[1]王勇,李水明,何曼文,等.人工解析提高串联质谱鉴定肽段的数据利用度[J].深圳大学学报理工版,2013,30(No.5(441-550)):538-544.[doi:10.3724/SP.J.1249.2013.05538]
 Wang Yong,Li Shuiming,He Manwen,et al.Improving data utilization of tandem time-of flight mass spectrometry for peptides identification by manual interpretation[J].Journal of Shenzhen University Science and Engineering,2013,30(No.5(441-550)):538-544.[doi:10.3724/SP.J.1249.2013.05538]
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人工解析提高串联质谱鉴定肽段的数据利用度()
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《深圳大学学报理工版》[ISSN:1000-2618/CN:44-1401/N]

卷:
第30卷
期数:
2013年No.5(441-550)
页码:
538-544
栏目:
生物工程
出版日期:
2013-09-02

文章信息/Info

Title:
Improving data utilization of tandem time-of flight mass spectrometry for peptides identification by manual interpretation
文章编号:
20130516
作者:
王勇1 李水明1 何曼文2 冯里茹2
1)深圳大学生命科学学院 深圳市海洋生物资源与生态环境重点实验室,深圳 518060;
2)深圳大学生命科学学院 深圳市微生物基因工程重点实验室,深圳 518060
Author(s):
Wang Yong1 Li Shuiming1 He Manwen2 and Feng Liru2
1)College of Life Science, Shenzhen Key Laboratory of Marine Bioresources and Ecology, Shenzhen University, Shenzhen 518060, P.R.China
2)College of Life Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen 518060, P.R.China
关键词:
蛋白质组学 数据库搜索 基质辅助激光解吸电离–串联飞行时间质谱人工解析亚胺离子
Keywords:
proteomicsdatabase searchingmatrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF/TOF)manual explanationimmonium ions
分类号:
O 57.63
DOI:
10.3724/SP.J.1249.2013.05538
文献标志码:
A
摘要:
为降低蛋白质鉴定的假阴性,利用标准蛋白和实际样品,探讨影响基质辅助激光解吸电离–串联飞行时间质谱数据利用度的原因. 发现误差设置偏小、翻译后修饰、异常酶解和氨基酸突变等是导致蛋白质数据库检索不匹配目标肽段的主要原因. 实验表明,典型情况下一级和二级质谱误差可设定在0.3 Da. 对未与数据库匹配的串联质谱进行亚胺离子辅助的人工解析发现,色氨酸双氧化、丝氨酸乙酰胺化和半胱氨酸丙酰胺化等不常见修饰,酪氨酸与苯丙氨酸、天冬氨酸与谷氨酸两两之间的突变和非特异性酶解等现象,该研究可提高质谱鉴定的数据利用度.
Abstract:
To reduce the false negative for protein identification based on mass spectrometry (MS), standard proteins and practical samples were used to explore the influence of the data utilization on matrix-assisted laser desorption ionization-tandem time-of-flight mass spectrometry. It was found that mass tolerance, post-translational modification, irregular digestion and gene mutation were the main factors leading to the mismatch between protein database and targeted peptides. After manual explanation assisted by immonium ions in low m/z region, the mass error of first order MS and second order MS could be set to 0.3 Da typically. In addition, the dioxidation of tryptophan, propionamidation of cysteine, carbamidomethy serine and the methionine to lose 48 Da was detected as an uncommon modification. Furthermore, the mutation between tyrosine and phenylalanine and the mutation between aspartate and glutamate were also found. All the above factors can lead to the failure of matching tandem mass data by Mascot database searching. Results show that manual analysis of the “unused” MS/MS data will improve the protein and peptide identification utilization effectively.

参考文献/References:

[1] Mann M,Kelleher N L. Precision proteomics: the case for high resolution and highmass accuracy [J]. Proceedings of the National Academy of Sciences,2008,105(47):18132-18138.
[2] Bell A W,Deutsch E W,Au C E,et al. A HUPO test sample study reveals common problems in mass spectrometry-based proteomics[J]. Nature Methods,2009,6(6):423-430.
[3] Aebersold R. A stress test for mass spectrometry—based proteomics[J]. Nature Methods,2009,6(6):411-412.
[4] Savitski M M,Nielsen M L,Kjeldsen F,et al. Proteomics-grade de novo sequencing approach[J]. Journal of Proteome Research,2005, 4(6):2348-2354.
[5] Sun Hanchang,Zhang Jiyang,Liu Hui,et al. Algorithm development of peptide sequencing tandem mass spectrometry[J]. Progress in Biochemistry and Biophysics,2010,37(12):1278-1288.(in Chinese)
孙汉昌,张纪阳,刘辉,等.串联质谱图谱从头测序算法研究进展[J]. 生物化学与生物物理进展,2010,37(12):1278-1288.
[6] Xu Changming,Zhang Jiyang,Liu Hui,et al. Advance of peptide detectability prediction on mass spectrometry platform in proteomics[J]. Chinese Journal of Analytical Chemistry,2010,38(2):286-292.(in Chinese)
徐长明,张纪阳,刘辉, 等. 蛋白质组学质谱平台肽段可检测性预测研究进展[J]. 分析化学,2010,38(2):286-292.
[7] Vestal M L, Campbell J M. Tandem time-of-flight mass spectrometry[J]. Methods Enzymol, 2005,402:79-108.
[8] Mingyao Li M Y,Wang I X,Li Y,et al. Widespread RNA and DNA sequence differences in the human transcriptome[J]. Science,2011,333(6038):53-58.
[9] Medzihradszky K F,Campbell J M,Baldwin M A,et al. The characteristics of peptide collision-induced dissociation using a high-performance MALDI-TOF/TOF tandem mass spectrometer[J]. Analytical Chemistry, 2000,72(3):552-558.
[10] Yergey A L,Coorssen J R,Backlund P S,et al. De novo sequencing of peptides using MALDI/TOF-TOF[J]. Journal of the American Society for Mass Spectrometry,2002,13(7):784-791.
[11] Falick A M,Hines W M,Medzihradszky K F,et al. Low-mass ions produced from peptides by high-energy collision-induced dissociation in tandem mass-spectrometry[J]. American Society for Mass Spectrometry, 1993,4(11):882-893.
[12] Chi H,Sun R X,Yang B,et al. pNovo: de novo peptide sequencing and identification using HCD spectra[J]. Journal of Proteome Research, 2010,9(5):2713-2724.
[13] Hohmann L J,Eng J K,Gemmill A. Quantification of the compositional information provided by immonium ions on a quadrupole-time-of-flight mass spectrometer[J]. Analytical Chemistry, 2008,80(14):5596-5606.

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备注/Memo

备注/Memo:
Received:2013-03-14;Accepted:2013-06-06
Foundation:National Natural Science Foundation of China(21271131, 31070731)
Corresponding author:Associate professor Wang Yong. E-mail: wyong@szu.edu.cn
Citation:Wang Yong, Li Shuiming, He Manwen, et al. Improving data utilization of tandem time-of flight mass spectrometry for peptides identification by manual interpretation[J]. Journal of Shenzhen University Science and Engineering, 2013, 30(5): 538-544.(in Chinese)
基金项目:国家自然科学基金资助项目(21271131, 31070731)
作者简介:王勇(1970-),男(汉族),吉林省四平市人,深圳大学副教授、博士. E-mail:wyong@szu.edu.cn
引文:王勇, 李水明, 何曼文, 等. 人工解析提高串联质谱鉴定肽段的数据利用度[J]. 深圳大学学报理工版,2013,30(5):538-544.
更新日期/Last Update: 2013-09-02