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Sokolova"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Lc-msms","Proteomics","Drug target"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD061498"],"tissue":["Cell Culture"],"sample_protocol":["Cell work and proteome extraction HeLa cells (CCL-2) obtained from ATCC were grown at 37 °C in 5% CO2 in DMEM media supplemented with 2 mM L-Glutamine, 100 U/mL Pen/Strep, and 10% FBS. For proteome extraction, HeLa cell pellets were resuspended in 20 mM EPPS buffer at pH 8. Cells were lysed by 5 freeze-thaw cycles in liquid nitrogen, and the lysate was cleared by centrifugation at 14,000 g for 10 min. Protein concentration was then measured using a BCA Protein Assay kit. 0.5 mL of lysate at the final concentration of 1 mg/mL of protein was aliquoted for further analysis. Sample preparation Lysate samples were either incubated with vehicle (DMSO) or drugs at 10 µM concentration for 30 min at 25°C. For the digestion procedure, trypsin was added at a 1:100 w/w ratio. After every hour of digestion at 25°C over the 8 h timeframe, samples were loaded on a 3 kDa MWCO filter and centrifuged at 14,000 g for 10 min. The filtrate was collected, and buffer was added to the undigested protein above the filter. TMT16 reagents were added 4x by weight to each sample, followed by incubation for 2 h at room temperature (RT). The reaction was quenched by addition of 0.5% hydroxylamine. Samples within each TMT set were combined and reduced with DTT (final concentration10 mM) for 1 h at RT. Afterwards, iodoacetamide (IAA) was added to a final concentration of 50 mM followed by 1 h incubation in the dark. Samples were then acidified by trifluoroacetic acid (TFA), cleaned using Sep-Pak and dried using a DNA 120 SpeedVac™ concentrator (Thermo). The pooled samples were resuspended in 20 mM ammonium hydroxide and separated into 96 fractions on an XBrigde BEH C18 2.1 × 150 mm column (Waters; Cat#186003023), using a Dionex Ultimate 3000 2DLC system (Thermo Scientific) over a 48 min gradient of 1–63% B (B = 20 mM ammonium hydroxide in ACN) in three steps (1–23.5% B in 42 min, 23.5–54% B in 4 min and then 54–63%B in 2 min) at 200 µL min−1 flow. Fractions were then concatenated into 24 samples in sequential order (e.g. 1, 25, 49, 73). After resuspension in 0.1% FA (Fisher Scientific) to a concentration of 1 µg/ µL, each fraction was analyzed by LC-MS/MS. For the dose response experiment, lysate samples were aliquoted into 18 tubes at a final protein concentration of 1 mg/mL. Samples were then treated with either vehicle (DMSO) or methotrexate at concentrations ranging from 0 to 1000 nM and incubated for 30 min at 25°C. Trypsin was added to each sample at a 1:100 ratio, followed by incubation at 25°C for 2 h after which the digestion was inhibited by adding aprotinin. TMT reagents were added to each sample at a 4x weight ratio. After the 2 h long incubation at 25°C, the reaction was quenched by adding 50% hydroxylamine to a final concentration of 0.5%. Individually labeled TMT samples in each replicate were pooled and loaded onto the filter units and centrifuged at 14,000 g for 10 min, with the filtrate (containing peptides in EPPS) retained for further processing. DTT was added to a final concentration of 10 mM, followed by incubation at 37°C for 30 min. IAA was added to a final concentration of 50 mM and incubated for 30 min at RT in the dark. Samples were acidified with TFA to pH 2-3 and cleaned using SepPak. After drying, samples were fractionated like above into 24 fractions.  LC-MS/MS analysis Samples (ca. 1 µg) were loaded onto a 50 cm column (EASY-Spray, 75 µm internal diameter (ID), PepMap C18, 2 µm beads, 100 Å pore size) connected to an Easy-nLC 1000 pump (Thermo Fisher Scientific) and eluted with a 150-min gradient reaching from 3% to 95% of buffer B (98% ACN, 0.1% FA, 2% H2O) in buffer A (0.1% FA, 2%ACN, 98% H2O) at a flow rate of 300 nL/min. Mass spectra were acquired with an Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Fisher Scientific) in the data-dependent acquisition (DDA) mode at a nominal resolution of 120,000 for MS and 45,000 for MS/MS, in the m/z range from 375 to 1500. Peptide fragmentation was performed via higher-energy collision dissociation (HCD) with normalized energy set at 33%."