We removed PSMs from the data table identified as part of a contaminating protein from the sample preparation steps or being highly expressed in most cells. We then reduced the variable columns of the Protein Discoverer result table and retained only those referring to the mass spectrometry TMT run and to the isolation interference percentage in addition to the PSM expression values. We next filtered the PSMs with respect to isolation interference and retained only those with less than 70% of spectrum overlap. We experimented with several interference thresholds and settled on a rather high value to increase the number of PSMS without adding noise to the data. We plotted the total amount of abundance for each TMT run and each channel in a bar plot and removed cell without abundances.