{"doi":"10.7554/elife.58783","title":"FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data","abstract":"Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without knowledge of the types of modifications involved. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.","journal":"eLife","year":2020,"id":110188,"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":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9512,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":525032,"name":"Konstantin Kahnert","orcid":"0000-0002-8454-4894","position":1,"is_corresponding":false},{"id":109112,"name":"Jan Muntel","orcid":"0000-0003-2320-5829","position":2,"is_corresponding":false},{"id":525033,"name":"Ruchi Chauhan","orcid":"0000-0002-6921-6112","position":3,"is_corresponding":false},{"id":525034,"name":"Bernhard Y. Renard","orcid":"0000-0003-4589-9809","position":4,"is_corresponding":false},{"id":109120,"name":"Judith A. Steen","orcid":"0000-0002-8167-0772","position":5,"is_corresponding":false},{"id":109119,"name":"Hanno Steen","orcid":"0000-0003-0179-6648","position":6,"is_corresponding":false},{"id":43281,"name":"Christoph N. Schlaffner","orcid":"0000-0003-2717-3406","position":0,"is_corresponding":true}],"reference_count":47,"raw_metadata":null,"created_at":"2026-07-18T23:12:57.988348Z","pmid":"33284109","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":[]}