一种基于iSRM策略的蛋白质组质谱数据分析工具

张伟, 卫军营, 贾婷, 徐长明, 张纪阳, 朱云平, 钱小红, 张养军, 谢红卫

张伟, 卫军营, 贾婷, 徐长明, 张纪阳, 朱云平, 钱小红, 张养军, 谢红卫. 一种基于iSRM策略的蛋白质组质谱数据分析工具[J]. 质谱学报, 2013, 34(1): 15-22. DOI: 10.7538/zpxb.2013.34.01.0015
引用本文: 张伟, 卫军营, 贾婷, 徐长明, 张纪阳, 朱云平, 钱小红, 张养军, 谢红卫. 一种基于iSRM策略的蛋白质组质谱数据分析工具[J]. 质谱学报, 2013, 34(1): 15-22. DOI: 10.7538/zpxb.2013.34.01.0015
ZHANG Wei, WEI Jun-ying, JIA Ting, XU Chang-ming, ZHANG Ji-yang, ZHU Yun-ping, QIAN Xiao-hong, ZHANG Yang-jun, XIE Hong-wei. A Data Processing Tool for Mass Spectrometry Data from iSRM Strategy in Proteomics[J]. Journal of Chinese Mass Spectrometry Society, 2013, 34(1): 15-22. DOI: 10.7538/zpxb.2013.34.01.0015
Citation: ZHANG Wei, WEI Jun-ying, JIA Ting, XU Chang-ming, ZHANG Ji-yang, ZHU Yun-ping, QIAN Xiao-hong, ZHANG Yang-jun, XIE Hong-wei. A Data Processing Tool for Mass Spectrometry Data from iSRM Strategy in Proteomics[J]. Journal of Chinese Mass Spectrometry Society, 2013, 34(1): 15-22. DOI: 10.7538/zpxb.2013.34.01.0015
张伟, 卫军营, 贾婷, 徐长明, 张纪阳, 朱云平, 钱小红, 张养军, 谢红卫. 一种基于iSRM策略的蛋白质组质谱数据分析工具[J]. 质谱学报, 2013, 34(1): 15-22. CSTR: 32365.14.zpxb.2013.34.01.0015
引用本文: 张伟, 卫军营, 贾婷, 徐长明, 张纪阳, 朱云平, 钱小红, 张养军, 谢红卫. 一种基于iSRM策略的蛋白质组质谱数据分析工具[J]. 质谱学报, 2013, 34(1): 15-22. CSTR: 32365.14.zpxb.2013.34.01.0015
ZHANG Wei, WEI Jun-ying, JIA Ting, XU Chang-ming, ZHANG Ji-yang, ZHU Yun-ping, QIAN Xiao-hong, ZHANG Yang-jun, XIE Hong-wei. A Data Processing Tool for Mass Spectrometry Data from iSRM Strategy in Proteomics[J]. Journal of Chinese Mass Spectrometry Society, 2013, 34(1): 15-22. CSTR: 32365.14.zpxb.2013.34.01.0015
Citation: ZHANG Wei, WEI Jun-ying, JIA Ting, XU Chang-ming, ZHANG Ji-yang, ZHU Yun-ping, QIAN Xiao-hong, ZHANG Yang-jun, XIE Hong-wei. A Data Processing Tool for Mass Spectrometry Data from iSRM Strategy in Proteomics[J]. Journal of Chinese Mass Spectrometry Society, 2013, 34(1): 15-22. CSTR: 32365.14.zpxb.2013.34.01.0015

一种基于iSRM策略的蛋白质组质谱数据分析工具

A Data Processing Tool for Mass Spectrometry Data from iSRM Strategy in Proteomics

