Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada.
Anal Chim Acta. 2023 Sep 1;1272:341467. doi: 10.1016/j.aca.2023.341467. Epub 2023 Jun 1.
Liquid chromatography mass spectrometry (LC-MS) has been increasingly used for metabolome analysis. One of the critical steps in the LC-MS metabolome analysis workflow is related to metabolite identification. Among the measured parameters, peak mass is commonly used to search against a database for potential metabolite matches. Higher accuracy mass measurement allows the use of a narrower mass tolerance window for mass search. While various types of mass analyzers can routinely measure a peak mass with an error of less than a few ppm, mass measurement accuracy is not uniform for peaks with different intensities, particularly for quadrupole time-of-flight (QTOF) MS. Herein we present a simple and convenient method to determine the relation between peak intensity and mass error in LC-QTOF-MS-based metabolome analysis, followed by intensity-dependent mass search (IDMS) of a database for metabolite matches. This method is based on running a series of sodium formate mass calibrants, as part of the standard operating procedure (SOP) in LC-MS data acquisition, and then curve-fitting the measured mass errors and peak intensities. We show that, in two different quadrupole time-of-flight (QTOF) mass analyzers, mass accuracy is generally reduced as peak intensity decreases, which is independent of m/z values in the range commonly used for metabolite detection (e.g., m/z < 1000). We demonstrate the improvement in metabolite matches using IDMS in the analyses of dansyl labeled standards and human urine samples. We have implemented the IDMS method in the freely available MCID database at www.mycompoundid.org, which is composed of 8021 known human endogenous metabolites and their predicted metabolic products (375,809 compounds from one metabolic reaction and 10,583,901 compounds from two reactions).
液相色谱-质谱联用（LC-MS）已越来越多地用于代谢组学分析。LC-MS 代谢组学分析工作流程中的一个关键步骤与代谢物鉴定有关。在所测量的参数中，峰质荷比通常用于针对数据库搜索潜在的代谢物匹配。更高的质量测量精度允许使用更窄的质量搜索容限窗口。虽然各种类型的质谱仪通常可以以小于几个 ppm 的误差测量峰质荷比，但对于不同强度的峰，质量测量精度并不均匀，特别是对于四极杆飞行时间（QTOF）MS。本文介绍了一种简单方便的方法，用于确定基于 LC-QTOF-MS 的代谢组学分析中峰强度与质量误差之间的关系，然后对数据库进行基于强度的质量搜索（IDMS）以寻找代谢物匹配。该方法基于运行一系列甲酸钠质量校准标准品，作为 LC-MS 数据采集标准操作规程（SOP）的一部分，然后对测量的质量误差和峰强度进行曲线拟合。我们表明，在两种不同的四极杆飞行时间（QTOF）质谱仪中，质量精度通常随着峰强度的降低而降低，这与通常用于代谢物检测的 m/z 值范围（例如，m/z <1000）无关。我们通过使用 IDMS 分析丹磺酰标记标准品和人尿样，证明了代谢物匹配的改进。我们已经在免费提供的 MCID 数据库中实现了 IDMS 方法，该数据库包含 8021 种已知的人类内源性代谢物及其预测的代谢产物（来自一个代谢反应的 375,809 种化合物和来自两个反应的 10,583,901 种化合物）。
