biostudies-literatureUnknownChang HYNIEHS NIH HHSNIGMS NIH HHSIsobaric 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 thbioRxiv : the preprint server for biology2025.05.27.656447https://www.ebi.ac.uk/biostudies/studies/S-EPMC12154698biostudies-literatureAnalysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.PMC12154698R01 GM094231U2C ES030164Leprevost FDVChang HYYu FHaynes SELi RWen BAvtonomov DZhang BNesvizhskii AIDeng YfalseAnalysis of isobaric quantitative proteomic data using TMT-Integrator and FragPipe computational platform.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 th2025-01-01T00:00:00Z2025 May2026-05-23T03:11:00.798Z2026-05-23T03:08:07.091ZS-EPMC121546984050172210.1101/2025.05.27.656447