{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Berumen Sanchez G"],"funding":["National Science Foundation Graduate Research Fellowship Program","NIDDK NIH HHS","Vanderbilt Institute for Clinical and Translational Research","Concern Foundation","NCI NIH HHS","NIH HHS"],"pubmed_abstract":["Extracellular vesicles (EVs) are critical mediators of intercellular communication, and valuable sources of biomarkers for diagnostic and therapeutic applications. However, the complexity and heterogeneity of EVs present significant challenges for their proteomic characterization. Major challenges of EV samples include low yield, technical variability, and the need for sensitive and high throughput quantification approaches. In this study, we implement a tandem mass tag (TMT)-based MS workflow for comprehensive, quantitative proteomic profiling of isolated EVs. Through comparison with label-free quantitation (LFQ), we highlight the potential pitfalls and limitations of methodological choices in EV proteomic analyses. Our study integrates standard EV isolation with robust TMT labeling and h"],"journal":["Proteomics"],"pagination":["e70103"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12934204"],"repository":["biostudies-literature"],"pubmed_title":["Proteomics in Practice: A Case Study Highlighting Tandem Mass Tag-Based MS for Quantitative Profiling of Extracellular Vesicles and Application to Irradiated Fibroblasts."],"pmcid":["PMC12934204"],"funding_grant_id":["ConquerCancerNowAward","1937963","V0000039983","R00CA201304","2444112","R00 CA201304","T32DK101003","T32 DK101003"],"pubmed_authors":["Patel P","Berumen Sanchez G","Rafat M","Rose KL"],"additional_accession":[]},"is_claimable":false,"name":"Proteomics in Practice: A Case Study Highlighting Tandem Mass Tag-Based MS for Quantitative Profiling of Extracellular Vesicles and Application to Irradiated Fibroblasts.","description":"Extracellular vesicles (EVs) are critical mediators of intercellular communication, and valuable sources of biomarkers for diagnostic and therapeutic applications. However, the complexity and heterogeneity of EVs present significant challenges for their proteomic characterization. Major challenges of EV samples include low yield, technical variability, and the need for sensitive and high throughput quantification approaches. In this study, we implement a tandem mass tag (TMT)-based MS workflow for comprehensive, quantitative proteomic profiling of isolated EVs. Through comparison with label-free quantitation (LFQ), we highlight the potential pitfalls and limitations of methodological choices in EV proteomic analyses. Our study integrates standard EV isolation with robust TMT labeling and h","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Dec","modification":"2026-07-16T21:34:49.915Z","creation":"2026-07-12T03:09:09.539Z"},"accession":"S-EPMC12934204","cross_references":{"pubmed":["41472394"],"doi":["10.1002/pmic.70103"]}}