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Data processing  The raw data from mass spectrometry was analyzed by MaxQuant, version 1.5.3.825. The Andromeda search engine26 searched MS/MS data against the International Protein Index database (human version 2014_02, 89,054 entries). Cysteine carbamidomethylation was used as a fixed modification, whereas N, Q-deamidation was selected as a variable modification. Trypsin/P was selected as enzyme specificity. No more than two missed cleavages were allowed. For all other parameters, the default settings were used."],"omics_type":["Proteomics"],"labhead":["Roman Zubarev"],"instrument_platform":[""],"labhead_affiliation":["Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["bohdana.sokolova@ki.se"],"publication":["41653152 Sokolova B, Gharibi H, Jafari M, Lyu H, Lovera S, Gaetani M, Saei AA, Zubarev RA. Above-Filter Digestion Proteomics Reveals Drug Targets and Localizes Ligand Binding Site. J Proteome Res. 2026 25(3):1556-1570 10.1021/acs.jproteome.5c00927"],"submitter_affiliation":["Karolinska Institutet"],"submitter_country":["Sweden"],"pubmed_abstract":["Identifying how drugs interact with proteins is fundamental to understanding their therapeutic effects and side effects. While numerous chemical proteomics methods exist for determining protein targets of drugs, each exhibits \"blind spots,\" necessitating complementary approaches. We introduce Above-Filter Digestion Proteomics (AFDIP), which monitors trypsin digestion rates that decrease at ligand-binding sites, while potentially increasing elsewhere. Molecular dynamics simulations showed that these changes relate to backbone flexibility. Using AFDIP, we identified targets of various drugs and metabolites, allowing two-dimensional analysis with the drug concentration as the second dimension. The method identifies binding sites within ≤10 Å of crystallography-determined locations with improved resolution (≤5 Å) for larger proteins. Compared with existing proteolysis approaches, AFDIP offers simpler sample preparation, deeper proteome analysis, and broader sequence coverage. AFDIP addresses the blind spots of current techniques and provides structural insights, enhancing the chemical proteomics toolkit."],"pubmed_title":["Above-Filter Digestion Proteomics Reveals Drug Targets and Localizes Ligand Binding Site."],"pubmed_authors":["Sokolova Bohdana B, Gharibi Hassan H, Jafari Maryam M, Lyu Hezheng H, Lovera Silvia S, Gaetani Massimiliano M, Saei Amir Ata AA, Zubarev Roman A RA"],"additional_accession":[]},"is_claimable":false,"name":"Above-Filter Digestion Proteomics reveals drug targets and localizes ligand binding site","description":"While a number of efficient chemical proteomics methods are available for determining protein targets of pharmaceutical drugs, each approach exhibits its own “blind spot” and development of complementary techniques is needed. Here, we introduce the Above-Filter Digestion Proteomics (AFDIP) approach based on the monitoring of the rate of trypsin digestion. Digestion rate is decreased at the site of ligand binding to its target protein, while other sites may simultaneously experience an increase the digestion rate. Molecular dynamics (MD) simulations revealed that this increase may be due to allosteric structural changes related to backbone flexibility. We showcase the utility of AFDIP for deconvoluting the targets of versatile drugs and metabolites. Like other techniques, AFDIP allows for a two-dimensional analysis, with the second dimension based on drug concentration. AFDIP exhibits structural resolution, identifying drug target binding sites within ≤10 Å, and 1for larger proteins often ≤5 Å of the crystallography-determined binding sites. Compared to earlier introduced limited proteolysis approaches, AFDIP provides easier sample preparation, deeper proteome analysis and broader sequence coverage. AFDIP is expected to find its place among the most efficient chemical proteomics methods currently available.","dates":{"publication":"2026-03-16","submission":"2025-03-05"},"accession":"PXD061498","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:376741","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:1211601","NEWT:876138","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NEWT:1390363","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:391619","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:105023","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NEWT:13164","NEWT:216129","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:8479","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:630","NEWT:334747","NEWT:61235","NEWT:15368","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:469008","NEWT:260707","NEWT:256318","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","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