biostudies-literatureKim JBundesministerium f?r Bildung und ForschungDeutsche ForschungsgemeinschaftEuropean Proteomics Infrastructure Consortium providing accessHORIZON EUROPE Marie Sklodowska-Curie Actions17227-17234https://www.ebi.ac.uk/biostudies/studies/S-EPMC11525931biostudies-literatureUnknown96(43)Accurate quantification of individual proteoforms is a crucial step in identifying proteome-wide alterations in different biological conditions. Intact proteoforms have been analyzed predominantly by liquid chromatography-mass spectrometry (LC-MS)-based top-down proteomics (TDP) and quantified primarily by the label-free quantification (LFQ) method, as it requires no additional costly labeling. In TDP, due to frequent coelution and complex signal structures, overlapping signals deriving from multiple proteoforms complicate accurate quantification. Here, we introduce FLASHQuant for MS1-level LFQ analysis in TDP, which is capable of automatically resolving and quantifying coeluting proteoforms. In benchmark tests performed with both spike-in proteins and proteome-level mixture data sets, FLAAnalytical chemistryFLASHQuant: A Fast Algorithm for Proteoform Quantification in Top-Down Proteomics.PMC11525931W-de.NBI-022823839765502-A4BTholey AKohlbacher OKim JWinkels KJeong KKaulich PTfalseFLASHQuant: A Fast Algorithm for Proteoform Quantification in Top-Down Proteomics.Accurate quantification of individual proteoforms is a crucial step in identifying proteome-wide alterations in different biological conditions. Intact proteoforms have been analyzed predominantly by liquid chromatography-mass spectrometry (LC-MS)-based top-down proteomics (TDP) and quantified primarily by the label-free quantification (LFQ) method, as it requires no additional costly labeling. In TDP, due to frequent coelution and complex signal structures, overlapping signals deriving from multiple proteoforms complicate accurate quantification. Here, we introduce FLASHQuant for MS1-level LFQ analysis in TDP, which is capable of automatically resolving and quantifying coeluting proteoforms. In benchmark tests performed with both spike-in proteins and proteome-level mixture data sets, FLA2024-01-01T00:00:00Z2024 Oct2025-04-04T01:02:19.598Z2025-04-04T01:02:19.598ZS-EPMC115259313942429010.1021/acs.analchem.4c03117