biostudies-literatureCupp-Sutton KANIH NIAIDNIAID NIH HHSOklahoma Center for the Advancement of Science and TechnologyNCI NIH HHSe5187https://www.ebi.ac.uk/biostudies/studies/S-EPMC12649780biostudies-literatureUnknown60(11)Protein function can vary due to changes in primary structure, such as post-translational modification (PTM), truncation, or amino acid replacement, and functional proteomics methods focus on elucidating changes in the function of proteins in biological pathways. Thermal proteome profiling (TPP) is a powerful functional proteomics approach that analyzes the thermal stability of proteins by exposing them to a temperature gradient to facilitate thermal denaturation, followed by analysis of the remaining folded proteins. Current TPP methods, however, utilize bottom-up methods that require protein digestion and can obscure relevant information regarding the structure of the intact proteoform. In this study, we have developed a top-down (TD) TPP approach to study intact proteoform stability as Journal of mass spectrometry : JMSTop-Down Thermal Proteome Profiling (TD-TPP) for Functional Characterization of the Intact Proteoforms in Complex Samples.PMC12649780R01AI141625R01 AI141625U19 AI062629HR23-169R61 CA2979642U19AI062629Cupp-Sutton KAGuo YWu SWelborn TfalseTop-Down Thermal Proteome Profiling (TD-TPP) for Functional Characterization of the Intact Proteoforms in Complex Samples.Protein function can vary due to changes in primary structure, such as post-translational modification (PTM), truncation, or amino acid replacement, and functional proteomics methods focus on elucidating changes in the function of proteins in biological pathways. Thermal proteome profiling (TPP) is a powerful functional proteomics approach that analyzes the thermal stability of proteins by exposing them to a temperature gradient to facilitate thermal denaturation, followed by analysis of the remaining folded proteins. Current TPP methods, however, utilize bottom-up methods that require protein digestion and can obscure relevant information regarding the structure of the intact proteoform. In this study, we have developed a top-down (TD) TPP approach to study intact proteoform stability as 2025-01-01T00:00:00Z2025 Nov2026-06-05T18:46:46.813Z2026-05-20T03:13:33.195ZS-EPMC126497804106915010.1002/jms.5187