Isobaric mass tagging (e.g., TMT) has become a common technique in mass spectrometry for relative quantification of proteins. However, there are a couple of factors that impede accurate quantification of complex proteomic samples. One of these factors is co-isolation of peptides, which leads to systematic under/overestimation of quantitative ratios of the isobaric tags [2]. Co-isolation interference has been addressed using various kinds of approaches, such as using MS³ experiments [3]. Due to the fast acquisition speed and efficient quadrupole isolation the Q-Exactive Plus/Q-Exactive HF can be used to address some of these challenges. The effect of several parameters (isolation window, normalized collision energy (NCE), source fragmentation, and others) on the protein quantification accuracy and precision is discussed.