Shotgun lipidomics exploits the unique chemical and physical properties of lipid classes and individual molecular species to facilitate the high-throughput analysis of a cellular lipidome on a large scale directly from the extracts of biological samples. A platform for comprehensive analysis of lysophospholipid (LPL) species based on shotgun lipidomics has not been established. Herein, after extensive characterization of the fragmentation pattern of individual LPL class and optimization of all experimental conditions including developing new methods for optimization of collision energy, and recovery and enrichment of LPL classes from the aqueous phase after solvent extraction, a new method for comprehensive and quantitative analysis of LPL species was developed. This newly developed method was applied for comprehensive analysis of LPL species present in mouse liver samples. Remarkably, the study revealed significant accumulation of LPL species in the liver of ob/ob mice. Taken together, by exploiting the principles of shotgun lipidomics in combination with a novel strategy of sample preparation, LPL species present in biological samples can be determined by the established method. We believe that this development is significant and useful for understanding the pathways of phospholipid metabolism and for elucidating the role of LPL species in signal transduction and other biological functions.