{"doi":"10.64898/2026.05.05.721470","title":"Analysis of Confounding Factors in Reactive Cysteine Profiling Reveals Enhanced Chromatin-Protein Association via CDK7 Inhibition by THZ1","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>Recent advances in activity-based proteome profiling (ABPP) have enabled global mapping of cysteine ligandability, uncovering novel biological insights and opportunities for identifying disease vulnerabilities. While both live cell-based and native lysate-based ABPP have been applied, how cysteine ligandability differs between these systems and what factors influence these measurements remain unclear. Building on our previous development of a high-throughput TMT-ABPP workflow for native lysates, here we adapt the protocol for live cells and systematically compare cysteine ligandability across both platforms. Our analysis reveals three major contributors to the discrepancies: in-cellulo cysteine accessibility, protein abundance changes, and protein relocalization. Notably, we highlight that CDK7 inhibitor THZ1 induces substantial protein relocalization and promotes chromatin binding. Together, these results provide a practical framework for ABPP experimental design and data interpretation, supporting more accurate application of ABPP in functional proteomics and drug discovery.</jats:p>","journal":null,"year":null,"id":611594,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1574145,"name":"Shaoxian Li","orcid":null,"position":1,"is_corresponding":false},{"id":515459,"name":"Bohui Li","orcid":null,"position":2,"is_corresponding":false},{"id":1574146,"name":"Daniel M. Richards","orcid":null,"position":3,"is_corresponding":false},{"id":461478,"name":"Kevin Dong","orcid":"0000-0002-2341-8472","position":4,"is_corresponding":false},{"id":491068,"name":"Uthpala Seneviratne","orcid":null,"position":5,"is_corresponding":false},{"id":1574147,"name":"Wankyu Lee","orcid":null,"position":6,"is_corresponding":false},{"id":1574148,"name":"Anthony Iannetta","orcid":null,"position":7,"is_corresponding":false},{"id":1327847,"name":"Hua Xu","orcid":"0000-0002-7401-307X","position":8,"is_corresponding":false},{"id":107041,"name":"Steven P. Gygi","orcid":"0000-0001-7626-0034","position":9,"is_corresponding":false},{"id":228749,"name":"Qing Yu","orcid":"0000-0003-0468-5353","position":10,"is_corresponding":false},{"id":271814,"name":"Ka Yang","orcid":"0000-0001-8937-7397","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Analysis of Confounding Factors in Reactive Cysteine Profiling Reveals Enhanced Chromatin-Protein Association via CDK7 Inhibition by THZ1","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>Recent advances in activity-based proteome profiling (ABPP) have enabled global mapping of cysteine ligandability, uncovering novel biological insights and opportunities for identifying disease vulnerabilities. While both live cell-based and native lysate-based ABPP have been applied, how cysteine ligandability differs between these systems and what factors influence these measurements remain unclear. Building on our previous development of a high-throughput TMT-ABPP workflow for native lysates, here we adapt the protocol for live cells and systematically compare cysteine ligandability across both platforms. Our analysis reveals three major contributors to the discrepancies: in-cellulo cysteine accessibility, protein abundance changes, and protein relocalization. Notably, we highlight that CDK7 inhibitor THZ1 induces substantial protein relocalization and promotes chromatin binding. Together, these results provide a practical framework for ABPP experimental design and data interpretation, supporting more accurate application of ABPP in functional proteomics and drug discovery.</jats:p>","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"42146579","pmcid":null,"openalex_id":"https://openalex.org/W7160549468","authors":[],"funders":[{"funder_name":"","grant_id":"CA282268","title":null},{"funder_name":"","grant_id":"GM67945","title":null},{"funder_name":"NCI NIH HHS","grant_id":"K22 CA282268","title":null}],"total_grants":3,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"green","license":"https://www.biorxiv.org/about/FAQ#license","oa_locations":[{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13174481/","host_type":"repository"},{"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13174481/","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.64898/2026.05.05.721470","host_type":"publisher"},{"url":"https://doi.org/10.64898/2026.05.05.721470","host_type":"repository"},{"url":"https://pubmed.ncbi.nlm.nih.gov/42146579","host_type":"repository"}],"fields_of_study":["Protein Degradation and Inhibitors","Click Chemistry and Applications","Genomics and Chromatin Dynamics"],"mesh_terms":[],"keywords":["Proteome","Cysteine","Proteomics","Profiling (computer programming)","Drug discovery","Workflow"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-01T20:57:45.829990Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}