Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences
文献类型：期刊论文
| 作者 | Lu,Zhuang2; Wang,Leheng3; Liu,Chao3; Wang,Wenping3; Xiu,Liyun3; Li,You3; Chi,Hao3; Yuan,Zuofei3; Wang,Haipeng3; Jia,Wei2 |
| 刊名 | BMC Bioinformatics
 |
| 出版日期 | 2009-01-30 |
| 卷号 | 10期号:Suppl 1 |
| ISSN号 | 1471-2105 |
| DOI | 10.1186/1471-2105-10-S1-S50 |
| 英文摘要 | AbstractBackgroundPeptide 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 post-translational modifications is a major reason.ResultsThis 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.ConclusionExperiments 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. |
| 语种 | 英语 |
| WOS记录号 | BMC:10.1186/1471-2105-10-S1-S50 |
| 出版者 | BioMed Central |
| 源URL | [http://119.78.100.204/handle/2XEOYT63/3958]  |
| 专题 | 中国科学院计算技术研究所期刊论文_2009年英文 |
| 通讯作者 | Fu,Yan; He,Si-Min; Qian,Xiaohong |
| 作者单位 | 1.Chinese Academy of Sciences; Key Lab of Intelligent Information Processing 2.State Key Laboratory of Proteomics-Beijing Proteome Research Center-Beijing Institute of Radiation Medicine 3.Chinese Academy of Sciences; Institute of Computing Technology |
| 推荐引用方式 GB/T 7714 | Lu,Zhuang,Wang,Leheng,Liu,Chao,et al. Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences[J]. BMC Bioinformatics,2009,10(Suppl 1). |
| APA | Lu,Zhuang.,Wang,Leheng.,Liu,Chao.,Wang,Wenping.,Xiu,Liyun.,...&Sun,Ruixiang.(2009).Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences.BMC Bioinformatics,10(Suppl 1). |
| MLA | Lu,Zhuang,et al."Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences".BMC Bioinformatics 10.Suppl 1(2009). |
入库方式： OAI收割
来源：计算技术研究所
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