Infrared spectroscopy of fragments from doubly protonated tryptic peptides.

Most proteins in proteomics are identified from tandem mass spectra of doubly protonated tryptic peptides. Statistical studies indicate that these spectra fall into two distinct classes. IR spectroscopy experiments and DFT calculations performed on model b(2) ions show that peptides producing Class I spectra form protonated oxazolone ions (see figure) and not protonated diketopiperazines as proposed elsewhere.