Mass spectrometry has become the preferred tool for peptide sequencing, but it still has trouble differentiating between the isomeric amino acids leucine and isoleucine. Most MS methods can’t distinguish between them. The methods that can tell the difference produce difficult-to-interpret spectra or are limited to peptides with only one leucine or isoleucine. Albert T. Lebedev of Moscow State University, in Russia, and coworkers overcome these problems with a so-called MS3 method, which they used to sequence frog peptides containing leucine, isoleucine, or both (Anal. Chem. 2014, DOI: 10.1021/ac501200h). The method uses electron-transfer dissociation to cleave N–Cα bonds in multiply protonated peptides. That process results in formation of z ions with an odd number of electrons. Those ions are fragmented again using higher-energy collisions to produce w ions, which are characteristic of the isomeric amino acids. The researchers successfully used the method to sequence six peptides isolated from frog skin secretions, ranging from 15 to 37 amino acids and containing a total of 22 leucine and isoleucine residues. Each peptide contained at least one and as many as seven of the isomeric residues.