biostudies-literatureZhang YGerman Tuberous Sclerosis FoundationEuropean Respiratory SocietyDeutsche ForschungsgemeinschaftRijksuniversiteit GroningenStichting TSC FondsAmt der Tiroler LandesregierungDutch Research Council (NWO)the PARC partnership which has received funding from the European Union's Horizon Europe Research and Innovation ProgrammeEuropean CommissionUniversit??t Innsbruck10893-10906https://www.ebi.ac.uk/biostudies/studies/S-EPMC9366746biostudies-literatureUnknown94(31)With increasing sensitivity and accuracy in mass spectrometry, the tumor phosphoproteome is getting into reach. However, the selection of quantitation techniques best-suited to the biomedical question and diagnostic requirements remains a trial and error decision as no study has directly compared their performance for tumor tissue phosphoproteomics. We compared label-free quantification (LFQ), spike-in-SILAC (stable isotope labeling by amino acids in cell culture), and tandem mass tag (TMT) isobaric tandem mass tags technology for quantitative phosphosite profiling in tumor tissue. Compared to the classic SILAC method, spike-in-SILAC is not limited to cell culture analysis, making it suitable for quantitative analysis of tumor tissue samples. TMT offered the lowest accuracy and the highestAnalytical chemistryComparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics.PMC9366746INST 337/16-1INST 337/15-1184.034.01910105701431682618903812616R3201703-00121754688INST 152/837-1TH 1358/3- 1Pfander PBischoff RHorvatovich PLOpitz CASchluter HKoncarevic SThedieck KZhang YKwiatkowski MDreyer BGovorukhina NHeberle AMKrisp CfalseComparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics.With increasing sensitivity and accuracy in mass spectrometry, the tumor phosphoproteome is getting into reach. However, the selection of quantitation techniques best-suited to the biomedical question and diagnostic requirements remains a trial and error decision as no study has directly compared their performance for tumor tissue phosphoproteomics. We compared label-free quantification (LFQ), spike-in-SILAC (stable isotope labeling by amino acids in cell culture), and tandem mass tag (TMT) isobaric tandem mass tags technology for quantitative phosphosite profiling in tumor tissue. Compared to the classic SILAC method, spike-in-SILAC is not limited to cell culture analysis, making it suitable for quantitative analysis of tumor tissue samples. TMT offered the lowest accuracy and the highest2022-01-01T00:00:00Z2022 Aug2026-05-09T19:29:20.868Z2025-02-19T03:23:53.206ZS-EPMC93667463588073310.1021/acs.analchem.2c01036