An integrated landscape of mRNA and protein isoforms [PacBio]

On the one hand, standard shotgun (that is, bottom-up) proteomics involves digestion of proteins into peptides. While this approach identifies many proteins, it results in a loss of isoform information.

On the other hand, mass spectrometric analysis of intact proteins (that is, top-down proteomics) distinguishes protein isoforms but only covers a small subset of the proteome. We developed peptide correlation profiling (PepCP) as a method to obtain protein-level information from peptide-centric (that is, bottom-up proteomic) data: First, proteins are fractionated by SDS-PAGE to polypeptides of different length. Second, individual protein fractions are digested into peptides.