Factors that contribute to the complexity of protein digests

High-throughput proteomics is one of the most dynamically developing research areas. Frequently, the whole protein content of a cell is digested, fractionated and analyzed in a completely automated way, including data analysis. Not only are proteins identified this way, but quantitative studies are also performed, and posttranslational modifications and covalently labeled derivatives are identified. Because the presence of unexpected and/or unconsidered contaminants or covalently modified peptides can lead to data misinterpretation in such an environment, it is mandatory that we attempt to identify, understand and evaluate the factors that can contribute to the complexity of protein digest mixtures.