Abstract: Improved methods of performing proteomic analysis are described wherein single cell samples are placed into nanowells disposed on chips that also contain a booster sample of known peptides. Once the samples are placed, these singles cells are lysed and peptides are extracted. These peptides are then labeled using TMT labels and combined with labeled boosting peptides to form a mixed sample. The mixed sample is then separated using an LC separation system and the separated sample is then passed through a mass spectrometer to acquire data of the peptide characterization data from the separated sample. Various modifications and alterations to the MS acquisition process that enhance the effectiveness of the process are also described.