Filtering Methods for Mass Spectrometry-based Peptide Identification Processes

Tandem mass spectrometry (MS/MS) is a powerful tool for identifying peptide sequences. In a typical experiment, incorrect peptide identifications may result due to noise contained in the MS/MS spectra and to the low quality of the spectra. Filtering methods are widely used to remove the noise and improve the quality of the spectra before the subsequent spectra identification process. However, existing filtering methods often use features and empirically assigned weights. These weights may not reflect the reality that the contribution (reflected by weight) of each feature may vary from dataset to dataset. Therefore, filtering methods that can adapt to different datasets have the potential to improve peptide identification results. This thesis proposes two adaptive filtering methods; denoising and quality assessment, both of which improve efficiency and effectiveness of peptide identification. First, the denoising approach employs an adaptive method for picking signal peaks that is more suitable for the datasets of interest. By applying the approach to two tandem mass spectra datasets, about 66% of peaks (likely noise peaks) can be removed. The number of peptides identified later by peptide identification on those datasets increased by 14% and 23%, respectively, compared to previous work (Ding et al., 2009a). Second, the quality assessment method estimates the probabilities of spectra being high quality based on quality assessments of the individual features. The probabilities are estimated by solving a constraint optimization problem. Experimental results on two datasets illustrate that searching only the high-quality tandem spectra determined using this method saves about 56% and 62% of database searching time and loses 9% of high-quality spectra. Finally, the thesis suggests future research directions including feature selection and clustering of peptides