Assessing data quality of peptide mass spectra obtained by quadrupole ion trap mass spectrometry.

An algorithm is introduced to assess spectral quality for peptide CID spectra acquired by a quadrupole ion trap mass spectrometer. The method employs a quadratic discriminant function calibrated with manually classified 'bad' and 'good' quality spectra, producing a single 'spectral quality' score. Many spectra examined that do not have significant matches are assessed to have good spectral quality, indicating that advances in search methods may yield substantial improvements in results.