Figure 3. decoMS2 applied to amino acid standards.

Amino acid standards were mixed and analyzed by LC/MS², using a 9 Da MS² isolation window. Because the amino acid standards were inadequately separated, each of their MS² spectra were contaminated by additional precursors in the collision cell. (a) The experimental MS² spectra for 4 representative amino acids are shown on the top of each plot. The standard MS² spectra for each of these amino acids as obtained from pure model compounds is shown on the bottom. Fragments that match in the 2 spectra are colored black, while fragments that do not match are colored red. (b) After the application of decoMS2, the top experimental MS² spectra of each amino acid are highly consistent with the MS² spectra from their respective amino acid standards.