Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences
Background: Peptide identification via tandem mass spectrometry is the basic task of current proteomics research. Due to the complexity of mass spectra, the majority of mass spectra cannot be interpreted at present. The existence of unexpected or unknown protein posttranslational modifications is a major reason.Results: This paper describes an efficient and sequence database-independent approach to detecting abundant post-translational modifications in high-accuracy peptide mass spectra. The approach is based on the observation that the spectra of a modified peptide and its unmodified counterpart are correlated with each other in their peptide masses and retention time. Frequently occurring peptide mass differences in a data set imply possible modifications,while small and consistent retention time differences provide orthogonal supporting evidence.We propose to use a bivariate Gaussian mixture model to discriminate modification-related spectral pairs from random ones. Due to the use of two-dimensional information, accurate modification masses and confident spectral pairs can be determined as well as the quantitative influences of modifications on peptide retention time.Conclusions: Experiments on two glycoprotein data sets demonstrate that our method can effectively detect abundant modifications and spectral pairs. By including the discovered modifications into database search or by propagating peptide assignments between paired spectra, an average of 10% more spectra are interpreted.
Yan Fu Chao Liu Leheng Wang Ruixiang Sun Wen Gao Xiaohong Qian Si-Min He Wei Jia Zhuang Lu Haipeng Wang Zuofei Yuan Hao Chi You Li Liyun Xiu Wenping Wang
Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China Key Lab of Int Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China State Key Laboratory of Proteomics-Beijing Proteome Research Center-Beijing Institute of Radiation M
国际会议
The 7th Asia-Pacific Bioinformatics Conference(第七届亚太生物信息学大会)
北京
英文
568-578
2009-01-01（万方平台首次上网日期，不代表论文的发表时间）