Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/peptides.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/proteinGroups.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/mqpar.xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/mzTab.mzTabftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_EGFP_benzo_2_Slot1-4_1_2777.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_EGFP_3_Slot1-8_1_2781.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_A104R_1_Slot1-12_1_2786.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_EGFP_benzo_3_Slot1-5_1_2778.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_A104R_benzo_2_Slot1-10_1_2784.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_EGFP_2_Slot1-7_1_2780.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_A104R_3_Slot1-14_1_2788.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_A104R_2_Slot1-13_1_2787.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_EGFP_1_Slot1-6_1_2779.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_A104R_benzo_1_Slot1-9_1_2783.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_EGFP_benzo_1_rep_Slot1-3_1_2803.d.zipftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067191/KD_A2_A104R_benzo_3_Slot1-11_1_2785.d.zipprimaryOK200katarzyna.dolata@fli.deKatarzyna DolataData-dependent acquisitionAffinity purification coupled with mass spectrometry proteomicsMass SpectrometryBottom-up proteomicsAfrican swine fever virus-like integrated (asfli)-elementsA104r proteinAfrican swine fever virusA104r interactomehttps://www.ebi.ac.uk/pride/archive/projects/PXD067191Epithelial CellTransfection For affinity purification, WSL cells were plated in a 6-well plate and transfected with 2.4 μg of GFP-tagged expression constructs or GFP control according to the manufacturer’s recommendations (K2 Transfection System, Biontex). For each bait, n = 3 independent biological replicates were prepared for affinity purification. Affinity purification A total of 5 x 106 WSL cells (expressing GFP or A104R-GFP) were mock-infected or infected with cell culture-adapted ASFV Armenia 2008 at a multiplicity of infection (MOI) of 2 PFU/cell. After 24 hours, cells were washed thrice with PBS and lysed on ice in 1 ml cold immunoprecipitation (IP) buffer [(50 mM Tris-HCl, pH 7.4, 150 mM NaCl, 1 mM MgCl2) supplemented with 0.5% Nonidet P40 substitute (NP-40; Sigma-Aldrich #I8896) and cOmplete mini EDTA-free protease inhibitor cocktail (Roche, #04693159001)]. To distinguish between DNA/RNA-dependent and -independent protein-protein interactions we lysed cells under two conditions: (1) lysis buffer supplemented with benzonase (25 U/ml, Sigma-Aldrich #E8263), (2) lysis buffer without benzonase. Cells were lysed by sonication 3x30sec, 80% amplitude (Branson Digital Sonifier 450) and incubated on a tube rotator for 30 min at 4°C and another 30 min on a thermomixer at 37°C with constant shaking at 900 rpm. Lysates were cleared by centrifugation at 13,000 x g and 4°C for 15 min. 50 µl of each lysate was removed for immunoblotting (whole cell lysate fraction). GFP-trap agarose beads (50 µl, Chromotek) were washed twice in IP buffer and incubated with the remaining lysate for 1 h with constant rotation at 4 °C. Beads were washed twice with 1 ml of IP buffer containing 0.05% NP-40 followed by two washes in detergent-free IP buffer. 