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Gaetani"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Lc-ms","Machanism of action","Drug traget deconvolution","Proteomics","Partial proteolysis","Tmt"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD069119"],"tissue":["Hela Cell"],"sample_protocol":["HOLSER  Hela cells were collected and washed with PBS twice. The cells were resuspended in 20 mM EPPS (Merck, E9502) buffer at pH 8.2 containing protease inhibitors (Thermo Fisher Scientific, Cat. 78439) and were subjected to three freeze/thaw cycles to lyse the cells. The protein concentration was measured using a rapid protein quantification assay kit (Thermo Fisher Scientific, Pierce 660 nm) according to the manufacturer’s protocol. Then the lysate was diluted to 1 mg/mL with the lysis buffer (EPPS buffer at pH 8.2). 50 μL of cell lysates were incubated with 5 μL of the ligand solution in DMSO or DMSO only for 30 min at 25 °C in three replicates. The final concentration of the ligand was 10 μM for MTX, 10 μM for staurosporine and 2 μM for rapamycin. Limited trypsinolysis was carried out at an enzyme-to-substrate ratio of 1:1 (wt/wt) for a total duration of 4 min. Specifically, 10 µL of trypsin (Sigma-Aldrich, T1426) 5 mg/mL stock solution was added to 50 µg of protein sample. The mixture was gently and thoroughly mixed for 30 s using a multichannel pipette to ensure even distribution. The samples were then incubated at 25 °C for 3.5 min in ThermoMixer F1.5 (Eppendorf), being shaken at 1,000 rpm. For carrier proteome samples, trypsin digestion was carried out for 8 h. Proteolysis was stopped by adding 165 µL of 8 M guanidine hydrochloride (GdmCl) in 20 mM EPPS buffer (pH 8.2), resulting in a final concentration of 6 M GdmCl. To perform alkylation of free cysteine residues by carbamidomethylation, tris(2-carboxyethyl) phosphine (TCEP) and iodoacetamide (IAA) were added to the digested protein samples to final concentrations of 10 mM and 40 mM, respectively. The mixture was subsequently incubated at 95 °C for 5 min. Then the samples were diluted to a final concentration of 1 M guanidine GdmCl using 20 mM EPPS buffer (pH 8.2). The peptide samples were labelled using 16 TMTpro reagents (Thermo Fisher Scientific, Cat. A44520) according to the manufacturer’s instructions. The labelling reaction was quenched by 50% hydroxylamine (Thermo Fisher Scientific, Cat. 15225753). After pooling together the individually labeled samples, the peptides were acidified by trifluoroacetic acid (TFA) to a final concentration of 1% and desalted using C18 Sep-Pak cartridge. The cartridge was first conditioned by washing twice with 1 mL of 100% acetonitrile (ACN), followed by two washes with 1 mL of 0.1% TFA to equilibrate the resin. Acidified peptide samples were then loaded onto the cartridge and washed twice using 5% ACN with 0.1% formic acid (FA). Peptides were eluted from the cartridge using 50% ACN with 0.1% FA in two steps of 300 µL each. The eluates were collected and subsequently dried. Prior to LC-MS/MS analysis, dried peptides were reconstituted and fractionated by high-performance liquid chromatography with a Dionex Ultimate 3000 UPLC system (Thermo Fisher Scientific) as previously described29, 30. The generated 96 fractions were concatenated into 48 by pooling together every fourth fraction. For LC-MS/MS analysis, 1 µg of each pooled fraction was injected and analyzed. NanoLC-MS/MS analysis NanoLC-MS/MS analyses were performed on an Orbitrap Exploris 480 mass spectrometer equipped with an EASY electrospray ionization source and connected online with an Ultimate 3000 nanoflow UPLC system (all - Thermo Fisher Scientific) as previously descibed for TMT-based quantitative protoemics. HDX MS  Recombinant KPNA2 was kindly provided by Saei’s lab at Karolinska Institutet. Recombinant FKBP3 protein was obtained from Elabscience (PKSH032876). For HDX labeling, 4 μL of KPNA2 (5 μM) or FKBP3 (10 μM) was mixed with 36 μL of stock buffer prepared in D₂O (Sigma, 151882) and incubated at 10 °C for 30 s. The buffer composition for KPNA2 was 20 mM Tris-HCl, 50 mM NaCl, 2.5 mM DTT, pH 8.0, whereas for FKBP3 it was 20 mM Tris-HCl, 1 mM DTT, pH 8.0. After adding 1 volume of ice-cold 1.8M guanidine hydrochloride in 0.8% formic acid, the samples were analyzed in an automated HDX-MS system (TRAJAN) in which injected samples were automatically digested, cleaned and separated at 4 °C. Samples were digested using enzymeate BEH pepsin column (WATERS) followed by a 3-min desalting step using 0.1% FA at 100 µL/min. Peptic peptides were then separated by a 21 mm I.D × 50-mm length C18/3 µm column using a 21 min/10%–90% acetonitrile gradient in 0.1% formic acid at 40 µL/min. An Orbitrap Fusion Lumos mass spectrometer (Thermo Fisher Scientific) operated at 60,000 resolution at m/z 200 was used for analysis."