Detection of co-eluted peptides using database search methods
Detection of co-eluted peptides using database search methods
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DOI：
10.1186/1745-6150-3-27
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发表时间：
2008-07-02
期刊：
影响因子：
5.5
通讯作者：
Yu, Yi-Kuo
中科院分区：
文献类型：
--
作者：
Alves, Gelio;Ogurtsov, Aleksey Y.;Yu, Yi-Kuo
背景：当前的实验技术，特别是那些应用液相色谱质谱法的技术，已经使高通量蛋白质组学研究成为可能。然而，吞吐量的增加也引起了对识别或量化准确性的担忧。大多数实验程序在给定的 MS 扫描中仅选择几个相对最强的母离子，每个母离子分别进行碎片化 (MS2)，而具有相似色谱保留时间的大多数其他次要共洗脱肽被忽略，并且其信息丢失。 结果：我们通过计算研究了在给定 LC/MS 实验期间通过选择两个或三个最强母离子进行同时碎片化来增强信息检索的可能性。通过叠加多个 MS2 光谱创建一组光谱，每个光谱都可以通过高置信度测试的所有搜索方法进行识别，以模仿共洗脱肽的光谱。生成的卷积光谱用于评估几种数据库搜索方法的能力 - SEQUEST、Mascot、X！ Tandem、OMSSA 和 RAld_DbS - 从共洗脱肽的叠加光谱中识别真正的肽。我们表明，使用这些模拟光谱，所有数据库搜索方法最终都会获得通过使用共洗脱肽的复合光谱识别出的真实肽的数量。公开同行评审：由 Vlad Petyuk（由 Arcady Mushegian 提名）、King Jordan 和 Shaamil Sunyaev 评审。如需完整评论，请访问审稿人评论部分。
Background: Current experimental techniques, especially those applying liquid chromatography mass spectrometry, have made high-throughput proteomic studies possible. The increase in throughput however also raises concerns on the accuracy of identification or quantification. Most experimental procedures select in a given MS scan only a few relatively most intense parent ions, each to be fragmented (MS2) separately, and most other minor co-eluted peptides that have similar chromatographic retention times are ignored and their information lost.Results: We have computationally investigated the possibility of enhancing the information retrieval during a given LC/MS experiment by selecting the two or three most intense parent ions for simultaneous fragmentation. A set of spectra is created via superimposing a number of MS2 spectra, each can be identified by all search methods tested with high confidence, to mimick the spectra of co-eluted peptides. The generated convoluted spectra were used to evaluate the capability of several database search methods - SEQUEST, Mascot, X! Tandem, OMSSA, and RAld_DbS - in identifying true peptides from superimposed spectra of co-eluted peptides. We show that using these simulated spectra, all the database search methods will gain eventually in the number of true peptides identified by using the compound spectra of co-eluted peptides.Open peer review: Reviewed by Vlad Petyuk (nominated by Arcady Mushegian), King Jordan and Shamil Sunyaev. For the full reviews, please go to the Reviewers' comments section.