This talk will describe an approach for using mass spectrometry and arrays of self-assembled monolayers to perform quantitative experiments in high throughput. The arrays are prepared by immobilizing small molecules, proteins, peptides and carbohydrates to self-assembled monolayers of alkanethiolates on gold. This arrays are then treated with reactants—either chemical reagents or enzymes—and then analyzed using the SAMDI technique to identify the masses of substituted alkanethiolates in the monolayer and therefore a broad range of reactivities and post-translational modifications—including kinase, protease, methyltransferase and carbohydrate-directed modifications—and for discovering chemical reactions. This talk will describe applications to high throughput experiments, including the discovery of reactions, the use of carbohydrate arrays to discover novel enzymes, the preparation of peptide arrays to profile the enzyme activities in cell lysates and high-throughput screening to discover novel reactions and small molecular modulators. These examples illustrate the broad capability of the SAMDI method to profile and discover molecular activities in the molecular sciences.