Current Practices in LC-MS Untargeted Metabolomics: A Scoping Review on the Use of Pooled Quality Control Samples

Untargeted metabolomics
is an analytical approach with numerous
applications serving as an effective metabolic phenotyping platform
to characterize small molecules within a biological system. Data quality
can be challenging to evaluate and demonstrate in metabolomics experiments.
This has driven the use of pooled quality control (QC) samples for
monitoring and, if necessary, correcting for analytical variance introduced
during sample preparation and data acquisition stages. Described herein
is a scoping literature review detailing the use of pooled QC samples
in published untargeted liquid chromatography–mass spectrometry
(LC-MS) based metabolomics studies. A literature query was performed,
the list of papers was filtered, and suitable articles were randomly
sampled. In total, 109 papers were each reviewed by at least five
reviewers, answering predefined questions surrounding the use of pooled
quality control samples. The results of the review indicate that use
of pooled QC samples has been relatively widely adopted by the metabolomics
community and that it is used at a similar frequency across biological
taxa and sample types in both small- and large-scale studies. However,
while many studies generated and analyzed pooled QC samples, relatively
few reported the use of pooled QC samples to improve data quality.
This demonstrates a clear opportunity for the field to more frequently
utilize pooled QC samples for quality reporting, feature filtering,
analytical drift correction, and metabolite annotation. Additionally,
our survey approach enabled us to assess the ambiguity in the reporting
of the methods used to describe the generation and use of pooled QC
samples. This analysis indicates that many details of the QC framework
are missing or unclear, limiting the reader’s ability to determine
which QC steps have been taken. Collectively, these results capture
the current state of pooled QC sample usage and highlight existing
strengths and deficiencies as they are applied in untargeted LC-MS
metabolomics.

非靶向代谢组学（Untargeted metabolomics）是一类具有诸多应用场景的分析方法，可作为高效的代谢表型分析平台，用于表征生物系统内的小分子化合物。代谢组学实验中，数据质量的评估与验证往往颇具挑战。为此，研究人员常采用混合质控（pooled quality control, QC）样本，以监测分析过程的变异，并在必要时校正样本制备与数据采集阶段引入的分析偏差。本文将介绍一项范围综述（scoping literature review），其聚焦已发表的基于液相色谱-质谱联用（liquid chromatography–mass spectrometry, LC-MS）的非靶向代谢组学研究中混合质控样本的应用情况。研究团队首先开展文献检索，对检索得到的论文列表进行筛选，并随机抽取符合纳入标准的文献。最终纳入分析的109篇文献均由至少5名评审员独立审阅，围绕混合质控样本的使用情况回答预设问题。综述结果显示，混合质控样本的使用已在代谢组学领域得到较为广泛的应用；且无论研究规模大小，该方法在不同生物类群与样本类型中的使用频率均较为接近。但值得注意的是，尽管多数研究均制备并分析了混合质控样本，却仅有极少数研究提及利用混合质控样本提升数据质量。这表明该领域仍有充足的改进空间，可进一步推广混合质控样本在质量报告、特征过滤、分析漂移校正以及代谢物注释等场景中的应用。此外，本研究采用的调研方法，也让我们得以评估混合质控样本制备与使用方法的报告中存在的歧义性。分析结果显示，质控流程的诸多细节均存在缺失或表述模糊的问题，导致读者无法准确判断研究中实施了哪些质控步骤。综上，本综述的结果清晰呈现了当前非靶向LC-MS代谢组学研究中混合质控样本的应用现状，并点明了该应用场景下现存的优势与不足。