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2026/06/PXD073251/3118_Lumik3_Uldrijan_120IS_HCD-low_P18_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik3_Uldrijan_120IS_HCD_ID18_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik2_Uldrijan_120IS_HCD-low_P15_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik1_Uldrijan_120IS_HCD_ID07_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik1_Uldrijan_120IS_HCD-low_P05_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik2_Uldrijan_120IS_HCD_ID16_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik1_Uldrijan_120IS_HCD-low_P02_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik2_Uldrijan_120IS_HCD-low_P12_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik1_Uldrijan_120IS_HCD_ID04_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik3_Uldrijan_120IS_HCD-low_P22_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik3_Uldrijan_120IS_HCD_ID19_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik3_Uldrijan_120IS_HCD_ID22_1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073251/3118_Lumik2_Uldrijan_120IS_HCD_ID13_1.rawprimary200OKzdrahal@sci.muni.czDavid PotesilMass SpectrometryBottom-up proteomicsLc-msHumanRocaglamide aMeljusoMelanomaEif4fA375Pd184352Small-moleculeMekEif4aCell lineInhibitorCi-1040https://www.ebi.ac.uk/pride/archive/projects/PXD073251Cell CultureSamples preparation for LC-MS analyses Individual cell pellets were solubilized using SDT buffer (4% sodium dodecyl sulphate, 100mM dithiothreitol, 100mM TrisHCl, pH 7.6) and processed by filter-aided sample preparation (FASP) method (cit1) with some modifications. The samples were mixed with 8M UA buffer (8M urea in 100 mM Tris-HCl, pH 8.5), loaded onto the Microcon device with MWCO 30 kDa (Merck Millipore) and centrifuged at 7,000× g for 30 min at 20°C. The retained proteins were washed (all centrifugation steps after sample loading done at 14,000× g) with 200 μL UA buffer. The final protein concentrates kept in the Microcon device were mixed with 100 μL of UA buffer containing 50 mM iodoacetamide and incubated in the dark for 20 min. After the next centrifugation step, the samples were washed three times with 100 μL UA buffer and three times with 100 μL of 50 mM NaHCO3. Trypsin (enzyme:protein ratio of 1:50, sequencing grade, Promega) was added onto the filter and the mixture was incubated for 18 h at 37°C. The tryptic peptides were eluted by centrifugation followed by two additional elutions with 50 μL of 50mM NaHCO3. Peptides were then cleaned by liquid-liquid extraction (3 iterations) using water saturated ethyl acetate (cit2). 1/10 of the cleaned FASP eluate was taken out for direct LC-MS measurements, evaporated completely in SpeedVac concentrator (Thermo Fisher Scientific). Peptides were further transferred into LC-MS vials using 50 μL of 2.5% FA in 50% ACN and 100 μL of pure ACN and with addition of polyethylene glycol (final concentration 0.001%) and concentrated in a SpeedVac concentrator. Phosphopeptides were enriched from the remaining 9/10 of the cleaned FASP eluate after complete solvent evaporation (SpeedVac concentrator) using High-Select™ TiO2 Phosphopeptide Enrichment Kit (Thermo Fisher Scientific, Waltham, Massachusetts, USA) according to manufacturer protocol. Resulting phosphopeptides were extracted into LC-MS vials by 2.5% formic acid (FA) in 50% acetonitrile (ACN) and 100% ACN with addition of polyethylene glycol (final concentration 0.001%) and concentrated in a