Modeling Experimental Design for Proteomics

The complexity of proteomes makes good experimental design essential for their successful investigation. Here, we describe how proteomics experiments can be modeled and how computer simulations of these models can be used to improve experimental designs. Key words: Proteomics, Mass spectrometry, Experimental design, Simulations, Modeling The proteomics researcher that aims at comprehensive proteome analysis using mass spectrometry (MS)-based methods will face experimental challenges. These challenges are due to the many different proteins encoded by a genome, the rich variation of protein posttranslational modifications, and the large concentra-tion differences between different proteins. The range of protein concentrations have been measured to be six orders of magni-tude in Saccharomyces cerevisiae (1) and estimated to be larger than ten orders of magnitude in body fluids (2). In contrast to these wide abundance ranges, the MS detection methods typi