Universal metrics for quality assessment of protein identifications by mass spectrometry
Universal metrics for quality assessment of protein identifications by mass spectrometry
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DOI：
10.1074/mcp.m500426-mcp200
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发表时间：
2006-07-01
影响因子：
7
通讯作者：
Brown, Alistair J. P.
中科院分区：
文献类型：
--
作者：
Stead, David A.;Preece, Alun;Brown, Alistair J. P.
越来越多的大型蛋白质组学数据集正在变得可用。在试图解释这些数据集并将其与其他形式的基因组数据整合的过程中，研究人员越来越意识到数据质量对蛋白质鉴定的重要性。我们提出了三个简单而通用的指标，描述了通过肽质量指纹鉴定蛋白质质量的不同方面。命中率给出了质谱中信噪比的指示，质量覆盖率测量了匹配的蛋白质序列的数量，而过量的极限消化肽反映了肽质量指纹之前消化的完整性。接收器操作特征图表明，在验证最先进的蛋白质鉴定软件系统（Mascot）的结果时，新的度量，即极限消化肽的过剩，可以比搜索分数更准确地区分正确匹配和随机匹配，特别是当与其他两个度量，命中率和质量覆盖率相结合时。在报告蛋白质鉴定实验时，对指标的使用提出了建议。
Increasing numbers of large proteomic datasets are becoming available. As attempts are made to interpret these datasets and integrate them with other forms of genomic data, researchers are becoming more aware of the importance of data quality with respect to protein identification. We present three simple and universal metrics that describe different aspects of the quality of protein identifications by peptide mass fingerprinting. Hit ratio gives an indication of the signal-to-noise ratio in a mass spectrum, mass coverage measures the amount of protein sequence matched, and excess of limit-digested peptides reflects the completeness of the digestion that precedes the peptide mass fingerprinting. Receiver-operating characteristic plots show that the novel metric, excess of limit-digested peptides, can discriminate between correct and random matches more accurately than search score when validating the results from a state-of-the-art protein identification software system (Mascot) especially when combined with the two other metrics, hit ratio and mass coverage. Recommendations are made regarding the use of the metrics when reporting protein identification experiments.