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Ciona intestinalis is a solitary ascidian that lives in temperate waters around the globe. C. intestinalis in Rhode Island exhibit normal embryonic development at water temperatures between 10° C and 18° C. This thesis is interested in what changes occur in the ovary tissue at temperatures above 18° C and below 10° C. A preliminary study to assess the reproductive fitness of C. intestinalis, found that C. intestinalis raised at 22 °C had lower embryo viability when compared to the normal temperature range. 22 °C was chosen to mimic the high temperature predicted in some climate change models (IPCC, 2014). During the coldest part of the winter when temperatures drop below 8 °C, feeding slows, the production of gametes ceases, and much of the ovary tissue is resorbed (Dybern, 1965). Ovary samples were collected from animals reared at 18 °C, 22 °C, and from a non-temperature controlled tank at 8 ºC. The samples were processed and sequenced by mass spectrometry. The data showed a decrease in the number of proteins produced between 18 ºC and 22 ºC samples. It also showed that there were more proteins upregulated in 22 °C compared to the 18 °C samples. Over the winter, the number of proteins also decreases when compared to 18 °C, and metabolic pathways were downregulated. Due to the lack of methods for ecological studies dealing with proteomic data, new methods were developed for both tissue and data processing.