Optimizing methods for liquid chromatography coupled to mass spectrometry (LC–MS) is a nontrivial task. Here we present rawDiag, a software tool supporting rational method optimization by providing MS operator-tailored diagnostic plots of scan-level metadata. rawDiag is implemented as an R package and can be executed on the R command line or through a graphical user interface (GUI) for less experienced users. The code runs platform-independent and can process 100 raw files in <3 min on current consumer hardware, as we show in our benchmark. As a demonstration of the functionality of our package we include a real-world example taken from our daily core facility business.

中文翻译：

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rawDiag：支持自下而上蛋白质组学的Rational LC-MS方法优化的R包

液相色谱-质谱联用的优化方法是一项艰巨的任务。在这里，我们介绍了rawDiag，这是一种通过提供MS操作员量身定制的扫描级元数据诊断图来支持合理方法优化的软件工具。rawDiag是作为R包实现的，可以在R命令行上执行，也可以通过图形用户界面（GUI）针对经验不足的用户执行。正如我们在基准测试中所展示的，该代码与平台无关，并且可以在3分钟内在当前的消费类硬件上处理100个原始文件。为了说明我们软件包的功能，我们提供了一个来自日常核心设施业务的真实示例。