10 µl bead slurry was removed for immunoblotting (IP fraction). The remaining 40 µl beads prepared in at least three independent biological replicates for each bait were kept for mass spectrometric analysis. Sample preparation for mass spectrometry After IP, beads were suspended in 300 µl freshly made UA buffer [8 M urea, 100 mM Tris-HCl pH 8], loaded onto 10 kDa filter units (Sartorius), and centrifuged at 12,000 x g at 20°C for 30 min. Filter Aided Sample Preparation (FASP) trypsin digestion was performed as described previously [1]. Beads were trypsinized to digest the baits and the interacting proteins in 100 μl of digest buffer [1 M urea, 50 mM Tris-HCl pH 7.5 and 5 μg/mL Trypsin (Promega)]. Digestion was performed overnight at 37°C with shaking. The next day, the flow-through containing peptides was collected, and the samples were inactivated for 10 min at 95°C. Peptides were acidified with formic acid (1% final concentration) and de-salted using C18 100 µl tips (Thermo Scientific) according to the manufacturer’s instructions, dried by vacuum centrifugation, and reconstituted in 20 μl of 0.1% formic acid prior to mass spectrometry. 1. Wiśniewski, J.R.; Zougman, A.; Nagaraj, N.; Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 2009, 6, 359–362, doi:10.1038/nmeth.1322.PrideMS data acquisition and analysis Digested peptide mixtures were analyzed by LC-MS/MS on a timsTOF Pro (Bruker Daltonik), which was coupled online to a nanoElute nanoflow liquid chromatography system (Bruker Daltonik) via a CaptiveSpray nano-electrospray ion source. Peptides (corresponding to 100 ng) were separated on a reversed-phase C18 column (25 cm × 75 µm i.d., 1.6 µm, IonOpticks) with a binary buffer system of buffer A (water with 0.1% formic acid, v/v) and buffer B (acetonitrile with 0.1% formic acid, v/v). Peptides were separated running a gradient of 2–95% mobile phase B over 115 min (2% to 16% solvent B (0-60 min), 15-24% solvent B (60-90 min), 24%-34% solvent B (90-105 min), 35-95% solvent B (105-107 min) and 95% solvent B (107-115 mins) at a constant flow rate of 400 nl/min. The column temperature was controlled at 40 °C. MS analysis of eluting peptides was per-formed in ddaPASEF mode (1.1sec cycle time) as recommended by the manufacturer. Data processing protocol Mass spectrometry raw files were processed with MaxQuant (v.2.0.2.0) [2] (Cox and Mann 2008). Peptide search was performed against an ENSEMBL [3] Sus scrofa proteo-me database (v.11.1.2021-11-10) and an NCBI ASFV Georgia (v.FR682468.2) proteome database. The following modifications were included in the search parameters: trypsin di-gestion with a maximum of 2 missed cleavages, carbamidomethylation of cysteine as fixed modification, protein N-terminal acetylation and oxidation of methionine as variable modifications. Mass error tolerance was set to 20 ppm for the full scan (MS1) and 40 ppm for MS/MS (MS2) spectra. False discovery rate (FDR) on peptide and protein level was set to 0.01, the minimum peptide length to seven amino acids, and the match between runs option was used with a 0.7 min match window and 20 min alignment time. The output files were analyzed using Perseus software (v.2.0.3.0) [4]. Proteins identified only by modified peptides, reverse hits, and contaminants were filtered out. Protein was considered identified if at least 2 unique peptides of this protein were found in 50% of the replicates. Proteins specifically binding to A104R baits were filtered out by removing the GFP background. The background list consists of proteins identified in our GFP negative controls and proteins identified as common protein contaminants for AP-MS experiments in HEK293 cells and deposited in the Contaminant Repository for Affinity Purification (CRAPome) [5]. Potential interactors were considered specific if they were identified only in GFP-bait pulldowns or if the log2 fold change (between GFP control and GFP-bait) was greater than 2 and the p-value of a two-sided t-test was <0.01. 2. Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26, 1367-1372, doi:10.1038/nbt.1511. 3. Aken, B.L.; Achuthan, P.; Akanni, W.; Amode, M.R.; Bernsdorff, F.; Bhai, J.; Billis, K.; Carvalho-Silva, D.; Cum-mins, C.; Clapham, P.; et al. Ensembl 2017. Nucleic Acids Res 2017, 45, D635-d642, doi:10.1093/nar/gkw1104. 