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["LC-MS/MS data were analyzed using Proteome Discoverer version 3.1 (Thermo Scientific). Database searches were performed against the UniProt human reference proteome (Proteome ID: UP000005640_9606; downloaded in May 2025), containing 20,663 reviewed protein entries, for peptide and protein identification and quantification. TMT reporter ion abundances were normalized on the total abundance in a given TMT channel.    The HDX-MS raw files were searched using  MASCOT v2.5.1 search engine using  single sequence-based databases for each recombinant proteins analyzed. The HDExaminer software (Sierra Analytics) was used to process all HDX-MS data."],"omics_type":["Proteomics"],"labhead":["Massimiliano Gaetani"],"instrument_platform":[""],"labhead_affiliation":["Chemical Proteomics, Division of Chemistry I, Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm, Sweden"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["massimiliano.gaetani@ki.se"],"publication":["42017605 Lyu H, Gharibi H, Meng Z, Sokolova B, Lundström S, Zhang X, Zubarev RA. Peptide-to-Protein Data Aggregation Using Fisher's Method Improves Target Identification in Chemical Proteomics. Anal Chem. 2026 98(17):12596-12602 10.1021/acs.analchem.5c08021"],"submitter_affiliation":["Karolinska Institutet"],"submitter_country":["Sweden"],"pubmed_abstract":["Protein-level statistical tests in proteomics, aimed at obtaining p-values, are conventionally made on protein abundances aggregated from peptide data. This integral approach overlooks peptide-level heterogeneity and ignores important information coded in individual peptide data, while protein p-values can also be obtained by Fisher's method of combining peptide p-values using chi-square statistics. Here, we test this latter approach across diverse chemical proteomics data sets based on assessments of protein expression, solubility, and protease accessibility. Using the top four peptides ranked by their p-values consistently outperformed protein-level analysis and avoided biases introduced by the inclusion of deviant peptides or the imputation of missing peptide values. Fisher's method provides a simple and robust strategy, improving identification of regulated/shifted proteins in diverse proteomics assays."],"pubmed_title":["Peptide-to-Protein Data Aggregation Using Fisher's Method Improves Target Identification in Chemical Proteomics."],"pubmed_authors":["Lyu Hezheng H, Gharibi Hassan H, Meng Zhaowei Z, Sokolova Bohdana B, Lundström Susanna S, Zhang Xuepei X, Zubarev Roman A RA"],"additional_accession":[]},"is_claimable":false,"name":"HigH-ratiO partiaL proteolysiS with carriER proteome (HOLSER) Enables  Global Structure Profiling and Site-resolved Elucidation of Ligand-Protein Interactions","description":"Understanding how cellular proteins interact with their environment, including endogenous and exogeneous molecules, is critical for elucidating mechanisms of cellular regulation and drug action. Partial proteolysis-based techniques offer peptide-level resolution of ligand-induced conformational changes but are limited by modest proteome coverage and depth, as well as sensitivity to the experimental conditions. To overcome these limitations, we developed higH ratiO partiaL proteolysiS with carriER proteome (HOLSER), an efficient workflow that features extended digestion time for low peptide yield variability and tandem mass tag (TMT)-based multiplexing that includes full digests for enhanced proteome depth and sequence coverage as well as higher precision of abundance measurements. We demonstrate HOLSER capabilities across diverse usage cases, including global proteome structure profiling, kinase target mapping, and structural mapping of the FKBP-mTOR complex in response to rapamycin. HOLSER reveals domain-specific stabilization and identifies peptides in direct contact with ligands, providing a powerful and scalable platform for simultaneous probing structural changes