Abstract：
Mass spectrometry is broadly employed to study complex molecular mechanisms in various biological and environmental fields, enabling \'omics\' research such as proteomics, metabolomics, and lipidomics. As study cohorts grow larger and more complex with dozens to hundreds of samples, the need for robust quality control (QC) measures through automated software tools becomes paramount to ensure the integrity, high quality, and validity of scientific conclusions from downstream analyses and minimize the waste of resources. Since existing QC tools are mostly dedicated to proteomics, automated solutions supporting metabolomics are needed. To address this need, we developed the software PeakQC, a tool for automated QC of MS data that is independent of omics molecular types (i.e., omics-agnostic). It allows automated extraction and inspection of peak metrics of precursor ions (e.g., errors in mass, retention time, arrival time) and supports various instrumentations and acquisition types, from infusion experiments or using liquid chromatography and/or ion mobility spectrometry front-end separations and with/without fragmentation spectra from data-dependent or independent acquisition analyses. Diagnostic plots for fragmentation spectra are also generated. Here, we describe and illustrate PeakQC\'s functionalities using different representative data sets, demonstrating its utility as a valuable tool for enhancing the quality and reliability of omics mass spectrometry analyses.
摘要：
质谱广泛用于研究各种生物和环境领域的复杂分子机制。启用蛋白质组学等“组学”研究，代谢组学，和脂质组学。随着研究队列越来越大，越来越复杂，有数十到数百个样本，需要强大的质量控制（QC）措施，通过自动化的软件工具变得至关重要，以确保完整性，高质量,以及下游分析的科学结论的有效性，最大限度地减少资源浪费。由于现有的QC工具主要致力于蛋白质组学，需要支持代谢组学的自动化解决方案。为了满足这一需求，我们开发了PeakQC软件,一种独立于组学分子类型的MS数据自动QC工具(即，组学-不可知论者)。它允许自动提取和检查前体离子的峰值度量(例如，质量错误，保留时间,到达时间)，并支持各种仪器和采集类型，来自输注实验或使用液相色谱和/或离子迁移谱的前端分离，并且具有/不具有来自数据依赖性或独立采集分析的碎片谱。还生成了碎裂光谱的诊断图。这里,我们使用不同的代表性数据集描述和说明PeakQC的功能，证明其作为提高组学质谱分析质量和可靠性的有价值的工具的实用性。
