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首页> 外文期刊>Molecular & cellular proteomics: MCP >DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.
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DtaRefinery, a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra data sets.

机译：DtaRefinery，一种软件工具，用于消除串联质谱数据集中母离子质量测量中的系统误差。

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摘要

Hybrid two-stage mass spectrometers capable of both highly accurate mass measurement and high throughput MS/MS fragmentation have become widely available in recent years, allowing for significantly better discrimination between true and false MS/MS peptide identifications by the application of a relatively narrow window for maximum allowable deviations of measured parent ion masses. To fully gain the advantage of highly accurate parent ion mass measurements, it is important to limit systematic mass measurement errors. Based on our previous studies of systematic biases in mass measurement errors, here, we have designed an algorithm and software tool that eliminates the systematic errors from the peptide ion masses in MS/MS data. We demonstrate that the elimination of the systematic mass measurement errors allows for the use of tighter criteria on the deviation of measured mass from theoretical monoisotopic peptide mass, resulting in a reduction of both false discovery and false negative rates of peptide identification. A software implementation of this algorithm called DtaRefinery reads a set of fragmentation spectra, searches for MS/MS peptide identifications using a FASTA file containing expected protein sequences, fits a regression model that can estimate systematic errors, and then corrects the parent ion mass entries by removing the estimated systematic error components. The output is a new file with fragmentation spectra with updated parent ion masses. The software is freely available.
机译：近年来，能够同时进行高精度质量测量和高通量MS / MS裂解的混合型两级质谱仪已得到广泛应用，通过使用相对较窄的窗口，可以更好地区分真假MS / MS肽段。测量母离子质量的最大允许偏差。为了充分获得高精度母离子质量测量的优势，限制系统质量测量误差非常重要。基于我们先前对质量测量误差的系统偏差的研究，我们设计了一种算法和软件工具，可从MS / MS数据中的肽离子质量中消除系统误差。我们证明消除系统的质量测量误差允许使用更严格的标准，从理论上的单同位素肽质量偏离测量质量，从而减少了错误的发现和错误的肽鉴定阴性率。该算法的软件实现称为DtaRefinery，它读取一组碎片质谱图，使用包含预期蛋白质序列的FASTA文件搜索MS / MS肽段鉴定，拟合可以估算系统误差的回归模型，然后通过以下方法校正母离子质量条目：去除估计的系统误差成分。输出是一个新的文件，该文件具有带有更新的母体离子质量的碎片质谱图。该软件是免费提供的。

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