4. Tyanova, S.; Temu, T.; Sinitcyn, P.; Carlson, A.; Hein, M.Y.; Geiger, T.; Mann, M.; Cox, J. The Perseus computa-tional platform for comprehensive analysis of (prote)omics data. Nat Methods 2016, 13, 731-740, doi:10.1038/nmeth.3901. 5. Mellacheruvu, D.; Wright, Z.; Couzens, A.L.; Lambert, J.P.; St-Denis, N.A.; Li, T.; Miteva, Y.V.; Hauri, S.; Sardiu, M.E.; Low, T.Y.; et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nat Methods 2013, 10, 730-736, doi:10.1038/nmeth.2557.ProteomicsKatarzyna DolataInstitute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems,GermanyCOMPLETESus Scrofa Domesticus (domestic Pig)katarzyna.dolata@fli.de10.3390/V18020272Friedrich-Loeffler InstitutGermany10.6019/PXD067191falseFunctional analyses of the histone-like A104R protein of African swine fever virus and of a homologous pseudogene product found in soft tick genomesAfrican swine fever virus (ASFV) causes a fatal disease with up to 100% mortality in domestic pigs and wild boar (species Sus scrofa), leading to significant economic losses for swine production. Unlike other eukaryotic viruses, ASFV encodes a histone-like nucleic acid-binding protein, pA104R. The A104R gene is highly conserved and present in all ASFV isolates of different genotypes. Moreover, A104R-like sequences have been identified in the genomes of soft ticks, which can replicate and transmit ASFV. Using a virulent genotype IX field isolate from Kenya, we analyzed the importance of A104R for viral replication in a permissive wild boar cell line (WSL). In this study, we confirmed that A104R is not essential for in vitro replication of ASFV. Loss of A104R did not detectably affect viral DNA replication or RNA transcription, but led to a moderate reduction of virus titers and plaque sizes. Substitution of A104R by a similar ASFV-like element derived from the genome of an Ornithodoros moubata soft tick was not capable of rescuing the deletion mutant phenotype. In contrast, reintroduction of the authentic A104R open reading frame (ORF) into the deletion mutant fully restored wild-type virus growth properties. In accompanying studies, we verified the DNA binding activities of the ASFV-, and of the tick-derived A104R protein (pA104R), and performed mass spectrometric analyses of the pA104R interactome. These experiments revealed besides DNA-dependent co-precipitated proteins, also specific, DNA-independent protein-protein interactions of pA104R with other viral and cellular proteins.2026-03-042025-08-11PXD067191NEWT:330879NEWT:377960NEWT:2042546NEWT:259447NEWT:295546NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:59753NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:1073882NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:10034NEWT:661410NEWT:638632NEWT:224326NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:1589NEWT:135622NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:418106NEWT:10029NEWT:913645NEWT:641809NEWT:38815NEWT:317447NEWT:4688NEWT:7719NEWT:868565NEWT:135674NEWT:79329NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:295105NEWT:108061NEWT:60711NEWT:224308NEWT:3347NEWT:160621NEWT:212790NEWT:110368NEWT:1310161NEWT:77133NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:44688NEWT:44689NEWT:498211NEWT:347256NEWT:5518NEWT:398007NEWT:1527468NEWT:498217NEWT:498216NEWT:11320NEWT:246196NEWT:246197NEWT:145458NEWT:44685NEWT:161934NEWT:1148NEWT:5508NEWT:3329NEWT:419481NEWT:5507NEWT:410661NEWT:1140NCBITaxon:2157NEWT:1143NEWT:1287689NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:1182590NEWT:3712NEWT:3711NEWT:2065263NEWT:177437NEWT:10418NEWT:118698NEWT:1616117NEWT:118696NEWT:34865NEWT:52283NEWT:284812NEWT:8175NEWT:43330NEWT:1603293NEWT:44664NEWT:43346NEWT