2 final concentration was added to the samples and incubated for 1 h at 37 °C on a shaker at 300 rpm. For negative control, samples not treated with USP2 were taken and incubated for 1 h at 37 0C on a shaker at 300 rpm. From the final sample, 90 µg protein was used for total proteome analysis and 3 mg protein was used for GG-peptidome analysis. Protocol for total proteome and GG-peptidome were same as discussed before. DIA-PASEF data acquisition and DIA-NN analysis Peptides for analysis by LC-MS/MS were loaded on Evotip Pure C18 tips following the manufacturer’s protocol. Briefly, tips were rinsed with 20 µL Solvent B by centrifugation, conditioned by soaking in 1-propanol, equilibrated with 20 µL Solvent A by centrifugation, loaded with 2 µL of sample and 18 µL of solvent A, then centrifuged, washed with 20 µL solvent A by centrifugation, and wetted with 100 µL solvent a and a brief centrifugation step for 10 s. All centrifugation steps were 60 s at 800 g unless stated otherwise. Peptides were analysed using an Evosep One liquid chromatography system coupled to a timsTOF SCP mass spectrometer (Bruker) using the Whisper 20 samples per day method and a 75 µm x 150 mm C18 column with 1.7 µm particles and an integrated Captive Spray Emitter. Data were acquired using diaPASEF methods generated by diAID. Total proteome and ISG15 pulldown samples were analysed using a method with 24 variable-width PASEF frames, with two ion mobility windows per PASEF frame, covering a region between 300 – 1,200 m/z and 0.6 – 1.6 V s cm-2. diGly samples were analysed using a method with 12 variable width PASEF frames, with two ion mobility windows per frame, covering a region between 330 – 1,100 m/z and 0.69 – 1.57 V s cm-2. For both methods, the accumulation and ramp times were 100 ms and the collision energy was ramped linearly over the ion mobility range: 20 – 59 eV over 0.6 – 1.6 V s cm-2. Raw mass spectrometry files were label-free quantified using DIA-NN (version 1.8) in library-free mode using the Uniprot proteome UP000005640 (2022) as a FASTA file.PrideBioinformatic analysis of DIA data Peptide intensity table with the Label-free quantitation (LFQ) values was analyzed in Perseus (v1.6.2.3).52 Data were log2 transformed and filtered for identification in all three replicates in at least one group. Different peptide groups were selected for different analyses like total proteome, ISG15 interactome, and GG-peptidome. Principal component analysis (PCA) was performed for each analysis with default settings. Intensities were Z-scored by subtracting the mean and used for hierarchical clustering by Euclidean distance (pre-processed with k-means, 300 clusters, 1000 iterations). Missing values were imputed from the lower end of the normal distribution (default settings). A two-sided student’s t-test with permutation-based FDR was used to calculate the significance between IFN-β treatment and control at 0.05 FDR (p-value). For a detailed protocol of data analysis in Perseus, refer to https://cox-labs.github.io/coxdocs/interactions.html. Gene Ontology and STRING network analysis Cytoscape (v3.9.1)53 with apps STRING (protein-protein interaction, confidence cutoff = 0.4; default) was used to create and visualize the interaction networks using the UniProt gene IDs from the ISG15 IP (ISGylome) data set (siUSP24, IFN-β treated – siC, IFN-β treated) based upon their p-value (-log10 ≥ 1.3) and fold change (log2 ≥ 1.3). Gene Ontology (GO) analysis of the interconnected proteins was done using the Functional Enrichment option in Cytoscape, which generated the GO data against the human proteome. Following the GO analysis, data was exported as a “.csv” file, and the GO analysis graph was generated in GraphPad Prism5 software using the -log10 p-value (Adjusted p-value) indicated for each of the biological processes reported by the GO analysis.ProteomicsAdan Pinto-FernandezCOI-NDM (University of Oxford)PARTIALHomo Sapiens (human)adan.pintofernandez@ndm.ox.ac.ukNot availableUniversity of OxfordUnited KingdomfalseUSP24 is an ISG15 cross-reactive deubiquitinase that mediates IFN-I production by de-ISGylating the RNA helicase MOV10The interferon Stimulated Gene-15 (ISG15) is a ubiquitin-like modifier induced by type I Interferon (IFN-I) and plays a crucial role in the innate immune response against viral infections. ISG15 is conjugated to target proteins by an enzymatic cascade through a process called ISGylation. While USP18 is a well-defined deISGylase counteracting ISG15 conjugation, ISG15 cross-reactive deubiquitylating enzymes (DUBs) have also been reported. Our study reports USP24 as a novel ISG15 cross-reactive DUB identified through activity-based protein profiling (ABPP). We demonstrated that recombinant USP24 processed pro-ISG15 and ISG15-linked synthetic substrates in vitro. Moreover, the depletion of USP24 significantly increased the accumulation of ISG15 conjugates upon IFN-β stimulation. An extensive proteomic analysis of the USP24-dependent ISGylome, integrating total proteome, GG-peptidome, and ISG15 interactome data, identified MOV10 as a specific target of USP24 for deISGylation. Further validation in cells revealed that ISGylated MOV10 enhances IFN-β production, whereas USP24 deISGylates MOV10 to negatively regulate the innate immune response. This study showcase USP24's novel roles in modulating ISGylation, IFN-I production, and innate immune responses with therapeutic implications in infectious diseases, cancer, autoimmunity, and neuroinflammation.2026-05-132024-09-13PXD055843NEWT:3555NEWT:71647NEWT:330879NEWT:35554NEWT:32046NEWT:544496NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:1129NEWT:309807NEWT:55153NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:43186NEWT:428146NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:263737NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:1401257NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT: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:1149786NEWT: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:198107NEWT:9031NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT: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:520NEWT: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: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:9793NEWT:83906NCBITaxon:780NCBITaxon:1502NEWT:6282NEWT:1134506NEWT:255470NEWT:27457NEWT: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: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