Peptide Puzzle Pieces: Perceiving Peculiarly Produced Proteins

Jackson Eberwein, Sonoma State University

The Approach: In my previous post, I discussed some of the problems about Domoic Acid Toxicosis in California sea lions, closing with the potential benefit of finding a biomarker protein. The first step in finding anything is to take a good look! How does someone look at something as small as a protein, though? When trying to see which proteins are in a sample of blood plasma and count how many there are of each, it can get complicated. The way I am achieving this is by using an instrument called a mass spectrometer. With it, I can predict the identity and amount of each protein in a sample. The mass spectrometer is picky, however. To read my proteins, it wants them to be cut up first. 

Orbitrap mass spectrometer (right) with attached liquid chromatograph (left).

Proteins are similar in structure to a tangle of string. The tangle first has to be unraveled, then it is cut up into small bits called peptides. These peptides are put into the mass spectrometer to be read. The shape of each peptide is pretty unique, and that unique shape is used to detect and measure them. With the help of some very handy computer programs, peptide measurements can be compared to a California sea lion genetic database to predict the protein that each peptide came from and how many of those proteins there might have been in the sample. Once we have the names and amounts of the proteins in the sea lion samples, the protein differences between each sample can be looked at. This is where we look for our biomarker. If there are one or more proteins that appear at consistently different levels in sea lion samples with Domoic Acid Toxicosis than in samples without it, those proteins have potential as good biomarkers! 


I would like to thank Dr. Michael Janech, Dr. Benjamin Neely, Alison Bland, The Marine Mammal Center, & College of Charleston. Supported in part by the Fort Johnson REU Program, NSF DBI-1757899.


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