LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation
LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation
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DOI：
10.1093/bioinformatics/btac581
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发表时间：
2022-08-25
期刊：
影响因子：
5.8
通讯作者：
Lahoz, Agustin
中科院分区：
文献类型：
--
作者：
Isabel Alcoriza-Balaguer, Maria;Carlos Garcia-Canaveras, Juan;Lahoz, Agustin
动机：LipidMS最初设想使用片段化规则和数据独立采集（DIA）进行脂质注释。然而，数据依赖性采集（DDA）仍然是基于非靶向LC-MS/MS的脂质组学最广泛的采集模式。在这里，我们介绍了LipidMS 3.0，这是一个R软件包，它不仅在其管道中添加了DDA和新的脂质类，而且还提供了从预处理到整个数据分析工作流程所需的功能（即峰-峰、对齐和分组）到脂质注释。我们将新的工作流程应用于在全扫描中获得的加标68种代表性脂质标准品的商业人血清池的数据分析，DDA和DIA模式。当关注检测到的脂质标准品特征和总识别脂质时，LipidMS 3.0数据预处理性能与XCMS相似，但它补充了MS-DIAL返回的注释，提供了更高水平的结构信息和更少数量的错误注释。为了在经验不足的R编程用户中扩展和促进LipidMS 3.0的使用，工作流程也被实现为基于Web的应用程序。
Motivation: LipidMS was initially envisioned to use fragmentation rules and data-independent acquisition (DIA) for lipid annotation. However, data-dependent acquisition (DDA) remains the most widespread acquisition mode for untargeted LC-MS/MS-based lipidomics. Here, we present LipidMS 3.0, an R package that not only adds DDA and new lipid classes to its pipeline but also the required functionalities to cover the whole data analysis workflow from pre-processing (i.e. peak-peaking, alignment and grouping) to lipid annotation.Results: We applied the new workflow in the data analysis of a commercial human serum pool spiked with 68 representative lipid standards acquired in full scan, DDA and DIA modes. When focusing on the detected lipid standard features and total identified lipids, LipidMS 3.0 data pre-processing performance is similar to XCMS, whereas it complements the annotations returned by MS-DIAL, providing a higher level of structural information and a lower number of incorrect annotations. To extend and facilitate LipidMS 3.0 usage among less experienced R-programming users, the workflow is also implemented as a web-based application.