at the scale of the whole proteome, individual protein domains and specific binding sites.","dates":{"publication":"2026-06-08","submission":"2025-10-03"},"accession":"PXD069119","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:1131","NEWT:35795","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NEWT:1334565","NEWT:625351","NEWT:258594","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:247480","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:2315688","NEWT:592321","NEWT:1073882","NEWT:6819","NEWT:475174","NEWT:111205","NEWT:1599","NEWT:428386","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:32264","NEWT:12215","NEWT:1590","NEWT:10034","NEWT:33114","NEWT:1596","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NEWT:1748418","NCBITaxon:79857","NEWT:1096976","NEWT:3765","NEWT:3767","NEWT:1589","NEWT:135622","NEWT:4615","NEWT:672127","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:1582","NEWT:3760","NEWT:1584","NEWT:2086595","NEWT:36630","NEWT:1585","NEWT:383379","NEWT:381198","NEWT:418106","NCBITaxon:12721","NEWT:10029","NEWT:913645","NEWT:2492962","NEWT:641809","NEWT:1392488","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:3357","NEWT:111225","NEWT:7719","NEWT:29073","NEWT:5530","NEWT:868565","NEWT:135674","NEWT:1562698","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:2020713","NEWT:224308","NEWT:3347","NEWT:49928","NEWT:3349","NEWT:160621","NEWT:2502409","NEWT:212790","NEWT:110368","NEWT:1916073","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:410658","NEWT:5516","NEWT:44688","NEWT:44689","NEWT:370038","NEWT:498211","NEWT:345076","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:1310173","NEWT:200795","NEWT:2579791","NEWT:44685","NEWT:161934","NEWT:156587","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:260499","NEWT:410661","NEWT:329854","NEWT:1140","NCBITaxon:2157","NEWT:2066563","NEWT:2649329","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:150808","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:3714","NCBITaxon:37162","NEWT:270643","NEWT:3715","NEWT:1538","NEWT:2065263","NEWT:177437","NEWT:717966","NEWT:10891","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:28174","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:3704","NEWT:244366","NEWT:1246791","NEWT:176597","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:9006","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:926571","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:2714896","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:1608994","NEWT:33995","NEWT:55784","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2499525","NEWT:1122981","NEWT:2853422","NEWT:1122984","NEWT:487","NEWT:1538553","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:45972","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:2836","NEWT:376686","NEWT:237610","NEWT:95486","EFO:0001352","NEWT:119562","NEWT:1883446","NEWT:1233435","NEWT:118223","NEWT:11757","NEWT:987059","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:1509","NEWT:491","NEWT:460523","NEWT:45954","NEWT:235443","NEWT:1579","NEWT:1757312","NEWT:85694","NEWT:109786","NEWT:1922344","NEWT:108458","NEWT:5936","NEWT:85692","NEWT:321967","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:279010","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:415978","NEWT:1255228","NEWT:410289","NEWT:191701","NEWT:373153","NEWT:1640278","NEWT:9054","NEWT:472","NEWT:940825","NEWT:29459","NEWT:529507","NEWT:1071661","NEWT:1380096","NEWT:28128","NEWT:470","NEWT:41122","NEWT:5911","NEWT:1328300","NEWT:748693","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:11723","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166314","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:29488","NEWT:215402","NEWT:1547","NEWT:1290454","NEWT:3726","NEWT:906914","NEWT:81231006","NEWT:30455","NEWT:28141","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:3728","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:548","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:2126348","NEWT:5180","NEWT:256737","NEWT:299467","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:542","NEWT:2903","NEWT:185579","NEWT:872227","NEWT:13076","NEWT:2587410","NEWT:207340","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:2126337","NEWT:550","NEWT:10804","NEWT:33941","NEWT:554","NEWT:451516","NEWT:552",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