Matrix assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) has the ability to provide an enormous amount of information on the abundances and spatial distributions of molecules within biological cells. to the brain by axons Palomid 529 (P529) of retinal ganglion cells. Diseases of the retina including age related macular degeneration (AMD) retinitis pigmentosa and diabetic retinopathy happen when the functions of these cells are interrupted by molecular processes that are not fully understood. With this statement we demonstrate the use of high spatial resolution Palomid 529 (P529) MALDI IMS and FT-ICR tandem mass spectrometry in the knockout mouse model of Stargardt disease a juvenile onset form of macular degeneration. The spatial distributions and identity of lipid and retinoid metabolites are shown to be unique to specific retinal cell layers. Intro The mammalian retina is definitely a highly complex cells capable of transforming light of various wavelengths into signals that can be interpreted by the brain to produce images. The complex anatomy of the retina is definitely formed from a rich diversity of cells including light sensing neurons not found anywhere else in the body . The layered structure of the mammalian retina was first studied in depth more than 100 years ago although Leonardo Da Vinci depicted layers in the eye in his anatomical studies dating back as early as the Fifteenth century . Within these layers the unique cell forms of the retina have well-defined physiological functions the loss of which can result in eye diseases that cause loss of vision such as age-related macular degeneration (AMD)  diabetic retinopathy [4 5 Stargardt’s disease [6-8] and retinitis pigmentosa . MALDI IMS technology offers rapidly progressed over the past decade with significant improvements seen in instrumentation [10-12] laser Palomid 529 (P529) technology [13-15] and sample preparation [16-24] techniques. These advances provide for increased sensitivity reduced acquisition time and higher spatial resolution. Furthermore these improvements have broadened the application of MALDI IMS to biological tissues of smaller sample size and feature sizes than was previously possible [25-27]. Earlier studies of lipid distributions in cross sections of retinal cells using MALDI IMS included mouse  salamander  and pig cells . Hayasaka utilized a MALDI QIT-TOF instrument and observed a number of phospholipid varieties distributed in the varying Palomid 529 (P529) layers of a mouse retina at a spatial resolution of 50 μm . The identities of the lipid varieties were confirmed using MS/MS Palomid 529 (P529) analysis on the same sections. Roy utilized atmospheric pressure MALDI IMS to observe phospholipid varieties inside a salamander retina at high spatial resolution (8 μm). Images generated from signals unique to the outer and inner plexiform coating and signals originating from the inner and outer segments of the photoreceptors and RPE region were observed. EMR2 Lipid varieties present in the salamander retina were recognized using LCESI MS/MS analysis . Previously published work using bad ion mode analysis of rat and human being retinal cells had been performed using chloroform/methanol extraction of homogenized cells followed by LC-MS [31 32 to identify retinal lipids. However since the whole cells was homogenized the spatial distribution of these lipids in relation to the cell forms of the retina was lost. The gene (also known as gene have been shown to have elevated levels of phosphatidylethanolamine (PE) in the photoreceptor cell outer segments and accumulate retinoid metabolites such as N-retinylidene-N-retinylethanolamine (A2E) in the retinal pigment epithelium (RPE) following photoreceptor phagocytosis . These highly lipophilic side products of the retinoid visual cycle are major components of lipofuscin and may Palomid 529 (P529) be harmful to cells [35-38]. Therefore the processes including retinoid regeneration are of great interest for the understanding of retinal degenerative diseases [39-42]. For the purpose of the present work the high large quantity of A2E in the RPE coating provides definition of this single cell coating in MALDI IMS experiments. Here we present data from mouse. These experiments provide new evidence within the distributions of these crucial molecules in solitary cell layers.