Increasing confidence in proteomic spectral deconvolution through mass defect

Abstract Motivation Confident deconvolution of proteomic spectra is critical for several applications such as de novo sequencing, cross-linking mass spectrometry and handling chimeric mass spectra. Results In general, all deconvolution algorithms may eventually report mass peaks that are not compatible with the chemical formula of any peptide. We show how to remove these artifacts by considering their mass defects. We introduce Y.A.D.A. 3.0, a fast deconvolution algorithm that can remove peaks with unacceptable mass defects. Our approach is effective for polypeptides with less than 10 kDa, and its essence can be easily incorporated into any deconvolution algorithm. Availability and implementation Y.A.D.A. 3.0 is freely available for academic use at http://patternlabforproteomics.org/yada3. Supplementary information Supplementary information is available at Bioinformatics online.