Purification and Proteomic Analysis of Major Whey Proteins in a Nutritional Supplement: A Six‐Week Undergraduate Independent Project

We sought to create an undergraduate laboratory experience to introduce the field of proteomics and the associated mass spectrometric (MS) techniques alongside classic protein purification methodologies. Students were tasked with the purification and identification of one of the major proteins found in a whey‐based nutritional supplement with the ultimate goal of having students become the drivers of their independent projects. Two major challenges were 1) to complete the experiments in 4‐hour blocks over several weeks in a typical semester and 2) to train sixteen students per lab period on a single mass spectrometer. A six‐week project was developed where students spent four lab periods performing either ion‐exchange or gel filtration chromatography and SDS‐PAGE, and two lab periods gathering bottom‐up and top‐down proteomic data with a matrix‐assisted laser desorption ionization (MALDI) mass spectrometry. The resulting data, peptide mass fingerprints and tandem mass spectra, were analyzed via database searching (i.e. MASCOT) during these weeks or outside the laboratory periods. The abundance of literature on the major whey proteins in terms of the biology, purification, and even proteomic analyses allowed students to determine their mode of protein purification and conditions for MALDI‐MS. This project is fairly low cost and widely applicable to any institution with appropriate facilities. Support or Funding Information This work was funded in part by a grant from the Siena College Committee on Teaching and Faculty Development (RSM) and the Siena College School of Science (EEH). This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .