Sun Wei, Zhang Ling, Yang Ruifeng, Shao Chen, Zhang Zhengguo, Gao Youhe
Proteomics Research Center, Department of Physiology and Pathophysiology, School of Basic Medicine Peking Union Medical College, Beijing, PR China.
Rapid Commun Mass Spectrom. 2009 Jan;23(1):109-18. doi: 10.1002/rcm.3851.
Peptide retention time (RT) is independent of tandem mass spectrometry (MS/MS) parameters and can be combined with MS/MS information to enhance peptide identification. In this paper, we utilized peptide empirical RT and MS/MS for peptide identification. This new approach resulted in the construction of an Empirical Peptide Retention Time Database (EPRTD) based on peptides showing a false-positive rate (FPR) <or=1%, detected in several liquid chromatography (LC)/MS/MS analyses. In subsequent experiments, the RT of peptides with FPR >1% was compared with empirical data derived from the EPRTD. If the experimental RT was within a specified time range of the empirical value, the corresponding MS/MS spectra were accepted as positive. Application of the EPRTD approach to simple samples (known protein mixtures) and complex samples (human urinary proteome) revealed that this method could significantly enhance peptide identification without compromising the associated confidence levels. Further analysis indicated that the EPRTD approach could improve low-abundance peptides and with the expansion of the EPRTD the number of peptide identifications will be increased. This approach is suitable for large-scale clinical proteomics research, in which tens of LC/MS/MS analyses are run for different samples with similar components.
肽保留时间（RT）独立于串联质谱（MS/MS）参数，并且可以与MS/MS信息相结合以增强肽的鉴定。在本文中，我们利用肽经验保留时间和MS/MS进行肽的鉴定。这种新方法导致构建了一个基于在多次液相色谱（LC）/ MS/MS分析中检测到的假阳性率（FPR）≤1%的肽的经验肽保留时间数据库（EPRTD）。在随后的实验中，将FPR>1%的肽的保留时间与从EPRTD获得的经验数据进行比较。如果实验保留时间在经验值的指定时间范围内，则相应的MS/MS谱被接受为阳性。将EPRTD方法应用于简单样品（已知蛋白质混合物）和复杂样品（人尿蛋白质组）表明，该方法可以在不影响相关置信水平的情况下显著增强肽的鉴定。进一步分析表明，EPRTD方法可以改善低丰度肽，并且随着EPRTD的扩展，肽鉴定的数量将会增加。这种方法适用于大规模临床蛋白质组学研究，其中针对具有相似成分的不同样品进行数十次LC/MS/MS分析。
