Cross-over electrophoresis, an immunological method for analyzing blood residues on archaeological artifacts, is tested. Artifacts from three sites were utilized in the testing of this methodology. The sites are the Dietz site in south-central Oregon (282 artifacts), Konemehu in northern California (48 artifacts tested for Winthrop Associates), and Chimney Shelter in southwestern Oregon (3 artifacts from the Umpqua National Forest).

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On the broadest level this dissertation makes a methodological statement about the design of regional research in archaeology, especially for Cultural Resource Management. It advocates by example a revised concept and set of requirements for regional research design. This revision views regional research design as something different from project-specific design. Regional research design requires the archaeologist focus on the total research potential of a region, rather than those problems that fascinate an individual. The regional research design resembles an overview in taking this perspective, but differs by providing an archaeological research program. This program specifies how the potential of an area relates to the coordination of research effort between projects, the assessment of archaeological significance and the integration of small projects. At no time is the regional research design a cookbook. It can never realize the unique potential of a specific project, nor specify exact techniques for field work. A regional research design for southwestern Arizona provides the empirical illustration of the revised concept and requirements. As is typical of most CRM research, this area does not equate to either a physiographic or cultural unit but rather results from the Bureau of Land Management and the National Forest Service's division of Arizona into Class I overview units. The core of this research design is a synthesis of the environment, ethnography, and archaeology of the region. This synthesis and an historical consideration of archaeological research in the area provides the basis for identifying the major scientific issues which archaeologists have (or can) addressed in the region. This leads to the development of a research program for southwestern Arizona. The research program specifies a minimal representative data set that all projects in the region should collect.

Liquid chromatography-mass spectrometry (LC-MS) based proteomic methods have provided archaeologists with a powerful tool for the discovery and identification of proteins within artifacts. Traditionally, discovery-based methods have utilized a non-targeted full mass scan method in an attempt to identify all proteins present within a given sample. However, increased sensitivity is often needed to target specific proteins in order to test hypotheses. Proteins present within archaeological materials present a unique challenge, as they are often subjected to a variety of chemical transformations both before and after burial. Any preserved proteins will be present within a complex mixture of compounds, and full mass scans often fail to detect less abundant proteins of interest. Consistent and reliable targeted methods are needed to detect protein biomarkers. Taphonomic experimentation was employed as a means to identify the effect of particular processes and conditions on the preservation of mare's milk proteins. In addition, three LC-MS methods were evaluated for their efficiency in identifying mare's milk-specific peptide biomarkers from experimental pottery samples. The ability to reliably detect the presence of these species-specific peptides can help provide evidence about past cultural groups, including the origins of dairying and animal domestication.