Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold.
Comparison of Mascot and X!Tandem performance for low and high accuracy mass spectrometry and the development of an adjusted Mascot threshold.
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DOI：
10.1074/mcp.m700293-mcp200
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发表时间：
2008-05
期刊：
影响因子：
--
通讯作者：
Choudhary J
中科院分区：
文献类型：
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作者：
Brosch M;Swamy S;Hubbard T;Choudhary J
开发有效的序列数据库搜索算法以将从串联质谱获得的分子量和片段质量信息转化为高质量的肽和蛋白质分配是一个重大挑战。我们研究了Mascot和X！串联用于低精度和高精度质谱法常见的质量容差设置。我们证明了肽鉴定的灵敏度和特异性对于不同的质量耐受性设置可以有很大的不同，但是这种效果对于Mascot更显著。我们提出了一个调整后的Mascot阈值，它允许用户自由选择灵敏度和特异性之间的最佳权衡。将调整后的Mascot阈值与默认Mascot和X！串联评分阈值，并显示在相同的错误发现率为低和高精度质谱数据更敏感。
It is a major challenge to develop effective sequence database search algorithms to translate molecular weight and fragment mass information obtained from tandem mass spectrometry into high quality peptide and protein assignments. We investigated the peptide identification performance of Mascot and X!Tandem for mass tolerance settings common for low and high accuracy mass spectrometry. We demonstrated that sensitivity and specificity of peptide identification can vary substantially for different mass tolerance settings, but this effect was more significant for Mascot. We present an adjusted Mascot threshold, which allows the user to freely select the best trade-off between sensitivity and specificity. The adjusted Mascot threshold was compared with the default Mascot and X!Tandem scoring thresholds and shown to be more sensitive at the same false discovery rates for both low and high accuracy mass spectrometry data.