Protein identification using next-generation protein sequencing of in-gel digested proteins

Western blot is one of the most widely used methods for protein identification but achieving reliable and reproducible results depends on quality antibodies with validated specificity for the target protein. Furthermore, differences in amino acid sequences and isoforms cannot be easily differentiated by western blot if the size of the protein is similar. To overcome these limitations, non-antibody-based approaches are highly desired. In this application note, Quantum-Si describes an in-gel protein digestion and peptide extraction procedure compatible with Quantum-Si’s library preparation and protein sequencing workflows. This method can be used for the separation and enrichment of single proteins from complex mixtures using SDS-PAGE, followed by their identification on Quantum-Si’s Platinum^® next-generation protein sequencing instrument.