In the field of marine microbial ecology, many questions remain unanswered with regards to the physiological trade-offs made by phytoplankton to maximize growth (e.g., nutrient acquisition) and minimize loss (e.g., predation defenses). These tradeoffs, which occur at the cellular level, have wide reaching impacts on food web dynamics and global biogeochemical cycles. In the first chapter, we explored the use of a non-canonical amino acid (NCAA) technique, bioorthogonal non-canonical amino-acid tagging (BONCAT), in phytoplankton model systems. This technique has potential to work well in natural systems by enabling isolation of only newly synthesized proteins during an incubation period with the NCAA, reducing the complexity of natural proteomics and easing the elucidation of patterns. However, in testing BONCAT across several groups of cultured phytoplankton, we discovered that the NCAA molecule induced a stress response in the globally ubiquitous marine picocyanobacteria, Synechococcus sp. Therefore, in addition to confirming the uptake of modified amino acids by phytoplankton, chapter one investigated the implications of this stress response and limitations when using this technique to study marine microbial communities. In chapter two, we addressed our initial question by exploring tradeoffs at the protein level in a simplified culture system. This approach revealed insights into metabolic tradeoffs in response to predation pressure and nutrient stress. These insights into how phytoplankton negotiate these physiological tradeoffs at the protein level could ultimately allow for targeted proteomic studies in natural systems.