TMT quantitative proteomics

TMT quantification is performed by measuring the intensities of fragment reporter ions released from the labels in the tandem MS mode (MS2) during peptide fragmentation. Precursor ions are selected in the full scan mode (MS1) to be fragmented. Since ion selection step reduces the noise levels, it is advantageous. Ideally, only one selected precursor ion is fragmented during the precursor ion fragmentation. However, it is common that other precursor ions are caught within the specified m/z window and are fragmented together with the selected precursor in practice. This is precursor co-isolation or mixing. Isobaric Labelling works best with mass-spectrometers which allow MS3-level quantitation such as Thermo’s Fusion Orbitraps. The additional filtering step allows almost complete correction of co-isolation caused by contamination of MS1 precursors.