Preprocessing data in a reproducible and robust way is one of the current challenges in untargeted metabolomics workflows. Data curation in liquid chromatography–mass spectrometry (LC–MS) involves the removal of biologically non-relevant features (retention time, m/z pairs) to retain only high-quality data for subsequent analysis and interpretation. The present work introduces TidyMS, a package for the Python programming language for preprocessing LC–MS data for quality control (QC) procedures in untargeted metabolomics workflows. It is a versatile strategy that can be customized or fit for purpose according to the specific metabolomics application. It allows performing quality control procedures to ensure accuracy and reliability in LC–MS measurements, and it allows preprocessing metabolomics data to obtain cleaned matrices for subsequent statistical analysis. The capabilities of the package are shown with pipelines for an LC–MS system suitability check, system conditioning, signal drift evaluation, and data curation. These applications were implemented to preprocess data corresponding to a new suite of candidate plasma reference materials developed by the National Institute of Standards and Technology (NIST; hypertriglyceridemic, diabetic, and African-American plasma pools) to be used in untargeted metabolomics studies in addition to NIST SRM 1950 Metabolites in Frozen Human Plasma. The package offers a rapid and reproducible workflow that can be used in an automated or semi-automated fashion, and it is an open and free tool available to all users.

中文翻译：

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用于非目标代谢组学工作流程的预处理LC-MS数据的基于Python的管道

以可重现和强大的方式预处理数据是无目标代谢组学工作流程中的当前挑战之一。液相色谱-质谱（LC-MS）中的数据管理涉及去除生物学上无关的特征（保留时间，m / z对），仅保留高质量数据，以供后续分析和解释。本工作介绍了TidyMS，这是用于Python编程语言的软件包，用于预处理非目标代谢组学工作流程中的LC-MS数据，以进行质量控制（QC）程序。它是一种通用策略，可以根据特定的代谢组学应用进行定制或适合特定目的。它允许执行质量控制程序，以确保LC-MS测量的准确性和可靠性，并且允许对代谢组学数据进行预处理，以获得用于后续统计分析的纯化基质。该软件包的功能与LC-MS系统适用性检查，系统调节，信号漂移评估和数据管理的管道一起显示。实施这些应用程序是为了对与国家标准技术研究院（NIST;高甘油三酸酯，糖尿病和非裔美国人血浆库）开发的一套新的候选血浆参考材料相对应的数据进行预处理，这些数据还将用于非靶向代谢组学研究中NIST SRM 1950冷冻人血浆中的代谢产物。该软件包提供了一种快速且可重复的工作流程，可以以自动化或半自动化的方式使用，并且它是一个开放的免费工具，可供所有用户使用。