The Problem:   In the year 2100 Pittsburgh, Pennsylvania was chosen as the location for the Species Olympics. One event determined the fastest individual from each of the different species. Races included Homo sapiens, canines and equines to name a few. The Species Olympics requires blood testing for both drugs and species genetic identification for all medal winner. Unfortunately, these blood samples were mislabeled for many of the racers and after drug testing several species came up positive. The genetic test was OK -- all individual winners were of the correct species in their event. You as an expert in species determination by mass spectrometry, must take a blood sample known to come from a violator and determine what species should 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. In this case, size does matter.

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 aren’t 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 have before you the five samples of blood; serum albumin has been isolated from each. You must take each sample and, one by one, perform a tryptic digest and us mass spectrometry to find the masses of the peptide fragments. Once you have collected sound data, use a database such as MS-Fit or PROWL to determine the identity of the creature from which each sample came.