  • 摘要: 由于重复性好、定量精度高,基于质谱的选择反应监测(SRM)技术在蛋白质定量分析中的应用越来越广泛。智能选择反应监测(iSRM)是一种新型的SRM实验策略。针对该策略产生的质谱数据,开发了一个肽段定量信息提取工具——iSQuant。该工具使用MATLAB脚本语言编写,简便易用。利用重复实验数据和标准实验数据对iSQuant的性能评估表明,iSQuant具有优越的可重复性能,定量结果和理论丰度线性度很高。
    Abstract: In proteomics research, selected reaction monitoring (SRM) technology based on mass spectrometry has been widely applied in the protein quantitative analysis because of its high reproducibility and accuracy. Intelligent selected reaction monitoring (iSRM) technology is a new SRM experimental strategy. In order to process the mass spectrometry data produced by iSRM, a peptide quantitative information extraction tool called iSQuant is developed. iSQuant is written with MATLAB programming language, and thus is convenient and user-friendly. Finally, a replicated dataset and a standard dataset are used to evaluate the performances of iSQuant. The results show that iSQuant has superior reproducibility and linearity.
  • [1] AEBERSOLD R, MANN M. Mass spectrometrybased proteomics [J]. Nature, 2003, 422(6 928): 198-207.
    [2] YATES J R, RUSE C I, Nakorchevsky a proteo-mics by mass spectrometry: Approaches, advances, and applications [J]. Annu Rev Biomed Eng, 2009, 11(1): 49-79.
    [3] 张伟, 张纪阳, 刘辉, 等. 蛋白质质谱分析的无标记定量算法研究进展[J]. 生物化学与生物物理进展, 2011, 38(6): 506-518.
    [4] LANGE V, PICOTTI P, DOMON B, et al. Selected reaction monitoring for quantitative proteomics: A tutorial [J]. Mol Syst Biol, 2008, 4(10): 222-235.
    [5] PICOTTI P, AEBERSOLD R. Selected reaction monitoring-based proteomics: Workflows, potential, pitfalls and future directions [J]. Nat Methods, 2012, 9(6): 555-566.
    [6] BR-NSTRUP M. Absolute quantification strategies in proteomics based on mass spectrometry[J]. Expert Rev Proteomics, 2004, 1(4): 503-512.
    [7] YOST R A, ENKE C G. Triple quadrupole mass spectrometry for direct mixture analysis and structural elucidation[J]. Anal Chem, 1979, 51(12): 1251-1264.
    [8] YOST R A, ENKE C G. Selected ion fragmentation with a tandem quadrupole mass spectrometer[J]. J Am Chem Soc, 1978, 100(7): 2274-2275.
    [9] LIN D, TABB D L, YATES J R. Large-scale protein identification using mass spectrometry [J]. Biochim Biophys Acta, 2003, 1 646(1/2): 1-10.
    [10] KIYONAMI R, SCHOEN A, PRAKASH A, et al.Increased selectivity, analytical precision, and throughput in targeted proteomics [J]. Mol Cell Proteomics, 2011, 10(2): M110002931.
    [11] REITER L, RINNER O, PICOTTI P, et al. mP-rophet: Automated data processing and statistical validation for largescale SRM experiments [J]. Nat Methods, 2011, 8(5): 430-435.
    [12] MACLEAN B, TOMAZELA D M, SHULMAN N, et al. Skyline: An open source document editor for creating and analyzing targeted proteomics experiments [J]. Bioinformatics, 2010, 26(7): 966-968.
    [13] BRUSNIAK M Y, KWOK S T, CHRISTIANSEN M, et al. ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry [J]. BMC Bioinformatics, 2011, 12: 78.
    [14] LANGE V, MALMSTROM JA, DIDION J, et al.Targeted quantitative analysis of streptococcus pyogenes virulence factors by multiple reaction monitoring [J]. Mol Cell Proteomics, 2008, 7(8): 1489-1500.
    [15] MARTIN D B, HOLZMAN T, MAY D, et al. MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments [J]. Mol Cell Proteomics, 2008, 7(11): 2270-2278.
    [16] 卫军营, 张养军, 赵炎, 等. 质谱智能选择反应检测用于蛋白质绝对定量中母离子对确证的方法研究[J]. 分析化学, 2012, 40(1): 59-65.
    [17] SONG Y, HAO Y, SUN A, et al. Sample preparation project for the subcellular proteome of mouse liver [J]. Proteomics, 2006, 19(6): 5269-6277.
    [18] WANG G, WU W W, ZENG W, et al. Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes [J]. J Proteome Res, 2006, 5(5): 1214-1223.
    [19] COLAERT N, VANDEKERCKHOVE J, GEVAERT K, et al. A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision [J]. Proteomics, 2011, 11(6): 1110-1113.
    [20] AMERICA A H, CORDEWENER J H, Comparative LCMS: A landscape of peaks and valleys [J]. Proteomics, 2008, 8(4): 731-749.
    [21] VALOT B, LANGELLA O, NANO E, et al. MassChroQ: A versatile tool for mass spectrometry quantification [J]. Proteomics, 2011, 11(17): 3572-3577.
计量
  • 文章访问数:  911
  • HTML全文浏览量:  1
  • PDF下载量:  953
  • 被引次数: 0
出版历程
  • 刊出日期:  2013-01-19

目录

    /

    返回文章
    返回