R2DGC：R 中的二维气相色谱-质谱无阈值峰对齐和识别。
R2DGC: threshold-free peak alignment and identification for 2D gas chromatography-mass spectrometry in R.
机构信息
HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
Department of Genetics, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
出版信息
Bioinformatics. 2018 May 15;34(10):1789-1791. doi: 10.1093/bioinformatics/btx825.
SUMMARY
Comprehensive 2D gas chromatography-mass spectrometry is a powerful method for analyzing complex mixtures of volatile compounds, but produces a large amount of raw data that requires downstream processing to align signals of interest (peaks) across multiple samples and match peak characteristics to reference standard libraries prior to downstream statistical analysis. Very few existing tools address this aspect of analysis and those that do have shortfalls in usability or performance. We have developed an R package that implements retention time and mass spectra similarity threshold-free alignments, seamlessly integrates retention time standards for universally reproducible alignments, performs common ion filtering and provides compatibility with multiple peak quantification methods. We demonstrate that our package's performance compares favorably to existing tools on a controlled mix of metabolite standards separated under variable chromatography conditions and data generated from cell lines.
AVAILABILITY AND IMPLEMENTATION
R2DGC can be downloaded at https://github.com/rramaker/R2DGC or installed via the Comprehensive R Archive Network (CRAN).
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
综合二维气相色谱-质谱法是一种分析复杂挥发性化合物混合物的强大方法，但会产生大量原始数据，需要进行下游处理以对齐多个样品中感兴趣的信号（峰），并在下游统计分析之前将峰特征与参考标准库匹配。很少有现有的工具可以解决这一方面的分析问题，而那些现有的工具在可用性或性能方面存在不足。我们开发了一个 R 包，该包实现了保留时间和质谱相似度无阈值对齐，无缝集成了保留时间标准，以实现普遍可重复的对齐，执行常见离子过滤，并与多种峰定量方法兼容。我们证明，在受控制的代谢物标准混合物（在不同的色谱条件下分离）和细胞系产生的数据上，我们的包的性能优于现有工具。
可用性和实现
R2DGC 可在 https://github.com/rramaker/R2DGC 下载，或通过综合 R 档案网络 (CRAN) 安装。
联系信息
补充信息
补充数据可在生物信息学在线获得。
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