Unable to obtain a graduate research position, she worked as a food quality supervisor at A&P supermarkets and for a food lab in New York, testing the acidity of pickles and the color of egg yolk going into mayonnaise. She moved to a position at Johnson & Johnson that she hoped would be more promising, but ultimately involved testing the strength of sutures. In 1944, she left to work as an assistant to George H. Hitchings at the Burroughs-Wellcome pharmaceutical company (now GlaxoSmithKline) in Tuckahoe, New York. Hitchings was using a new way of developing drugs, by intentionally imitating natural compounds instead of through trial and error. Specifically, he was interested in synthesizing antagonists to nucleic acid derivatives, with the goal that these antagonists would integrate into biological pathways. He believed that if he could trick cancer cells into accepting artificial compounds for their growth, they could be destroyed without also destroying normal cells.Gertrude synthesized anti-metabolites of purines, and in 1950, she developed the anti-cancer drugs tioguanine and mercaptopurine.