|Using protein databases
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The Problem: In the year 2236 Pittsburgh, Pennsylvania was chosen as the location for the Species Olympics. Different events determine the fastest individual for each event. Species include homo sapien, canine and equine to name a few. After each event, a blood test is required of the winner to determine whether a drug enhanced their performance and to determine if the correct species ran the race. Unfortunately, these blood samples were mislabeled for many of the winners and after drug testing several of these individuals did indeed come up positive for drugs. You, as an expert in species determination by mass spectrometry, must take a blood sample that tested positive and determine what species cheated. You can solve this problem by identifying the species using a common blood protein, serum albumin. Once identified, the species in question will be removed of his/her medal.
Brief Background: We know that most non-human creatures share many biological traits with us. We can see a bird's wing as an analog for our arms; so is the fish's flipper, and the horse's front leg. Likewise, we have many internal organs in common. Our digestive system is similar to that of the aforementioned species. Our nervous system is also analogous. So it is not surprising that these similarities continue down to the molecular level, all the way down to our proteins. One such protein is serum albumin, a protein that comprises roughly 60% of human blood plasma and a large fraction in other creatures as well. Serum albumin is a carrier protein; to learn more about it, see the detailed background.
And yet, we are very different from other animals. We can distinguish between human arms, equine legs, and fins, and wings. While we share analogous structures with similar function, there are marked differences between these structures. Again, it is the same with proteins: similar in function and design, but quite distinguishable. Unfortunately, it is not as easy to distinguish between avian and human protein as it is to distinguish between an arm and a wing.
So what is a scientist to do? Well, thanks to the leaps proteomics has made in past few years, databases which contain millions of proteins now exist. When a protein is sequenced, researchers can compare it to known proteins. If there are not any matches, then they know they have a new protein. One of the many ways to identify unknown proteins is to use enzymes such as trypsin or chymotrypsin to "digest" large proteins into peptide fragments. Each unique protein will produce a unique pattern of fragments. Mass spectrometry comes into the picture when it is used to determine the masses of these fragments, and the "matching" of fragments (between the experimental data and database information) can be used to positively identify a protein. Mass spectrometry (using the right instrument) can be performed on intact proteins; however, many different proteins can have the same mass. By matching a number of peaks, the identity of a protein can be discovered with a higher degree of confidence.
The Experiment: You must take one or more of the 10 possible blood samples and identify what species donated the blood. This experiment will require an enzyme digestion and the use of mass spectrometry. You may determine the masses of all of the peptide fragments and enter this data into a protein database search engine or dissociate the peptides into product ions and enter this MS/MS data into a protein database search engine. The protein database search engines will tell you the top matches and will calculate a confidence score (e.g. MOWSE score) for all of your matches. Do not trust the top match without evaluating the information presented. Please note that the protein database search engines are a product from other researchers.
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