Development of a Differential Multiplex PCR Assay for the Supplemental Identification of Different Sources of Proteins

Background: Differentiation of proteins from multiple sources provides challenges in the accuracy using multiple and often disputed protein identification methods. The U.S. Pharmacopeia Food Chemical Codex does not include monographs for many protein sources, including milk proteins and soy protein isolate. Monographs that are included for proteins do not list a single comprehensive identification method but instead rely on a combined assessment of ash (total), fat, lactose, loss on drying, and protein content. A fast, inexpensive, and accurate protein source assay is tantamount to prevention of economic adulteration in protein powders. Objective: This study describes the development of a novel method to identify and differentiate animal proteins (cow protein powders as milk protein and whey protein) and plant proteins (soy protein powders). These proteins powders are of high importance to the food and dietary supplement industries, as they encompass the highest grossing and fastest growing protein sources in the global protein powder market. Methods: The developed method uses PCR amplification and gel electrophoresis of short chain DNA fragments found in processed protein powders to identify and differentiate the source of each powder. The original development was performed using reference materials of known identity and tested against an inclusivity panel of protein powders from commercial sources. Bands were identified using the Agilent Tapestation 4200 and Tapestation Analysis Software A.02.02 (SR1) using proprietary band analysis. Results: The developed method was found to be specific for the identification of each protein source, passing a computational (National Center for Biotechnology Information Basic Local Alignment Search Tool) exclusivity panel and an experimental inclusivity panel. The method was also able to detect multiple adulterants in concentrations as low as 1% (w/w). Conclusions: The developed method is fast, inexpensive, and accurate (100%) for the supplemental identification of cow and soy proteins and able to detect adulteration as low as 1% (w/w). Highlights: A new method can identify cow and soy proteins, and detect low levels of adulteration using DM-PCR.