A New Scoring Scheme for Peptide Sequence Tagging via Doubly Charged MS/MS Spectra

Peptide sequence tagging (PST) is one of the basic problems in computational proteomics. It is a flexible method which has been widely used in protein identification as well as mapping post-translational modifications (PTM) to peptides. In this work, we present a new scoring scheme for peptide sequence tagging via doubly charged tandem mass spectra. Four public datasets from different types of mass spectrometers (Thermo LTQ-FT, LTQ and LCQ, Waters/Micromass QTOF) are applied to test our scoring scheme and the results are compared with the widely used PST algorithm InsPecT. The results show that our method achieves higher accuracy and better performance than InsPecT. Based on the scoring scheme, we have developed a software tool named TVNovoTag, which is available at http://www.bprc.ac.cn/TVNovoTag/.