Charge-remote fragmentation has been well recognized as an effective approach for dissociation of long aliphatic chains. Herein, we exploited this approach for structural identification of all fatty acids including saturated, unsaturated, and modified ones by using electrospray ionization tandem mass spectrometry after one-step derivatization of a charge-carried reagent through an amidation reaction. We tested the approach with different charge-carried reagents with respect to the hydrophobicity, charge strength, and distance from the charge to the carboxyl group. We found that all of the derivatives with these reagents could yield informative charge-remote fragmentation patterns regardless of the different chemical and physical properties of the reagents. These informative fragmentation patterns all could be effectively used for structural elucidation of lipid species containing a carboxyl group. We further found that the distinguished charge-remote fragmentations of fatty acid isomers enabled us to determine the composition of these isomers without any chromatographic separation. Finally, the abundant fragments yielded from an individual derivatized moiety enabled us to sensitively quantify the individual species containing a carboxyl group. The described approach was a great extension to the multidimensional mass-spectrometry-based shotgun lipidomics for global analysis of fatty acids including isomers and modifications. We believe that this approach could greatly facilitate identification of the biochemical mechanisms underlying numerous pathological conditions.