Philip Anderson Shaffer was born in Martinsburg, West Virginia. He graduated from the University of West Virginia with a B.A. in 1900 and from Harvard University with a Ph.D. degree in 1904. At Harvard, Shaffer worked with Otto Folin and became interested in methods for the determination of organic substances in blood, urine, and milk. For a time, Shaffer served as a research biological chemist at the McLean Hospital in Waverly, Massachusetts, and from 1904 to 1910 he was an instructor in pathological chemistry at Cornell University Medical College. He then became professor of biological chemistry at the Washington University School of Medicine, St. Louis, Missouri, where he built up a strong department of physiological chemistry.
Shaffer's scientific work was varied in character. He studied metabolism in disease, nutrition in typhoid fever, protein metabolism in exophthalmic goiter, and protein metabolism in cystinuria. His studies on antiketogenesis were especially noteworthy and appeared in a series of papers in the Journal of Biological Chemistry. He also developed a means for purifying insulin for use in childhood diabetes and, with Alexis Hartmann, invented a test for measuring blood sugar levels, which became widely used. Later in his career, Shaffer studied the oxidations induced by sugars, the electrometric reduction potentials of sugars, and coupled reactions involving intermediate peroxides.
For many years, Shaffer served as secretary of the American Society of Biological Chemists, and he was president for two terms, 1923 and 1924.He also succeeded Russell H. Chittenden as the Society historian. He was elected to the National Academy of Sciences in 1928.