Trypsin Cleaves Exclusively C-terminal to

Almost all large-scale projects in mass spectrometry-based proteomics use trypsin to convert protein mixtures into more readily analyzable peptide populations. When searching peptide fragmentation spectra against se-quence databases, potentially matching peptide se-quences can be required to conform to tryptic specificity, namely, cleavage exclusively C-terminal to arginine or lysine. In many published reports, however, significant numbers of proteins are identified by non-tryptic pep-tides. Here we use the sub-parts per million mass accu-racy of a new ion trap Fourier transform mass spectrom-eter to achieve more than a 100-fold increased confidence in peptide identification compared with typical ion trap experiments and show that trypsin cleaves solely C-ter-minal to arginine and lysine. We find that non-tryptic pep