Abstract: Described herein is a method of analyzing a sample including molecules having two or more possible sites for ionization comprising: 1) separating ionized molecules of the sample according to ion mobility of the ionized molecules, and 2) analyzing the ionized molecules using mass spectrometry. Additionally described herein is a method of diagnosing and/or determining the progression of a disease or disorder associated with gangliosides and/or cardiolipins in a subject comprising: 1) separating ionized molecules in a biological sample from the subject according to ion mobility of the ionized molecules, and 2) analyzing the ionized molecules using mass spectrometry to identify and quantify gangliosides and/or cardiolipins in the sample.