A spectral clustering approach to MS/MS identification of post-translational modifications.

Unidentified tandem mass spectra typically represent 50-90% of the spectra acquired in proteomics studies. This manuscript describes a novel algorithm, "Bonanza", for clustering spectra without knowledge of peptide or protein identifications. Further analysis leverages existing peptide identifications to infer related, likely valid identifications. Significantly more spectra can be identified with this approach, including spectra with unexpected potential modifications or amino-acid substitutions.