Peptide digestion

You will remember that Mass Spectrometery is a technique that allows you to look at all of the proteins in a sample and the relative abundances of those proteins. This is accomplished by sending tiny bits of proteins whizzing down a machine to measure how long they are able to fly. The topic of the day is how one gets those tiny bits to shoot into a mass spectrometer. 

Proteins are macromolecules (this means that they are pretty big as far as molecules go but still too tiny to see with a light microscope) made up of amino acids. There are enzymes called proteases specially designed to chop up proteins into managable chunks when the cell needs to recycle them. I found this picture on a supplement site and was intrigued, the site recommends taking a protease supplement for all kinds of infections. This picture is rather misleading though, there are actually many kinds of proteases each which cleaves after a specific pattern of amino acids. This is important because knowing where a protease cuts helps you determine the sequence of the protein around the cut, in turn helping you to identify what protein you chopped up. The protease we use is Trypsin which cuts after pretty much any basic amino acid. I couldn't figure out which protease they were selling in the supplement. Probably trypsin since trypsin functions at low pH and this is a pill that you take, but who knows?
After digesting the proteins into little peptides, you need to get rid of the trypsin and some of the salts that were added. To do that you let the solution drip through tiny filters. They look pretty cool which is good because it takes a long time. Once you have clean little peptides, you lyophylize them. This is a fun word to say and just fancy for dehydrate.
Then you stick them in the little octopus vials and are ready to load them on the mass spectrometer.