Proteomics? What in the world is that!?

28 Jul 2017

One of the fields I am interested in is that of proteomics. The problem with that is that the average person probably has never heard that word in their life, so I usually tell people that I study proteins. While this certainly avoids a lot of confusion, saying that I study proteins is still a pretty vague answer. This post is designed to be an introduction to proteomics that anyone (including your grandma) can understand.

So what is proteomics? Proteomics is a cousin to genomics, which is something you may have heard of before. Genomics deals with figuring out what the genetic code of somebody/something is. Essentially genomics is figuring out what DNA is in your body. Your genetic code acts as the blueprint that all your body’s cells use when making proteins. If you think of the DNA as the instructions to a Lego set, you can think of the proteins as the Lego creation itself. The DNA dictates which proteins should be made. Proteomics deals with figuring out what proteins are actually being made in your body. This sounds like a fairly simple task, but each organ in your body makes varying amounts of protein, and cells will often make special modifications to proteins. The goal of proteomics is to decode all that information so that we have a better understanding of how cells work and so that we can develop better drugs to fight disease.

One of the tools that makes proteomics possible is the mass spectrometer, or mass spec for short. A spectrometer is something used to measure data, and in the case of a mass spec, we are measuring mass. Why measure mass? Knowing how much a protein weighs goes a long way in figuring out what the protein is. We can also perform some neat tricks with the mass that help us figure out what all the individual parts of the protein are. You could almost say we are working with a glorified bathroom scale, but let’s remember that we are talking about measuring proteins, so how we measure their mass is actually a bit different.

To measure the mass of proteins, the mass spectrometer will use magnetic and electric fields to throw the proteins at a detector. It’s sort of like if you decided to weigh all your kids’ Lego sets by launching them across your lawn with a catapult. If we know with how much force the catapult is launching the Legos, we can use the distance that each item travels to measure its mass. A mini Lego creation will travel much farther than a Lego house. This is how the mass spec works. The further down the detector a protein hits, the lighter it is; the closer a protein hits, the heavier it is. We can then calculate the mass of the protein since we know how hard the mass spectrometer is throwing the proteins.

However, there is a problem with this method. Proteins can often come in very similar, if not identical, masses. To further obfuscate things, proteins come in an extreme range of sizes and consequently weights. If we wanted to measure the mass of a life-size Lego replica of Batman with the catapult, the mini Lego creation would end up in the neighbors yard! On the other hand, if we decreased the strength of the catapult so that the mini Lego creation stayed in our yard, we could then no longer measure the mass of life-size Batman because it wouldn’t go anywhere. To get around this problem, scientists will actually chop the proteins up into smaller pieces.

To chop the proteins up into smaller pieces, scientists use a special protein called an enzyme that will chop other proteins at specific locations. The resulting pieces, called peptides, still vary in their mass, but the variation is much smaller. Rather than dealing with a range of mini Lego creation to life-size Batman, we are now dealing with a range of mini Lego creation to Lego house. However, we now have another problem. Rather than being able to weigh each Lego set, we are now only weighing chunks of our Lego sets. Unfortunately, the chunks of our Lego sets are now mixed up with each other! To further add to the confusion, there are now so many chunks that they are piling up all over the yard! It would look like we are worse off than before when it comes to using a mass spectrometer, but us sneaky chemists still have a few tricks up our sleeves.

Let’s first examine the problem of everything now overlapping since we have so many chunks. An important method used by chemists is chromatography. This is sort of an awkward word, but essentially chromatography means we are separating out chemicals. I’m going to use an analogy to explain how chromatography works. Let’s say you are the principal of a school and you want to help prevent overcrowding when school lets out. To do so, you are going to let the kindergarteners leave first, and then move on up through the grades until you get to the sixth graders. As each class gets out, you’ll see a trickle of students coming out the doors (the kids who just can’t wait to get out of school), then you’ll see the main body of students coming out, and then you’ll see a few stragglers. Then you’ll see the same process repeat with the next grade up. This is exactly how chromatography works. A chemist will put all their chemicals on one side of a column, and then they’ll control the conditions that dictate what gets to move through the column. The result is that their chemicals come out the other end of the column one-by-one. With proteomics, we are usually dealing with so many different peptides that we can’t separate them one-by-one with chromatography, but we can separate them enough so that only a few come out at a time. It’s okay if the kindergarteners come out with the fourth graders because we can still see that they are different ages; likewise we don’t mind if several peptides are analyzed at the same time because they most likely have different masses. If we return to our Lego analogy, we are now grabbing small bucketfuls of Lego chunks from our pile of Lego chunks, catapulting and measuring those chunks, cleaning up the yard, and then repeating with the next bucketful. The process is much slower, but we are making sure we remain in the bounds of our yard, and we avoid the problem of trying to measure too much at once.

Okay, so we’ve solved the problem of too much stuff at once, but now what about the problem of not knowing what Lego chunk goes with what set? We chemists once again have another trick up our sleeves. You see, since we know what the genetic code of humans is, we know what proteins humans theoretically can make. Since we know what proteins can be found in humans, we don’t really care that we broke our proteins up into smaller pieces and then mixed them together. If we have the DNA for our Lego sets, AKA the instruction manuals, mixing up our Lego chunks isn’t the end of the world because we can pick up any given piece and figure out which Lego set it belongs to. A particular Lego piece might be shared between two Lego sets, but since Lego sets often come with unique pieces, we can still figure out which Lego sets we have in our pile of Legos. It’s the same thing with the peptides. We are looking to see what peptides we have and then we are matching them back to the potential proteins that a human can make.

The last hurdle we need to clear is how we can use mass to figure out what a certain peptide (or Lego chunk) is. The neat thing about a mass spectrometer is that once it finds a peptide, it can then smash that peptide and look at those pieces. How does that work? The building blocks of proteins (and peptides) are called amino acids. They are sort of like Lego pieces. When the mass spectrometer smashes a peptide, it will break the peptide in between the amino acids. If you bought one hundred Lego houses and then threw them against a wall, you would end up with lots of different sized chunks. If you arranged these chunks from smallest to biggest (or lightest to heaviest in the case of peptides), the gaps in between will tell you what piece is there. For example, let’s say I have a chunk of the Lego house with a door, and the same chunk of the house but without the door. If I were to weigh each chunk, the difference between the two chunks would be the weight of the door. When the mass spectrometer breaks the peptides, we use those gaps to figure out the sequence of the peptide. That sequence is then what we use to match the peptide back to a protein.

I know we just covered a lot of information and we used a lot of analogies, so let’s summarize everything.

1. We have a collection of Lego sets that we want to identify.
2. We break those Lego sets up into roughly equal chunks (but we are not breaking them down to individual pieces).
3. We catapult the chunks across our yard and measure how far each chunk went. This gives us the mass of each chunk.
4. Next we take each collection of chunks and we smash them against a wall.
5. We organize the smashed pieces from smallest to largest.
6. The differences between masses will tell us which Lego pieces we have in each chunk.
7. We take our list of pieces and go through the instruction manuals until we find which set(s) those pieces came from.

The analogy isn’t perfect because we can see the Lego sets with our eyes and figure things out that way, but with proteins we aren’t able to see them.

If you are interested in a more technical introduction to proteomics, the Wikipedia page on the subject gives a brief overview.

If you’ve made it to the end of this post, I want to thank you for reading and I hope your understanding of proteomics is a little better than it was before you got here.