Isobaric peptide labeling on digital microfluidics for quantitative proteomics of low cell numbers is facilitated by low critical micellar concentration detergents

We developed protocols for isobaric TMT labeling on digital microfluidics (DMF) devices enabling the quantitative proteome analysis of approximately 25 mammalian cells per channel by subsequent bottom-up proteome analysis by LC-MS. This comprised identification of a compatible detergent for digestion, on-chip labeling, and LC-MS. Application of the method in a TMT 6-plex sample analysis enabled the relative quantification 648 proteins (2 unique peptides for quantification) from a total of 125 cell equivalents.