pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization

5 years ago

pSite: Amino Acid Confidence Evaluation for Quality Control of De Novo Peptide Sequencing and Modification Site Localization

Wen-Feng Zeng, Hao Chi, Zhen-Lin Chen, Chao Liu, Rui-Min Wang, Xiu-Nan Niu, Si-Min He, Zhao-Wei Wang, Wen-Jing Zhou, Hao Yang

MS-based de novo peptide sequencing has been improved remarkably with significant development of mass-spectrometry and computational approaches but still lacks quality-control methods. Here we proposed a novel algorithm pSite to evaluate the confidence of each amino acid rather than the full-length peptides obtained by de novo peptide sequencing. A semi-supervised learning approach was used to discriminate correct amino acids from random one; then, an expectation-maximization algorithm was used to adaptively control the false amino-acid rate (FAR). On three test data sets, pSite recalled 86% more amino acids on average than PEAKS at the FAR of 5%.

Publisher URL: http://dx.doi.org/10.1021/acs.jproteome.7b00428

DOI: 10.1021/acs.jproteome.7b00428