Geoduck clams (Panopea generosa) are an increasingly important fishery and aquaculture product in the United States while also holding essential ecological roles. These long-lived clams are highly fecund, but sustainable hatchery production of genetically diverse larvae is hindered by the lack of sexual dimorphism, resulting in asynchronous spawning of broodstock, unequal sex ratios, and low numbers of breeders. Assays of gonad physiology could indicate both sex and maturation stage. Proteomic profiles were determined for three reproductive maturation stages in both male and female clams using data dependent acquisition (DDA), or whole proteome profiling, of gonad proteins. Gonad proteomes became increasingly divergent between males and females as maturation progressed. The DDA data was used to develop targets analyzed with selected reaction monitoring (SRM) in gonad tissue as well as hemolymph. The SRM assay yielded a suite of indicator peptides that can be used as an efficient assay to non-lethally determine geoduck sex and maturation stage pre-spawning. These results lay the foundation for the development of field-based tools to assess reproductive status in marine mollusks.