Universal metrics for quality assessment of protein identifications by mass spectrometry

Increasing numbers of large proteomic datasets are becoming available. As attempts are made to interpret these datasets and integrate them with other forms of genomic data, researchers are becoming more aware of the importance of data quality with respect to protein identification. We present three simple and universal metrics that describe different aspects of the quality of protein identifications by peptide mass fingerprinting. Hit ratio gives an indication of the signal-to-noise ratio in a mass spectrum, mass coverage measures the amount of protein sequence matched, and excess of limit-digested peptides reflects the completeness of the digestion that precedes the peptide mass fingerprinting. Receiver-operating characteristic plots show that the novel metric, excess of limit-digested peptides, can discriminate between correct and random matches more accurately than search score when validating the results from a state-of-the-art protein identification software system (Mascot) especially when combined with the two other metrics, hit ratio and mass coverage. Recommendations are made regarding the use of the metrics when reporting protein identification experiments.