As a pioneering biochemist, Downes was instrumental in establishing the biological importance of the inositol glycerophospholipids and their metabolites. Among his other discoveries are the identification of the mechanism of action for the drug
lithium, which has since been used in the treatment of manic depression, and the breakthrough in finding the biochemical pathway that is the most common source of mutations leading to human cancers. As a result of this work, many new avenues have opened up into the discovery of new drugs and to deeper levels of understanding regarding many common diseases. In his capacity as Principal he has focused on fostering research links between academia and industry particularly in his own field of life sciences; his tenure has however seen financial challenges following Government cutbacks in funding. As former Convenor of
Universities Scotland, Downes has spoken out against the
UK's decision to exit the European Union citing the potential adverse effect on research funding and freedom of movement for staff and students. Downes was knighted in the Queen's 2015 Birthday Honours, "For services to Higher Education and Life Sciences." It was announced on 2 July 2018 that Sir Pete would be succeeded as Principal and Vice-Chancellor by Professor Andrew Atherton on 1 January 2019. Following the end of his term at Dundee, Downes was appointed chairman of
Dynamic Earth in March 2019, the geology-based visitor attraction in
Holyrood, Edinburgh. ==Honours and awards==