Introduction

While liquid chromatography coupled to mass spectrometric detection in the selected reaction monitoring detection mode offers the best quantification sensitivity for omics, the number of target analytes is limited, must be predefined and specific methods developed. Data independent acquisition (DIA), including SWATH using quadrupole time of flight or orbitrap mass spectrometers and generic acquisition methods, has emerged as a powerful alternative technique for quantitative and qualitative analyses since it can cover a wide range of analytes without predefinition.

Objectives

Here we review the current state of DIA, SWATH-MS and highlight novel acquisition strategies for metabolomics and lipidomics and opportunities for data analysis tools.

Method

Different databases were searched for papers that report developments and applications of DIA and in particular SWATH-MS in metabolomics and lipidomics.

Results

DIA methods generate digital sample records that can be mined retrospectively as further knowledge is gained and, with standardized acquisition schemes, used in multiple studies. The different chemical spaces of metabolites and lipids require different specificities, hence different acquisition and data processing approaches must be considered for their analysis.

Conclusions

Although the hardware and acquisition modes are well defined for SWATH-MS, a major challenge for routine use remains the lack of appropriate software tools capable of handling large datasets and large numbers of analytes.

中文翻译：

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代谢组学和脂质组学的SWATH-MS：定性和定量分析的关键方面。

介绍

尽管液相色谱与质谱联用在选定的反应监测检测模式下提供了最佳的组学定量灵敏度，但目标分析物的数量有限，必须预先定义并开发特定的方法。数据独立采集（DIA），包括使用四极飞行时间或Orbitrap质谱仪和通用采集方法的SWATH，已成为一种强大的替代技术，可用于定量和定性分析，因为它无需预先定义即可覆盖多种分析物。

目标

在这里，我们回顾了DIA，SWATH-MS的当前状态，并重点介绍了代谢组学和脂质组学的新型采集策略以及数据分析工具的机会。

方法

在不同的数据库中搜索了报道DIA（特别是SWATH-MS）在代谢组学和脂质组学领域的发展和应用的论文。

结果

DIA方法生成数字样本记录，可以随着获得更多知识而追溯性地对其进行挖掘，并且可以使用标准化的采集方案将其用于多项研究。代谢物和脂质的不同化学空间需要不同的特异性，因此必须考虑不同的采集和数据处理方法进行分析。

结论

尽管为SWATH-MS定义了良好的硬件和采集模式，但常规使用的主要挑战仍然是缺乏能够处理大型数据集和大量分析物的适当软件工具。