Assessment of diet currently relies on self-reporting, such as food logs, 24 hour recalls and food frequency questionnaires. Self-reporting of diet is inaccurate due to memory lapses, lying and biased language. A molecular-based approach to assess diet would allow accurate reporting of diet for researchers, medical professionals and patients. We performed metaproteomic analysis of five human stool samples collected from a free-eating individual over five consecutive days (25Jun18-29Jun18). The free-eating individual maintained a food log during the sample collection period. We used these samples to develop a molecular-based approach for assessing diet.