SpeedVac concentrator). LC-MS analysis of peptides LC-MS/MS analyses of all peptide mixtures (2 peptide solutions for each sample – 1 not enriched; 2 enriched on phosphopeptides using TiO2 enrichment kit) were done using RSLCnano system connected to Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific). Prior to LC separation, tryptic digests were online concentrated and desalted using trapping column (100 μm × 30 mm, column compartment temperature of 40ºC) filled with 3.5-μm X-Bridge BEH 130 C18 sorbent (Waters). After washing of trapping column with 0.1% FA, the peptides were eluted (flow rate - 300 nl/min) from the trapping column onto an analytical column (Acclaim Pepmap100 C18, 3 µm particles, 75 μm × 500 mm; column compartment temperature of 40ºC, Thermo Fisher Scientific) by using 100 min long nonlinear gradient program (1-56% of mobile phase B; mobile phase A: 0.1% FA in water; mobile phase B: 0.1% FA in 80% ACN; 0 min: 1% B, 70 min: 30% B, 100 min: 56% B) for analysis of phosphopeptides enriched fraction and not enriched peptide mixture. Equilibration of the trapping column and the analytical column was done prior to sample injection to sample loop. The analytical column outlet was directly connected to the Digital PicoView 550 (New Objective) ion source with sheath gas option and SilicaTip emitter (New Objective; FS360-20-15-N-20-C12) utilization. ABIRD (Active Background Ion Reduction Device, ESI Source Solutions) was installed. MS data were acquired in a data-dependent strategy with cycle time for 3 seconds and with survey scan (350-2000 m/z). The resolution of the survey scan was 60000 (200 m/z) with a target value of 4×105 ions and maximum injection time of 50 ms. HCD MS/MS (30% relative fragmentation energy, normal mass range) spectra were acquired with a target value of 5.0x104. The MS/MS spectra were recorded in Orbitrap at resolving power of 30 000 (200 m/z) and the maximum injection time for MS/MS was 500 or 54 ms for analysis of phosphopeptides enriched fraction or not enriched peptide mixture, respectively. Dynamic exclusion was enabled for 60 s after one MS/MS spectra acquisition. The isolation window for MS/MS fragmentation was set to 1.6 m/z. Inspect the raw data as part of the PRIDE upload for more details on methods used.PrideNot availableThe analysis of the mass spectrometric RAW data files was carried out using the MaxQuant software (version 1.6.1.0) using default settings unless otherwise noted. MS/MS ion searches were done against modified cRAP database (based on http://www.thegpm.org/crap, 112 protein sequences) containing protein contaminants like keratin, trypsin etc., and UniProtKB protein database for Homo sapiens (https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/reference_proteomes/Eukaryota/UP000005640/UP000005640_9606.fasta.gz; version 2018-05 from 2025-05-18, number of protein sequences: 20,996). Oxidation of methionine, deamidation (N, Q), acetylation (protein N-terminus) and phosphorylation (S, T, Y; only data for solutions enriched on phosphopeptides) as optional modifications, and trypsin/P enzyme with 2 allowed miss cleavages and minimal peptide length 6 aminoacids were set. Peptides and proteins with FDR threshold <0.01 and proteins having at least one unique or razor peptide were considered only. Match between runs was set separately for all enriched and not enriched peptide solution analyses. Please inspect provided files related to the MaxQuant search as part of the PRIDE