{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"submitter":["Chang HY"],"funding":["NIEHS NIH HHS","NIGMS NIH HHS"],"pubmed_abstract":["Isobaric mass tags, such as iTRAQ and TMT, are widely utilized for peptide and protein quantification in multiplex quantitative proteomics. We present TMT-Integrator, a bioinformatics tool for processing quantitation results from TMT and iTRAQ experiments, offering integrative reports at the gene, protein, peptide, and post-translational modification site levels. We demonstrate the versatility of TMT-Integrator using five publicly available TMT datasets: an <i>E. coli</i> dataset with 13 spike-in proteins, the clear cell renal cell carcinoma (ccRCC) whole proteome and phosphopeptide-enriched datasets from the Clinical Proteomic Tumor Analysis Consortium, and two human cell lysate datasets showcasing the latest advances with the Astral instrument and TMT 35-plex reagents. Integrated into th"],"journal":["bioRxiv : the preprint server for biology"],"pagination":["2025.05.27.656447"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12154698"],"repository":["biostudies-literature"],"pubmed_title":["Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform."],"pmcid":["PMC12154698"],"funding_grant_id":["R01 GM094231","U2C ES030164"],"pubmed_authors":["Leprevost FDV","Chang HY","Yu F","Haynes SE","Li R","Wen B","Avtonomov D","Zhang B","Nesvizhskii AI","Deng Y"],"additional_accession":[]},"is_claimable":false,"name":"Analysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.","description":"Isobaric mass tags, such as iTRAQ and TMT, are widely utilized for peptide and protein quantification in multiplex quantitative proteomics. We present TMT-Integrator, a bioinformatics tool for processing quantitation results from TMT and iTRAQ experiments, offering integrative reports at the gene, protein, peptide, and post-translational modification site levels. We demonstrate the versatility of TMT-Integrator using five publicly available TMT datasets: an <i>E. coli</i> dataset with 13 spike-in proteins, the clear cell renal cell carcinoma (ccRCC) whole proteome and phosphopeptide-enriched datasets from the Clinical Proteomic Tumor Analysis Consortium, and two human cell lysate datasets showcasing the latest advances with the Astral instrument and TMT 35-plex reagents. Integrated into th","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 May","modification":"2026-05-23T03:11:00.798Z","creation":"2026-05-23T03:08:07.091Z"},"accession":"S-EPMC12154698","cross_references":{"pubmed":["40501722"],"doi":["10.1101/2025.05.27.656447"]}}