Integrating Carbamylation and Ultraviolet Photodissociation Mass Spectrometry for Middle-Down Proteomics

The most popular bottom-up proteomics workflow uses trypsin to enzymatically cleave proteins C-terminal to lysine and arginine residues prior to LCMS/MS analysis of the resulting peptides. The high frequency of these residues generates short peptides, some of which are too small or uninformative for optimal analysis and which potentially contribute to gaps in sequence coverage of proteins. Analysis of larger peptides, termed "middle-down", has the potential to span greater sections of protein sequences if the larger peptides are adequately characterized based on their fragmentation patterns. We describe a strategy to generate larger peptides in conjunction with successful characterization by ultraviolet photodissociation (UVPD) for MS/MS analysis in a middle-down workflow, as demonstrated for proteins from E. coli lysates. The larger peptides are produced via modification of lysine residues by carbamylation of proteins. Carbamylation of proteins followed by tryptic digestion produced peptides similar to those expected from Arg-C proteolysis, yet with fewer missed and nonspecific cleavages. UVPD provides excellent sequence coverage of the larger peptides that are often less well characterized by traditional collision-based activation methods.