串联质谱谱库搜索鉴定技术综述

doi:10.3969/j.issn.1000-3428.2012.07.088

计算机工程 ›› 2012, Vol. 38 ›› Issue (7): 269-272. doi: 10.3969/j.issn.1000-3428.2012.07.088

串联质谱谱库搜索鉴定技术综述

王耀君^1,2，孙世伟²，卜东波²，刘金刚¹

(1. 首都师范大学计算机科学联合研究院，北京 100048；2. 中国科学院计算技术研究所计算生物研究组，北京 100190)

收稿日期:2011-08-17 出版日期:2012-04-05 发布日期:2012-04-05
作者简介:王耀君(1985－)，男，硕士，主研方向：计算生物学，谱库搜索技术；孙世伟、卜东波、刘金刚，博士
基金资助:
国家自然科学基金资助项目(30800189)；北京市自然科学基金资助项目(5102029)

Survey on Spectrum Library Search Identification Technology for Tandem Mass Spectra

WANG Yao-jun ^1,2, SUN Shi-wei ², BU Dong-bo ², LIU Jin-gang ¹

(1. Join Faculty of Computer Scientific Research, Capital Normal University, Beijing 100048, China; 2. Bioinformatics Group, Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China)

Received:2011-08-17 Online:2012-04-05 Published:2012-04-05

摘要/Abstract

摘要： 介绍蛋白质质谱鉴定领域的串联质谱谱库搜索技术，分析谱库搜索技术的基本原理，从多个角度阐述当前主流的谱库搜索方法，并对其优缺点进行比较，针对目前蛋白质质谱鉴定技术所存在的优缺点，设计其改进思路，论述目前谱库搜索技术所面临的问题以及未来的研究趋势。

关键词: 蛋白质鉴定, 串联质谱, 谱库搜索, 质谱鉴定

Abstract: The emerging approach of tandem mass spectra spectrum library searching in peptide identifications field is introduced. The basic principles of spectrum library building and searching are discussed. The review summarizes populate methods of spectrum library searching from different views, describes its advantages and limitations and provides a primer for researchers with interests in adopting this new approach for data analysis. The future outlook on the evolution and utility of spectrum libraries is also discussed and some optional cut-in points for study are supposed.

Key words: protein identification, tandem mass spectra, spectrum library search, mass spectrometry

中图分类号:

TP311.52

王耀君, 孙世伟, 卜东波, 刘金刚. 串联质谱谱库搜索鉴定技术综述[J]. 计算机工程, 2012, 38(7): 269-272.

WANG Yao-Jun, SUN Shi-Wei, BO Dong-Bei, LIU Jin-Gang. Survey on Spectrum Library Search Identification Technology for Tandem Mass Spectra[J]. Computer Engineering, 2012, 38(7): 269-272.

http://www.ecice06.com/CN/Y2012/V38/I7/269

参考文献

[1] Sadygov R G, Cociorva D, Yates J R. Large-scale Database Searching Using Tandem Mass Spectra: Looking up the Answer in the Back of the Book[J]. Nature Methods, 2004, 1(3): 195-202.
[2] 邵明芝, 徐云, 王颖, 等. 基于串联质谱的快速肽段鉴定算法[J]. 计算机工程, 2010, 36(18): 214-216.
[3] 乔彦涛, 缪佳铮, 孙世伟, 等. 串联质谱的蛋白质序列鉴定技术综述[J]. 计算机科学与探索, 2010, 4(2): 97-107.
[4] Lam H, Deutsch E W, Eddes J S, et al. Building Consensus Spectral Libraries for Peptide Identification in Proteomics[J]. Nature Methods, 2008, 5(10): 873-875.
[5] Beavis R C, Craig R, Cortens J C, et al. Using Annotated Peptide Mass Spectrum Libraries for Protein Identification[J]. Journal of Proteome Research, 2006, 5(8): 1843-1849.
[6] Wu Zhan, Lajoie G, Ma Bin. MSDash: Mass Spectrometry Database and Search[J]. Computational Systems Bioinformatics/ Life Sciences Society Computational Systems Bioinformatics Conference, 2008, 7(1): 63-71.
[7] Maccoss M J, Frewen B E, Merrihew G E, et al. Analysis of Peptide MS/MS Spectra from Large-scale Proteomics Experiments Using Spectrum Libraries[J]. Analytical Chemistry, 2006, 78(16): 5678-5684.
[8] Stein S E, Scott D R. Optimization and Testing of Mass-spectral Library Search Algorithms for Compound Identification[J]. Journal of the American Society for Mass Spectrometry, 1994, 5(9): 859-866.
[9] Yates J R, Morgan S F, Gatlin C L, et al. Method to Compare Collision-induced Dissociation Spectra of Peptides: Potential for Library Searching and Subtractive Analysis[J]. Analytical Chemistry, 1998, 70(17): 3557-3565.
[10] Bandeira N, Tsur D, Frank A, et al. Protein Identification by Spectral Networks Analysis[EB/OL]. (2010-11-21). http://www. springerprotocols.com/Abstract/doi/10.1007/978-1-60761-977-2_11.
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