Lipids play many biological roles including membrane formation, protection, insulation, energy storage, and cell division. These functions have brought great interest to lipidomic studies for understanding their dysregulation in toxic exposure, inflammation, and diseases. However, lipids have shown to be analytically challenging due to their highly isomeric nature and vast concentration ranges in biological matrices. Therefore, powerful multidimensional techniques such as those integrating

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... d chromatography, ion mobility spectrometry, collision induced dissociation, and mass spectrometry (LC-IMS-CID-MS) have recently been implemented to separate lipid isomers as well as provide structural information and increased feature identification confidence. These multidimensional datasets are however extremely large and highly complex, resulting in challenges in data processing and annotation. Here, we have overcome these challenges by developing sample-specific multidimensional libraries using the freely available software Skyline. Specifically, the human plasma library developed for this work contains over 500 unique, experimentally validated lipids, which is combined with adapted Skyline functions for highly confident lipid annotations such as indexed retention time (iRT) for retention time prediction and IMS drift time filtering for increased sensitivity and selectivity. For broad comparison with other lipidomic studies, this human plasma database was initially used to annotate LC-IMS-CID-MS data from a NIST SRM 1950 extract, giving comparable results to previous studies. This workflow was then utilized to assess matched plasma and bronchoalveolar lavage fluid (BALF) samples from patients with varying degrees of smoke inhalation injury to identify potential lipid-based patient prognostic and diagnostic markers.