data upload for more details. Protein intensities reported in proteinGroups.txt file and evidence intensities reported in evidence.txt file (output of MaxQuant program) were further processed using the software container environment (https://github.com/OmicsWorkflows), version 3.6.1a.ProteomicsZbynek ZdrahalProteomics Core Facility and Research Group Proteomics, CEITEC-MU, Masaryk University, Brno, Czech RepublicPARTIALHomo Sapiens (human)42050705 Vadovičová N, Lešková A, Koždoňová K, Smolková K, Valčíková B, Kafka F, Potěšil D, Zdráhal Z, Vacek O, Víchová R, Souček K, Uldrijan S. Translational control of AMPK activity in melanoma. Cell Commun Signal. 2026 24(1):348 10.1186/s12964-026-02901-4david.potesil@ceitec.muni.czProteomics Core Facility and Research Group Proteomics CEITEC-MU Masaryk University Brno, Czech RepublicCzech RepublicTranslational control of AMPK activity in melanoma.Vadovičová Natália N, Lešková Anna A, Koždoňová Kateřina K, Smolková Karolína K, Valčíková Barbora B, Kafka Filip F, Potěšil David D, Zdráhal Zbyněk Z, Vacek Ondřej O, Víchová Ráchel R, Souček Karel K, Uldrijan Stjepan SfalseLC-MS analysis of human melanoma cell line response to eIF4F inhibition and MEK inhibitionThe project aimed to identify changes at the protein level in human melanoma cells treated with the eIF4F inhibitor rocaglamide A, the MEK inhibitor PD184352 (CI-1040), and their combination. A375 and MelJuso human melanoma cell lines were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, and 2 mM L-glutamine and maintained at 37 °C in a humidified atmosphere containing 5% CO2. For the analysis, both cell lines were seeded in 10-mm dishes and, the following day, treated with 100 nM rocaglamide A (DRG), 500 nM PD184352/CI-1040 (MEKi), and their combination (DRG_MEKi). Negative controls (CTR) were treated with an equivalent volume of DMSO. 20 h post-treatment, cells were washed with PBS, collected, and pelleted.2026-06-152026-01-19PXD073251NEWT:6945NEWT:184922NEWT:6703NEWT:3555NEWT:71647NEWT:2NEWT:157546NEWT:474186NEWT:35554NEWT:38942NEWT:307972NEWT:32046NEWT:1496NEWT:544496NEWT:2102NEWT:2042546NEWT:259447NEWT:45351NEWT:43179NEWT:4513NEWT:180454NEWT:5722NEWT:1247NEWT:6938NEWT:1129NEWT:55153NCBITaxon:10407NEWT:1736309NEWT:309800NEWT:281395NEWT:10360NEWT:1211601NEWT:876138NEWT:47664NEWT:317548NEWT:3654NEWT:237561NEWT:5833NEWT:6928NEWT:10036NEWT:36745NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:272563NEWT:224326NEWT:1333499NCBITaxon:79857NEWT:1096976NEWT:82688NEWT:95648NEWT:3885NEWT:3888NEWT:5821NEWT:1589NEWT:135622NCBITaxon:4896NEWT:6915NEWT:3649NEWT:101510NEWT:28903NEWT:3880NEWT:272559NEWT:28909NEWT:515849NEWT:3641NEWT:383379NEWT:466585NEWT:10029NEWT:913645NEWT:1000589NEWT:85963NEWT:85962NEWT:143361NEWT:317447NEWT:4688NEWT:7955NEWT:7959NEWT:2261NEWT:31156NEWT:398580NEWT:4442NEWT:4565NEWT:1264690NEWT:515619NEWT:192875NEWT:34305NEWT:59729NEWT:2164133NCBITaxon:183674NEWT:224308NEWT:167387NEWT:84645NEWT:44586NEWT:626528NEWT:3347NEWT:139927NEWT:4558NEWT:209285NEWT:5888NEWT:211586NEWT:747078NEWT:1282NEWT:1283NEWT:931281NEWT:4550NEWT:1000561NEWT:294381NEWT:197NEWT:1390363NEWT:77133NEWT:288705NEWT:29176NEWT:145481NCBITaxon:79824NEWT:4787NCBITaxon:4563NEWT:5755NEWT:44689NEWT:3218NEWT:5759NEWT:1736231NEWT:556182NEWT:1270NEWT:374990NEWT:1392NEWT:498217NEWT:156471NEWT:2242NEWT:4784NEWT:11320NEWT:360106NEWT:156476NEWT:286NEWT:391619NEWT:360104NEWT:246196NEWT:287NEWT:246197NEWT:10117NEWT:10239NEWT:10116NEWT:1280NEWT:1735272NEWT:83334NEWT:83332NEWT:44685NEWT:317513NEWT:161934NEWT:1148NEWT:580240NEWT:5508NEWT:294128NEWT:5507NEWT:11676NEWT:55571NEWT:35500NEWT:1140NEWT:100226NEWT:4530NEWT:1143NEWT:4896NEWT:75058NEWT:13616NEWT:1390NEWT:1094343NEWT:1336795NEWT:644042NEWT:296543NEWT:316435NEWT:42157NEWT:1773NEWT:1895NEWT:1182590NEWT:3712NEWT:82380NEWT:1034304NEWT:105023NEWT:866628NEWT:935293NEWT:64152NEWT:4924NEWT:749200NEWT:375146NEWT:9378NEWT:990346NEWT:145953NEWT:257309NEWT:100816NEWT:263NEWT:230741NEWT:52283NEWT:284812NEWT:8175NCBITaxon:1313NEWT:43330NEWT:1603293NEWT:408169NEWT:44544NEWT:47946NEWT:4911NEWT:645463NEWT:3702NEWT:129249NEWT:1077286NEWT:243277NEWT:990119NEWT:2850NEWT:408172NEWT:227321NEWT:408170NEWT:493760NEWT:106590NEWT:260710NEWT:257313NEWT:3827NEWT:400772NEWT:3708NEWT:128161NEWT:332648NEWT:930945NEWT:106592NEWT:536231NEWT:46704NEWT:1436733NEWT:460519NEWT:1187947NEWT:572307NEWT:1432138NEWT:269796NEWT:10312NEWT:1424507NCBITaxon:1773NEWT:1194599NEWT:54571NEWT:9598NEWT:8030NEWT:9483NEWT:1513458NCBITaxon:40559NEWT:1639NEWT:188229NEWT:3818NEWT:480NEWT:4909NEWT:67767NEWT:759272NEWT:432359NEWT:46835NEWT:1182263NEWT:109757NEWT:943146NEWT:2711NEWT:300852NEWT:1502NEWT:376686NEWT:95486NEWT:9103NEWT:508771NEWT:1883446NEWT:29159NEWT:253NEWT:10306NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:8022NEWT:145943NCBITaxon:4932NEWT:595536NEWT:240906NEWT:593117NEWT:89920NEWT:29158NEWT:3635NEWT:5811NEWT:235443NEWT:180923NEWT:108458NEWT:272623NEWT:272624NEWT:411483NEWT:884019NEWT:198215NEWT:411490NEWT:983964NEWT:118499NEWT:169963NEWT:32644NEWT:527796NEWT:225117NEWT:746128NEWT:499175NEWT:109779NEWT:43665NEWT:1266464NEWT:1715989NEWT:476272NEWT:3747NEWT:195051NEWT:367830NEWT:1255228NEWT:178616NEWT:649908NEWT:410289NEWT:373153NEWT:375451NEWT:352472NEWT:357NEWT:1071661NEWT:360094NEWT:470NEWT:41364NEWT:1313NEWT:411469NEWT:84023NEWT:559292NEWT:39491NCBITaxon:5811NEWT:29491NEWT:411464NEWT:411460NEWT:2014887NEWT:2762NEWT:1174673NEWT:1328426NEWT:562NEWT:411470NEWT:33952NEWT:2094720NCBITaxon:2697049NEWT:571256NCBITaxon:138NEWT:40483NEWT:28038NEWT:1663NEWT:1423NEWT:4932NEWT:3603NEWT:2759NEWT:3847NEWT:38293NEWT:1428NEWT:327159NEWT:178876NEWT:1660NEWT:327160NEWT:573NEWT:9031NEWT:1872122NEWT:7091NEWT:108931NEWT:241368NEWT:1055524NEWT:42528NEWT:190802NEWT:9778NEWT:150475NEWT:303NEWT:9417NEWT:7111NEWT:347515NEWT:1216979NEWT:7237NEWT:9534NEWT:5180NEWT:256737NEWT:9541NEWT:115104NEWT:1121114NEWT:663NEWT:1081927NEWT:1238993NEWT:67825NEWT:187878NEWT:185579NEWT:941442NEWT:220668NEWT:13076NEWT:1821314NEWT:1249668NEWT:7108NEWT:317NEWT:5286NEWT:7227NEWT:7469NEWT:885318NEWT:9402NEWT:9644NEWT:415540NEWT:550NEWT:675060NEWT:4081NEWT:334542NEWT:273068NEWT:554NEWT:27592NEWT:98334NEWT:426428NEWT:451516NEWT:63459NEWT:1276815NEWT:36185NEWT:588858NEWT:1225786NEWT:9639NCBITaxon:11071NEWT:242231NEWT:7574NEWT:1715256NEWT:197221NEWT:7215NEWT:575412NEWT:929793NEWT:29204NEWT:28112NEWT:2172103NEWT:6494NEWT:7460NEWT:6491NEWT:507601NEWT:643680NCBITaxon:6157NEWT:42752NEWT:746360NEWT:6239NEWT:89764NEWT:470150NEWT:162425NEWT:216257NEWT:102169NEWT:543734NEWT:9986NEWT:4054NEWT:73239NEWT:226186NEWT:1268063NEWT:8782NEWT:1263854NEWT:118503NEWT:2059687NEWT:115357NEWT:435590NEWT:1902NEWT:160488NEWT:28104NEWT:1908NEWT:13164NEWT:216129NCBITaxon:2NEWT:985076NEWT:1215323NEWT:2664179NEWT:986NEWT:52641NEWT:7038NEWT:7159NEWT:6192NEWT:28532NCBITaxon:38727NEWT:353152NEWT:2829NEWT:366581NEWT:216599NEWT:216595NEWT:1194669NEWT:51329NEWT:40559NEWT:243230NEWT:8355NEWT:633NEWT:9685NEWT:7029NEW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