Selenium is an essential trace element incorporated as selenocysteine (Sec) in selenoproteins. Selenium has enjoyed increased attention in studies due to it playing an essential role in a variety of cellular processes. It is involved in protection against excess H2O2, heavy metal detoxification, and regulation of both the immune and reproductive systems. Selenium has been found to have been protective in a range of cancers, but also in many neurodegenerative disorders, including both Alzheimer’s and Parkinson’s disease, particularly when populations are deficient. On the other side having too much Se can be toxic and there are documented cases of acute exposure through poor manufacturing and quality control of supplements and through environmental exposure due to selenium-rich geological deposits. In this study, we investigated the effect of dietary selenium deficiency and supernutritial doses and how effects incorporation of SeCys into different selenoproteins in rat liver. We additionally used shotgun proteomics and identified nonselenoproteins regulated by dietary changes in Se. Our results confirm that selenium treatment results in increased selenium incorporation. Selenium-treated animals also showed a significant alteration of the expression of 30 separate proteins. We found that an increase in dietary selenium caused an upregulation of essential proteins such as glutathione peroxidase (Gpx1, an essential protein and the major selenoprotein in most animal tissue). There also changes in non-selenium containing proteins linked to energy production, lipid metabolism or protein synthesis pathways. This indicates the broad effect on cellular metabolism that can be perpetuated through changes in selenium exposure or deficiencies and begins to explain how this essential element can be involved in a wide variety of diseases.