:3702NEWT:1245466NEWT:244366NEWT:1246791NEWT:118694NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:52299NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:460519NEWT:1515NEWT:572307NEWT:1432138NEWT:1424507NEWT:1194599NEWT:272844NEWT:1303443NEWT:485NEWT:56636NEWT:2853422NEWT:1679718NEWT:480NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:1883446NEWT:1233435NEWT:109760NEWT:29031NEWT:235443NEWT:1757312NEWT:85694NEWT:108458NEWT:5936NEWT:320637NEWT:3750NEWT:983964NEWT:11706NEWT:32644NEWT:527796NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:3747NEWT:1116234NEWT:1255228NEWT:410289NEWT:373153NEWT:472NEWT:940825NEWT:529507NEWT:1071661NEWT:470NEWT:5911NCBITaxon:50557NEWT:39251NEWT:29491NEWT:101841NEWT:446NEWT:153481NEWT:2014887NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:63366NEWT:63367NEWT:215402NEWT:1547NEWT:9031NEWT:27292NEWT:1050722NEWT:108931NEWT:1293497NEWT:1055524NEWT:150475NEWT:267872NEWT:172269NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:8694NEWT:33936NEWT:8692NEWT:2903NEWT:185579NEWT:13076NEWT:1006581NEWT:8673NEWT:33940NEWT:550NEWT:554NEWT:451516NEWT:552NEWT:1325291NEWT:36185NEWT:1054211NEWT:1225786NEWT:51338NEWT:575412NEWT:28112NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:643680NEWT:214092NCBITaxon:6157NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:9986NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:8655NEWT:5147NEWT:28104NEWT:407821NEWT:568703NCBITaxon:2NEWT:568708NEWT:986NEWT:52641NEWT:28532NEWT:353152NEWT:40674NEWT:1194669NEWT:443906NEWT:519NEWT:2510939NEWT:7394NEWT:6063NEWT:1328388NEWT:1548728NEWT:667127NEWT:9557NEWT:377586NEWT:300641NEWT:39655NEWT:9554NEWT:256318NEWT:206411NCBITaxon:6191NEWT:229533NEWT:214053NEWT:80863NEWT:90675NEWT:52638NEWT:57075NEWT:1666905NEWT:8697NEWT:8695NEWT:884204NEWT:1123869NEWT:9544NEWT:9545NEWT:979NEWT:7370NEWT:83906NEWT:1134506NEWT:255470NEWT:38783NEWT:6426NEWT:33090NEWT:9935NEWT:287889NEWT:305959NEWT:13489NEWT:92867NEWT:92866NCBITaxon:3055NEWT:51750NEWT:202950NEWT:295027NCBITaxon:11320NEWT:632957NEWT:9925NCBITaxon:9606NEWT:90690NEWT:1436183NEWT:4232NEWT:416348NEWT:11298NEWT:7742NEWT:196627NEWT:200308NEWT:200302NEWT:870435NEWT:9913NEWT:9915NEWT:105841NEWT:2666255NEWT:999810NCBITaxon:5693NEWT:28995NEWT:1392998NEWT:380394NEWT:226900NEWT:1266738NEWT:231490NEWT:244704NEWT:7725NEWT:9909NEWT:9902NEWT:430615NEWT:72664NEWT:563041NEWT:36599NEWT:41949NEWT:326423NEWT:452467NEWT:198822NEWT:36111NEWT:326424NEWT:1678078NEWT:749906NEWT:418985NEWT:749907NEWT:150847NEWT:431947NEWT:69014NEWT:142809NEWT:302409NEWT:130821NEWT:27606NEWT:1519788NEWT:59202NEWT:9975NEWT:8643NEWT:1159899NEWT:502780NEWT:860688NEWT:13443NEWT:8644NEWT:5141NEWT:46360NCBITaxon:3044782NEWT:202914NEWT:160235NEWT:502779NEWT:297246NEWT:8639NEWT:1928434NEWT:8637NEWT:1114970NEWT:2096NEWT:192222NEWT:9963NEWT:1617910NEWT:2785785NEWT:411901NEWT:1298722NEWT:8626NEWT:186801NEWT:105884NCBITaxon:9615NEWT:8621NEWT:58334NEWT:58331NEWT:8624NEWT:5116NEWT:8623NEWT:5597NEWT:194439NCBITaxon:12637NEWT:38727NEWT:8618NEWT:70448NEWT:9940NEWT:1247190NEWT:118702NEWT:118700NEWT:2126719NEWT:118705NEWT:6945NEWT:2104NEWT:2627626NEWT:6943NEWT:157546NEWT:870726NEWT:91374NEWT:91373NEWT:474186NEWT:10136NEWT:38942NEWT:4762NEWT:307972NEWT:2102NEWT:34NEWT:38949NEWT:1299114NEWT:1590841NEWT:1276473NEWT:2282334NEWT:1247NEWT:70667NEWT:869728NEWT:6938NCBITaxon:39054NEWT:1736309NEWT:4751NEWT:194963NEWT:15819NEWT:109461NEWT:1085956NEWT:6928NEWT:1239NEWT:36745NEWT:400727NEWT:272563NEWT:11009NEWT:913998NEWT:68335NEWT:3885NEWT:3888NEWT:649408NEWT:6915NEWT:101510NEWT:3880NEWT:272559NEWT:216816NEWT:153151NEWT:515849NEWT:10141NEWT:95767NEWT:466585NEWT:1000589NEWT:85963NEWT:85962NEWT:42197NEWT:143361NEWT:1299NEWT:316407NEWT:1794699NCBITaxon:183674NEWT:167387NEWT:84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