LipidMS

LipidMS provides structural lipid annotation from untargeted liquid chromatography-data independent acquisition-mass spectrometry (LC-DIA-MS) data as an R package, linking precursor and fragment ions to assign subclass, fatty acyl, and fatty acyl position identifications.

Key Features:

• Implementation: Provided as an R package for analysis of LC-DIA-MS lipidomics datasets.
• Data type support: Operates on untargeted high-resolution liquid chromatography-data independent acquisition-mass spectrometry (LC-DIA-MS) data.
• DIA handling: Addresses DIA-specific challenges including loss of direct precursor–product linkage and high data dimensionality.
• Coelution score: Uses a coelution score to link coeluting precursor and fragment ions.
• Fragmentation and intensity rules: Applies fragmentation and intensity rules to corroborate precursor–fragment relationships and support annotations.
• Annotation levels: Reports three structural annotation levels—Subclass (e.g., PG(34:1)), Fatty Acyl (e.g., PG(16:0_18:1)), and Fatty Acyl Position (e.g., PG(16:0/18:1)).
• Benchmarking: Demonstrated higher accuracy and more informative structural annotations compared with existing DDA and DIA identification tools.

Scientific Applications:

• Untargeted lipidomics analyses: Enables structural annotation of lipid species in complex untargeted LC-DIA-MS experiments.
• Clinical lipidomics — NASH serum profiling: Applied to serum lipidomics of nonalcoholic steatohepatitis (NASH) patients, corroborating decreased lysophosphatidylcholines, phosphatidylcholines, and cholesterol esters, and increased phosphatidylethanolamines.
• Biomarker discovery: Facilitates identification of novel lipid species with potential utility as NASH biomarkers.

Methodology:

Integrates a coelution score with fragmentation and intensity rules to link precursor and fragment ions in LC-DIA-MS data and assign annotations at subclass, fatty acyl, and fatty acyl position levels.