Ion mobility conformational lipid atlas for high confidence lipidomics

Abstract

Lipids are highly structurally diverse molecules involved in a wide variety of biological processes. Here, we use high precision ion mobility-mass spectrometry to compile a structural database of 456 mass-resolved collision cross sections (CCS) of sphingolipid and glycerophospholipid species. Our CCS database comprises sphingomyelin, cerebroside, ceramide, phosphatidylethanolamine, phosphatidylcholine, phosphatidylserine, and phosphatidic acid classes. Primary differences observed are between lipid categories, with sphingolipids exhibiting 2–6% larger CCSs than glycerophospholipids of similar mass, likely a result of the sphingosine backbone’s restriction of the sn1 tail length, limiting gas-phase packing efficiency. Acyl tail length and degree of unsaturation are found to be the primary structural descriptors determining CCS magnitude, with degree of unsaturation being four times as influential per mass unit. The empirical CCS values and previously unmapped quantitative structural trends detailed in this work are expected to facilitate prediction of CCS in broadscale lipidomics research.

Large-scale lipid analysis with C=C location and sn-position isomer resolving power

“…PB reaction converts the C=C to an oxetane which can be preferentially fragmented by low-energy collisioninduced dissociation (CID). Other approaches include ion mobility spectrometry (IMS) 36,37 and alternative gas-phase ion activation [38][39][40][41][42][43][44] . These lipid characterizing methods were also compatible with mass spectrometry imaging (MSI) [45][46][47][48][49][50] .…”

Lipidomics from sample preparation to data analysis: a primer

“…The CCS value is a measure of the shape-and sizedependent mobility of an ion in IMS and is unique to every compound. In recent years there have been major efforts to establish lipid CCS databases for DTIMS and traveling wave IMS [65][66][67][68][69]. Blazenovic et al, for example, proposed a system of lipid annotation derived from accurate mass, retention time, CCS, and degree of unsaturation values as well as the number of carbons, which should promote the identification certainty for lipids from untargeted workflows [65].…”

“…Blazenovic et al, for example, proposed a system of lipid annotation derived from accurate mass, retention time, CCS, and degree of unsaturation values as well as the number of carbons, which should promote the identification certainty for lipids from untargeted workflows [65]. In a similar fashion, Leaptrot et al introduced an experimentally derived database of CCS values of glycerophospholipids and sphingolipids [67]. Their findings suggest that the main determinant of the CCS value is not fatty acyl chain length but rather the degree of fatty acyl unsaturation.…”

Trapped ion mobility spectrometry (TIMS) and parallel accumulation - serial fragmentation (PASEF) enable in-depth lipidomics from minimal sample amounts

“…The investigation of the correlation of lipids mass and ion mobility has been a long term interest in ion mobility spectrometry-based lipidomics 26,27 . TIMS and PASEF provide a very efficient way to extend the scope of such studies to complex biological samples.…”

“…This is particular interesting for lipidomics, as it provides an opportunity to separate otherwise unresolved isomers [22][23][24][25] . Furthermore, the chemical structure of lipids is closely linked to the CCS, which allows predictions by machine learning and could facilitate lipid identification [26][27][28][29] .…”