Program in Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
Bioinformatics. 2018 Oct 15;34(20):3589-3590. doi: 10.1093/bioinformatics/bty218.
Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis. Users are notified of detrimental instrument drift or errors by email. Also included are two shiny applications, targetId for real-time MS2 target identification, and peakMonitor to monitor targeted metabolites.
SimExTargId is publicly available under GNU LGPL v3.0 license at https://github.com/JosieLHayes/simExTargId, which includes a vignette with example data. SimExTargId should be installed on a dedicated data-processing workstation or server that is networked to the LC-MS platform to facilitate MS1 profiling of metabolomic data.
Supplementary data are available at Bioinformatics online.
液相色谱-质谱联用（LC-MS）是生物流体中小分子非靶向代谢组学分析的首选方法。本文介绍了 SimExTargId，这是一个用于代谢组学数据自主分析和实时观察实验运行的开源 R 包。这个同时进行的、全自动的（可选多线程）软件包是一个独立于供应商的格式转换（ProteoWizard）、基于 xcms 和 CAMERA 的峰提取、基于 MetMSLine 的预处理以及基于协变量的统计分析的包装器。用户将通过电子邮件收到有关仪器漂移或错误的通知。还包括两个 shiny 应用程序，targetId 用于实时 MS2 目标识别，peakMonitor 用于监测靶向代谢物。
SimExTargId 可在 https://github.com/JosieLHayes/simExTargId 下根据 GNU LGPL v3.0 许可证公开获取，其中包括一个带有示例数据的简介。SimExTargId 应安装在专用的数据处理工作站或服务器上，该工作站或服务器与 LC-MS 平台联网，以促进代谢组学数据的 MS1 分析。
补充数据可在生物信息学在线获取。
