Sphingoid base (SPH)
is a basic structural unit of all classes
of sphingolipids. A sphingoid base typically consists of an aliphatic
chain that may be desaturated between C4 and C5, an amine group at
C2, and a variable number of OH groups located at C1, C3, and C4.
Variations in the chain length and the occurrence of chemical modifications,
such as methyl branching, desaturation, and hydroxylation, lead to
a large structural diversity and distinct functional properties of
sphingoid bases. However, conventional tandem mass spectrometry (MS/MS)
via collision-induced dissociation (CID) faces challenges in characterizing
these modifications. Herein, we developed an MS/MS method based on
CID-triggered radical-directed dissociation (RDD) for in-depth characterization
of sphingoid bases. The method involves derivatizing the sphingoid
amine with 3-(2,2,6,6-tetramethylpiperidin-1-yloxymethyl)-picolinic
acid 2,5-dioxopyrrolidin-1-yl ester (TPN), followed by MS2 CID to unleash the pyridine methyl radical moiety for subsequent
RDD. This MS/MS method was integrated on a reversed-phase liquid chromatography–mass
spectrometry workflow and further applied for in-depth profiling of
total sphingoid bases in bovine heart and Caenorhabditis elegans. Notably, we identified and relatively quantified a series of unusual
sphingoid bases, including SPH id17:2 (4,13) and SPH it19:0 in C. elegans, revealing that the metabolic pathways of sphingolipids
are more diverse than previously known.