Gene expression differs among individuals and populations and is thought to be a major determinant of phenotypic variation. Although variation and genetic loci responsible for RNA expression levels have been analyzed extensively in human populations, our knowledge is limited regarding the differences in human protein abundance and the genetic basis for this difference. Here we have used quantitative mass spectrometry to determine protein abundance in cell lines as well as in a variety of human tissues. We will describe the variation in proteins between individuals and across tissues. Integrating genomic and transcriptomic data, we will discuss genetic regulation of protein abundance, and consider approaches of integrating protein abundance in studies of complex traits and diseases. This is joint work with Mike Snyder and others.