This new study at JPR is great -- and introduces a promising alternative to traditional enzymatic digestion!
In theory, ArgC is a great enzyme for shotgun proteomics. If you only cleave at the R residues and skip the lysines, we're going to have half the number of peptides floating around. Sure, the peptide chains will be longer, in general, but with normalized collision energy like the ones that are automatically working in the background of today's instruments -- this really isn't going to be a problem.
There are two problems with ArgC -- it is expensive (relative to sequencing grade trypsin...which used to be pretty expensive itself...though...only us old guys remember that...) and, honestly, ArgC has some specificity issues
Solution from this group? Why don't we just block the lysines!?!? They chemically modify the lysines in an E.coli digest and then digest with trypsin -- and it works! They get cheap digestion that ends up looking better than any ArgC digestion I've ever done.
Super interesting note here for us nerds -- they do their peptide mapping with a MALDI-Orbitrap XL! There are so few of these around (2 in Baltimore...which may be more than any city in the world!) and it always makes me happy to see one of these awesome things in use -- especially for proteomics.