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Zhang"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Lc-ms-ms","Proteomics","Partial proteolysis","Ligand-protein interaction"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD077592"],"tissue":["Epithelial Cell"],"sample_protocol":["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 alkylate free cysteine residues via carbamidomethylation, tris(2-carboxyethyl)phosphine (TCEP) was added to a final concentration of 10 mM, followed by incubation at 95 °C for 5 min. Subsequently, iodoacetamide (IAA) was added to a final concentration of 40 mM. The samples were then diluted to a final concentration of 1 M guanidine hydrochloride (GdmCl) using 20 mM EPPS buffer (pH 8.2). The peptide samples were labelled using 18 TMTpro reagents (Thermo Fisher Scientific, Cat. A52045) according to the manufacturer’s instructions. Three carrier channels were assigned to the lowest-mass reporter channels, followed by two empty channels to create a buffer region before the partial proteolysis samples. The labelling reaction was quenched by 0.5% 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 described15, 16. 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."],"repository":["Pride"],"quantification_method":["Not available"],"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.   Statistical analysis Statistical significance of peptide abundance changes between treated and untreated samples was assessed using two-sided, unpaired Welch’s t-test, with p-values (pp) calculated across biological triplicates. The peptide data were translated to the protein level by selecting top three peptides based on a combined score calculated as the absolute value of the log2 fold change in treated sample versus DMSO control multiplied by -log10(pp). The fold change for the protein was calculated as the average of those for the selected three peptides, and the protein p-value was obtained from the pp values by combining them using Fisher’s formula. All statistical analyses were conducted using R (version 4.5.0).  A p-value threshold of < 0.05 was considered statistically significant."],"omics_type":["Proteomics"],"labhead":["Massimiliano Gaetani"],"instrument_platform":[""],"labhead_affiliation":["1 Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden 2 Chemical Proteomics Unit, Science for Life Laboratory (SciLifeLab), SE-17 177 Stockholm, Sweden 3 Chemical Proteomics, Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), SE-17 177 Stockholm, Sweden"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["xuepei.zhang@ki.se"],"publication":["42610894 Zhang X, Gharibi H, Sokolova B, Meng Z, Lyu H, Saei AA, Gaetani M, Zubarev RA. High-Ratio Partial Proteolysis with Carrier Proteome (HOLSER) Enables Global Structure Profiling and Site-Resolved Elucidation of Ligand-Protein Interactions. Anal Chem. 2026 98(32):23939-23948 10.1021/acs.analchem.6c04688"],"submitter_affiliation":["Karolinska Institutet"],"submitter_country":["Sweden"],"pubmed_abstract":["Understanding how cellular proteins interact with their environment, including endogenous and exogenous 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 an extended digestion time for reduced peptide yield variability as well as tandem mass tag multiplexing that includes full digests for enhanced proteome depth and sequence coverage, as well as higher precision of peptide abundance measurements. We demonstrate HOLSER capabilities of probing structural changes on the scale of specific binding sites for kinase target mapping, individual protein domains for structural mapping of the FKBP-mTOR complex in response to rapamycin, as well as global proteome structure profiling."],"pubmed_title":["High-Ratio Partial Proteolysis with Carrier Proteome (HOLSER) Enables Global Structure Profiling and Site-Resolved Elucidation of Ligand-Protein Interactions."],"pubmed_authors":["Zhang Xuepei X, Gharibi Hassan H, Sokolova Bohdana B, Meng Zhaowei Z, Lyu Hezheng H, Saei Amir Ata AA, Gaetani Massimiliano M, 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 reduced peptide yield variability as well as tandem mass tag multiplexing that includes full digests for enhanced proteome depth and sequence coverage as well as higher precision of peptide abundance measurements. We demonstrate HOLSER capabilities of probing structural changes on the scale of specific binding sites for kinase target mapping, individual protein domains for structural mapping of the FKBP-mTOR complex in response to rapamycin as well as global proteome structure profiling.","dates":{"publication":"2026-09-14","submission":"2026-04-24"},"accession":"PXD077592","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:8655","NEWT:5147","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:2925","NEWT:214053","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:90690","NEWT:1436183","NEWT:4232","NEWT:416348","NEWT:11298","NEWT:7742","NEWT:196627","NEWT:200308","NEWT:242507","NEWT:200302","NEWT:870435","NEWT:9913","NEWT:9915","NEWT:105841","NEWT:2666255","NEWT:999810","NCBITaxon:5693","NEWT:28995","NEWT:1392998","NEWT:380394","NEWT:114796","NEWT:226900","NEWT:1266738","NEWT:231490","NEWT:244704","NEWT:7725","NEWT:9909","NEWT:9902","NEWT:430615","NEWT:563041","NEWT:72664","NEWT:36599","NEWT:41949","NEWT:326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