Microarray and gene expression analysis have been key in our understanding of molecular pathways underlying physiological responses. Arguably, a large number of microarray based studies in fish have examined steroid nuclear receptor signaling (e.g., estrogens, androgens) in the context of both physiology and toxicology. Following close behind the advances in gene expression analysis, novel proteomic tools are available that have been under utilized in fish endocrinology studies. Quantitative proteomic approaches include both gel based (e.g., 2D gel electrophoresis, 2-D Fluorescence Difference Gel Electrophoresis; DIGE) and non-gel based methods that can be separated further into labeling approaches such as stable isotope labeling (SILAC), isotope coded affinity tags (ICAT), and isobaric tagging (iTRAQ) and label-free approaches (e.g., spectral counting and absolute quantitation). This review summarizes quantitative proteomic approaches and describes a successful application of iTRAQ) to study changes in the liver proteome in fathead minnows in response to the androgen, 17beta-trenbolone. The challenge remains to integrate molecular datasets in such a manner as to be able to consider temporal effects and complex regulation at the level of the genome and proteome.