Honey bees play a crucial role in pollinating wild and cultivated vegetation, with substantial implications on our economy and food supply. Our scientific knowledge of bees consists largely of behavioral or macroscopic-level biological studies. Although in the past several decades there have been some advances in our knowledge of specific hormones, genes, and proteins, molecular biology of bees remain poorly understood relative to the depth to which we understand humans, and typical model organisms such as the mouse or fruit fly. This is due in part to the lack of available reagents for interrogating protein-specific information in standard assays such as Western blot, immunolocalization, and immunoaffinity purification, as well as a relatively difficult system for introducing small, interfering RNAs. Given the available genome sequence then, mass spectrometry-based proteomics techniques are ideally suited to studies in bees; starting from so little knowledge, the discovery-based nature of proteomics should allow for a very steep learning curve relative to better-studied systems such as fruit fly. To this end, twenty-two honey bee proteomics papers have been published since 2005. Here we present a brief summary of biochemical/molecular biological research in bees, including some of the challenges; we focus on the proteomics work to date, and relate these findings to recent transcriptomic work and proteomic studies in other social insects. We end with some speculation on where proteomics is most likely able to provide insight into bee biology where other methods would fail. As the general population and scientific community become increasingly aware of the value of honey bees to both our economy and ecosystem, proteomics will play an important role in improving our understanding of this beneficial insect.