共 28 条
Decision tree-driven tandem mass spectrometry for shotgun proteomics
被引:262
作者:

Swaney, Danielle L.
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机构:
Univ Wisconsin, Dept Chem, Madison, WI 53706 USA Univ Wisconsin, Dept Chem, Madison, WI 53706 USA

McAlister, Graeme C.
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机构:
Univ Wisconsin, Dept Chem, Madison, WI 53706 USA Univ Wisconsin, Dept Chem, Madison, WI 53706 USA

Coon, Joshua J.
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h-index: 0
机构:
Univ Wisconsin, Dept Chem, Madison, WI 53706 USA
Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA Univ Wisconsin, Dept Chem, Madison, WI 53706 USA
机构:
[1] Univ Wisconsin, Dept Chem, Madison, WI 53706 USA
[2] Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA
基金:
美国国家卫生研究院;
关键词:
D O I:
10.1038/nmeth.1260
中图分类号:
Q5 [生物化学];
学科分类号:
071010 ;
081704 ;
摘要:
Mass spectrometry has become a key technology for modern large-scale protein sequencing. Tandem mass spectrometry, the process of peptide ion dissociation followed by mass-to-charge ratio (m/z) analysis, is the critical component for peptide identification. Recent advances in mass spectrometry now permit two discrete, and complementary, types of peptide ion fragmentation: collision-activated dissociation (CAD) and electron transfer dissociation (ETD) on a single instrument. To exploit this complementarity and increase sequencing success rates, we designed and embedded a data-dependent decision tree algorithm (DT) to make unsupervised, real-time decisions of which fragmentation method to use based on precursor charge and m/z. Applying the DT to large-scale proteome analyses of Saccharomyces cerevisiae and human embryonic stem cells, we identified 53,055 peptides in total, which was greater than by using CAD (38,293) or ETD (39,507) alone. In addition, the DT method also identified 7,422 phosphopeptides, compared to either 2,801 (CAD) or 5,874 (ETD) phosphopeptides.
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页码:959 / 964
页数:6
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