Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra.
Spectral Library Search Improves Assignment of TMT Labeled MS/MS Spectra.
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光谱库搜索改善了标记为MS/MS Spectra的TMT分配。
DOI：
10.1021/acs.jproteome.8b00594
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发表时间：
2018-09-07
影响因子：
4.4
通讯作者：
Wang X
中科院分区：
文献类型：
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作者：
Shen J;Pagala VR;Breuer AM;Peng J;Bin Ma;Wang X
基于串联质量标签（TMT）的液相色谱-串联质谱（LC-MS/MS）是一种成熟的大规模多重蛋白定量方法。然而，在传统的序列数据库搜索过程中，tmt标记肽的识别受到标记的影响。在本研究中，我们的目的是利用谱库搜索来提高基于tmt的质谱数据的肽鉴定的敏感性和特异性。与未标记肽的MS/MS光谱相比，TMT标记肽的光谱通常显示增强的b离子，这表明TMT标记可以改变MS/MS片段过程中产物的离子模式。我们从数十个分析项目的数百万个肽谱匹配中编译了401168个高质量的独特肽的人类TMT谱库，匹配了14048个非冗余蛋白（13953个基因）。建立了类似大小的小鼠TMT谱库。随后，在库中添加诱饵光谱来评估错误发现率，并通过模拟null TMT数据集进行验证。通过去除TMT报告离子，选择合适的库构建方法，进一步优化库搜索性能。最后，我们利用光谱库对人类TMT数据集进行了检索，以证明光谱库的性能优于序列数据库。人类和小鼠的TMT库都向研究界公开提供。
Tandem mass tag (TMT)-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a proven approach for large-scale multiplexed protein quantification. However, the identification of TMT-labeled peptides is compromised by the labeling during traditional sequence database search. In this study, we aim to use spectral library search to increase the sensitivity and specificity of peptide identification for TMT-based MS data. Compared to MS/MS spectra of unlabeled peptides, the spectra of TMT-labeled counterparts usually display intensified b ions, suggesting that TMT labeling can alter product ion patterns during MS/MS fragementation. We compiled a human TMT spectral library of 401,168 unique peptides of high quality from millions of peptide-spectrum matches in tens of profiling projects, matching to 14,048 non-redundant proteins (13,953 genes). A mouse TMT spectral library of the similar size was also constructed. The libraries were subsequently appended with decoy spectra to evaluate false discovery rate, which was validated by a simulated null TMT dataset. The performance of library search was further optimized by removing TMT reporter ions and selecting an appropriate library construction method. Finally, we searched a human TMT dataset against the spectral library to demonstrate that the spectral library outperformed the sequence database. Both human and mouse TMT libraries were made publicly available to the research community.
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影响因子：
4.4
作者：
Dasari, Surendra;Chambers, Matthew C.;Tabb, David L.
通讯作者：
Tabb, David L.
影响因子：
7.4
作者：
Toghi Eshghi S;Shah P;Yang W;Li X;Zhang H
通讯作者：
Zhang H
影响因子：
32.4
作者：
Tan H;Yang K;Li Y;Shaw TI;Wang Y;Blanco DB;Wang X;Cho JH;Wang H;Rankin S;Guy C;Peng J;Chi H
通讯作者：
Chi H
影响因子：
4.4
作者：
Ahrne, Erik;Nikitin, Frederic;Mueller, Markus
通讯作者：
Mueller, Markus
DOI：
10.1007/978-1-4939-2425-7_17
发表时间：
2015-01-01
期刊：
PROTEIN-PROTEIN INTERACTIONS: METHODS AND APPLICATIONS, 2ND EDITION
影响因子：
--
作者：
Pagala, Vishwajeeth R.;High, Anthony A.;Peng, Junmin
通讯作者：
Peng, Junmin