S6-1.1 Thursday, Jan. 5 Experimental contexts and statistical choices: Challenges for interpreting the proteomics of environmental stress DOWD, W.W.; Loyola Marymount University email@example.com
Environmental physiology, toxicology, and ecology and evolution stand to benefit substantially from the relatively recent surge of ‘omics’ technologies into these fields. These approaches, and proteomics in particular, promise to elucidate novel and integrative functional responses of organisms to diverse environmental challenges, over a variety of time scales and at different levels of organization. However, application of proteomics to environmental questions suffers from several factors – some unique to omics technologies and some relevant to many related fields – that complicate interpretation of the data. I will explore two important contingencies in proteomics and how they challenge the interpretation of data regarding organisms’ responses to environmental stress: 1. Dependence of biological conclusions drawn from environmental stress proteomics studies on the choice of experimental conditions; and 2. Dependence of biological inferences from a single multivariate proteomics dataset on the choice of statistical methods. I draw upon both a review of the literature and data generated from my previous and ongoing proteomics studies of coastal marine animals: responses to episodes of hypoxia or anoxia in the rectal gland of the epaulette shark (Hemiscyllium ocellatum), and comparative proteomics of differential thermal tolerance in the gills of intertidal Mytilus mussel congeners. Although some of these experimental design and statistical issues await further critical assessment and debate, I conclude by offering some suggestions for meeting these challenges.