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Globotriaosylsphingosine (LysoGb3) is a biomarker for Fabry disease (OMIM 301500) that contains long-chain bases (LCBs) as a building block. There have been several studies proposing that LysoGb3 forms with distinct LCBs could be putative disease subtype-related biomarkers for this congenital disorder, however, there have been no detailed multiple reaction monitoring-based studies examining the LCB distribution in this lysosphingolipid. To achieve this, we established an assay procedure that aimed at elucidating the LCB-targeted lipidome using liquid chromatography&ndash, tandem mass spectrometry. Consistent with previous studies, we found d18:1 to be the major LCB species of the LysoGb3 in pooled human plasma, while some atypical LCBs, such as d18:2, d18:0, t18:1, d16:1, and d17:1, were detected as minor fractions. When the same methodology was applied to fetal bovine serum (FBS) as a positive control, we identified additional unique LCB species, such as t18:0, d20:1, t19:1, and t21:1, in herbivore LysoGb3. Furthermore, we found an elevation of sphingosine and LysoGb3, which are N-deacylated forms of ceramide and Gb3, respectively, in FBS, suggesting that ceramidase activity may be involved in this process. Thus, our LCB-targeted lipidomics data revealed that mammalian LCBs in glycosphingolipids have a greater variety of molecular species than previously expected.