{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["24(3)"],"submitter":["Matzanke T"],"pubmed_abstract":["The quantification of proteoforms, i.e., all molecular forms in which proteins can be present, by top-down proteomics provides essential insights into biological processes at the molecular level. Isobaric labeling-based quantification strategies are suitable for multidimensional separation strategies and allow for multiplexing of the samples. Here, we investigated cysteine-directed isobaric labeling by iodoTMT in combination with a gel- and gas-phase fractionation (GeLC-FAIMS-MS) for in-depth quantitative proteoform analysis. We optimized the acquisition workflow (i.e., the FAIMS compensation voltages, isolation windows, acquisition strategy, and fragmentation method) using a two-proteome mix to increase the number of quantified proteoforms and reduce ratio compression. Additionally, we implemented a mass feature-based quantification strategy in the widely used deconvolution algorithm FLASHDeconv, which improves and facilitates data analysis. The optimized iodoTMT GeLC-FAIMS-MS workflow was applied to quantitatively analyze the proteome of <i>Escherichia coli</i> grown under glucose or acetate as the sole carbon source, resulting in the identification of 726 differentially abundant proteoforms."],"journal":["Journal of proteome research"],"pagination":["1470-1480"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11894657"],"repository":["biostudies-literature"],"pubmed_title":["Cysteine-Directed Isobaric Labeling Combined with GeLC-FAIMS-MS for Quantitative Top-Down Proteomics."],"pmcid":["PMC11894657"],"pubmed_authors":["Tholey A","Takemori N","Kohlbacher O","Takemori A","Matzanke T","Jeong K","Kaulich PT"],"additional_accession":[]},"is_claimable":false,"name":"Cysteine-Directed Isobaric Labeling Combined with GeLC-FAIMS-MS for Quantitative Top-Down Proteomics.","description":"The quantification of proteoforms, i.e., all molecular forms in which proteins can be present, by top-down proteomics provides essential insights into biological processes at the molecular level. Isobaric labeling-based quantification strategies are suitable for multidimensional separation strategies and allow for multiplexing of the samples. Here, we investigated cysteine-directed isobaric labeling by iodoTMT in combination with a gel- and gas-phase fractionation (GeLC-FAIMS-MS) for in-depth quantitative proteoform analysis. We optimized the acquisition workflow (i.e., the FAIMS compensation voltages, isolation windows, acquisition strategy, and fragmentation method) using a two-proteome mix to increase the number of quantified proteoforms and reduce ratio compression. Additionally, we implemented a mass feature-based quantification strategy in the widely used deconvolution algorithm FLASHDeconv, which improves and facilitates data analysis. The optimized iodoTMT GeLC-FAIMS-MS workflow was applied to quantitatively analyze the proteome of <i>Escherichia coli</i> grown under glucose or acetate as the sole carbon source, resulting in the identification of 726 differentially abundant proteoforms.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Mar","modification":"2026-06-02T00:01:25.293Z","creation":"2025-04-04T13:11:08.353Z"},"accession":"S-EPMC11894657","cross_references":{"pubmed":["39885717"],"doi":["10.1021/acs.jproteome.4c00835"]}}