A system for quantitating lipids of a matrix sample using a differential mobility spectrometry device during a targeted multiple reaction monitoring acquisition experiment, comprising: a separation device configured to receive sequentially a first injection and a second injection of a matrix sample and to separate known lipid molecules of the matrix from the first injection and the second injection over time, wherein before the experiment the known lipid molecules of the matrix are grouped into lipid classes and the lipid classes are further grouped into a pass-through group that includes lipid classes without lipid molecules known to produce isobaric interferences with other lipid molecules and a mobility separation group that includes lipid classes with lipid molecules known to produce isobaric interferences; an ion source configured to receive separated lipid molecules from the separation device for the first injection and the second injection and to ionize the separated lipid molecules for the first injection and the second injection; a DMS device configured to receive a first beam of ions of the separated lipid molecules for the first injection and pass the first beam through without ion mobility separation, and to receive a second beam of ions of the separated lipid molecules for the second injection and sequentially mobility separate the second beam according to compensation voltage (CoV) values experimentally predetermined for each lipid class of the mobility separation group; a tandem mass spectrometer configured to receive the first ion beam from the DMS device, for a first plurality of cycles, perform an MRM scan for at least one MRM transition for each lipid molecule of each lipid class of the pass-through group, and store a first set of intensity values of each MRM scan for the first plurality of cycles, and to receive the second mobility separated ion beam from the DMS device, for a second plurality of cycles, perform an MRM scan for at least one MRM transition for each lipid molecule of each lipid class of the mobility separation group, and store a second set of intensity values of each MRM scan for the second plurality of cycles, wherein each MRM transition of each lipid molecules is experimentally predetermined; a processor in communication with the mass spectrometer and the DMS device configured to receive the first set of intensity values and the second set of intensity values, to receive MRM intensity and concentration values for known standards of the known lipid molecules of the matrix, and to quantitate each lipid molecule in the matrix sample by comparing the first set of intensity values and the second set of intensity values to the MRM intensity and concentration values for the known standards of the known lipid molecules of the matrix. a separation device configured to receive sequentially a first injection and a second injection of a matrix sample and to separate known lipid molecules of the matrix from the first injection and the second injection over time, wherein before the experiment the known lipid molecules of the matrix are grouped into lipid classes and the lipid classes are further grouped into a pass-through group that includes lipid classes without lipid molecules known to produce isobaric interferences with other lipid molecules and a mobility separation group that includes lipid classes with lipid molecules known to produce isobaric interferences; an ion source configured to receive separated lipid molecules from the separation device for the first injection and the second injection and to ionize the separated lipid molecules for the first injection and the second injection; a DMS device configured to receive a first beam of ions of the separated lipid molecules for the first injection and pass the first beam through without ion mobility separation, and to receive a second beam of ions of the separated lipid molecules for the second injection and sequentially mobility separate the second beam according to compensation voltage (CoV) values experimentally predetermined for each lipid class of the mobility separation group; a tandem mass spectrometer configured to receive the first ion beam from the DMS device, for a first plurality of cycles, perform an MRM scan for at least one MRM transition for each lipid molecule of each lipid class of the pass-through group, and store a first set of intensity values of each MRM scan for the first plurality of cycles, and to receive the second mobility separated ion beam from the DMS device, for a second plurality of cycles, perform an MRM scan for at least one MRM transition for each lipid molecule of each lipid class of the mobility separation group, and store a second set of intensity values of each MRM scan for the second plurality of cycles, wherein each MRM transition of each lipid molecules is experimentally predetermined; a processor in communication with the mass spectrometer and the DMS device configured to receive the first set of intensity values and the second set of intensity values, to receive MRM intensity and concentration values for known standards of the known lipid molecules of the matrix, and to quantitate each lipid molecule in the matrix sample by comparing the first set of intensity values and the second set of intensity values to the MRM intensity and concentration values for the known standards of the known lipid molecules of the matrix.