An automated tandem mass spectrometry based analysis employing precursor ion and neutral loss scans in a triple quadrupole mass spectrometer has been employed to identify and quantify changes in the abundances of glycerophospholipids extracted from retina and erythrocytes in a rat streptozotocin model of type 1 diabetes, 6 weeks and 36 weeks following induction of diabetes, compared to age matched nondiabetic controls. The utility of an 'internal standard' method compared to an 'internal standard free' method for quantification of differences in the abundances of specific lipid ions was evaluated in both retina and erythrocyte lipid extracts. In retina, equivalent results were obtained by using the internal standard and 'internal standard free' methods for quantification. In erythrocytes, the two methods of analysis yielded significantly different results, suggesting that factors intrinsic to particular sample types may influence the outcome of label-free lipidome quantification approaches.Overall increases (~25% to ~35%) in the abundances of major retina glycerophospholipid classes were demonstrated in rats at 6 weeks of diabetes, relative to control animals. However, at 36 weeks of diabetes, subsequent overall decreases in retina glycerophosphocholine and glycerophosphoethanolamine abundances of 16% and 33%, respectively, were observed. Additionally, retina and erythrocyte glycerophosphocholine lipids at both 6 week and 36 weeks of diabetes exhibited increased incorporation of linoleic acid((18:2n6)) and a decrease in docosahexaenoic acid (DHA((22:6n3))) content. Finally, an approximately 5-fold increase in the abundances of specific glycated glycerophosphoethanolamine (Amadori-GPEtn) lipids were observed in the retina of 36 week diabetic rats, with a corresponding 1.6 fold increase of Amadori-GPEtn lipids in diabetic erythrocytes.