LipidHunter Identifies Phospholipids by High-Throughput Processing of LC-MS and Shotgun Lipidomics Datasets

Lipids are dynamic constituents of biological systems, rapidly responding to any changes in physiological conditions. Thus, there is a large interest in lipid-derived markers for diagnostic and prognostic applications, especially in translational and systems medicine research. As lipid identification remains a bottleneck of modern untargeted lipidomics, we developed LipidHunter, a new open source software for the high-throughput identification of phospholipids in data acquired by LC-MS and shotgun experiments. LipidHunter resembles a workflow of manual spectra annotation. Lipid identification is based on MS/MS data analysis in accordance with defined fragmentation rules for each phospholipid (PL) class. The software tool matches product and neutral loss signals obtained by collision-induced dissociation to a user-defined white list of fatty acid residues and PL class-specific fragments. The identified signals are tested against elemental composition and bulk identification provided via LIPID MAPS search. Furthermore, LipidHunter provides information-rich tabular and graphical reports allowing to trace back key identification steps and perform data quality control. Thereby, 202 discrete lipid species were identified in lipid extracts from rat primary cardiomyocytes treated with a peroxynitrite donor. Their relative quantification allowed the monitoring of dynamic reconfiguration of the cellular lipidome in response to mild nitroxidative stress. LipidHunter is available free for download at https://bitbucket.org/SysMedOs/lipidhunter.脂质是生物系统中的动态组成成分，可快速响应生理条件的各类变化。因此，脂质衍生标志物在诊断与预后应用中的价值受到广泛关注，尤其在转化医学与系统医学研究领域。由于脂质鉴定仍是现代非靶向脂质组学的瓶颈问题，本研究开发了开源软件LipidHunter，用于高通量鉴定液相色谱-质谱联用（LC-MS）与鸟枪法实验所获数据中的磷脂。LipidHunter的分析流程模拟了人工谱图注释的工作模式，其脂质鉴定基于对各磷脂（PL）类别已定义的碎裂规则开展的MS/MS数据分析。该软件将碰撞诱导解离所获的产物离子与中性丢失信号，与用户自定义的脂肪酸残基列表及PL类别特异性片段进行匹配。通过LIPID MAPS数据库检索得到的元素组成与批量鉴定结果，对已识别的信号进行验证。此外，LipidHunter可生成信息丰富的表格与可视化报告，便于回溯关键鉴定步骤并开展数据质量控制。据此，本研究在经过氧亚硝基供体处理的大鼠原代心肌细胞脂质提取物中，鉴定出202种独立的脂质物种。通过对这些脂质的相对定量，可监测轻度氮氧化应激下细胞脂质组的动态重构型过程。LipidHunter可从https://bitbucket.org/SysMedOs/lipidhunter免费下载获取。