Mass Spectrometry: Study with Video Lessons, Practice Problems & Examples

Mass spectrometry is an analytical technique used to determine the molecular weight of unknown samples through electron impact ionization (EI). In EI, high-energy electrons create a radical cation by dislodging an electron from the molecule. The mass spectrometer then deflects these cations in a magnetic field, allowing for the measurement of their mass-to-charge ratio (m/z). The base peak represents the most abundant ion, often the molecular ion, while other peaks indicate fragmentation patterns. Understanding these concepts is crucial for interpreting mass spectra and identifying molecular structures.

Equipment and Theory

So guys, mass spec is an analytical technique that's used to weigh your sample. So you place a sample, an unknown molecule through a mass spectrometer, and it should tell you the weight of your molecule. Okay? Now the way this is accomplished usually is through a process called electron impact ionization or simply EI. This is the most common form of mass spec and it has to do with electrons hitting your sample at a very, very high speed. So guys, here I have the general scheme of how a mass spectrum works like the actual equipment. And what you do is you have your unknown sample. So in this case, you can tell that my sample is methane. I know it because I happen to draw it, but if I were out in the field, I might not know what the sample is, so I'm processing it through my mass spectrometer. And what's going to happen is it's going to go through a series of steps whereby at the end, I can actually tell what its molecular weight is. Let's go ahead and follow the bullet points. I'm going to go over how this machine works. So the first thing that happens is that electrons are going to be beamed at these molecules. Remember that I said that this is called electron impact ionization. So you're going to be shooting very high-energy electrons at your molecule and what this is going to do is it's going to generate a high-energy intermediate called a radical cation. So where is this happening? If we're looking at my diagram, this would happen right at the ionization phase. So your sample is actually first vaporized. It's turned into a gas. That's over here so that you're putting a gas through your mass spectrometer and then we're ionizing it. We're shooting this very fast single beam of electrons at the molecules and trying to break them apart essentially. When you break it apart, you're going to get something called the molecular ion. Now what a molecular ion is, is it's your same exact molecule, but it's with one thing missing. And what it is is that it's your molecule missing one electron. Let me show you how this works. Imagine that this carbon initially has 8 octet electrons. Right? Remember that every second row element, most of them want to have 8 electrons to fulfill their octet. Well, after I shoot these high-energy electrons at my molecule, what's going to happen is that one of them is going to get dislodged. That's what I'm counting on. I'm counting that one of these 8 electrons is going to go missing. It's going to just bounce off. And what's going to happen at the end is that we get this thing called the radical cation. So you can see that the radical cation is the same thing as before. It's the same molecule, but instead of having 2 electrons for this bond, I only have 1. Okay? So imagine that basically that electron is now one of them is missing. So that is what my radical cation is called, that's how it's made. And the reason it's called a radical cation is because first of all, it has a radical now, it just has one electron between those atoms instead of 2. But also, the entire molecule has a positive charge because as you can see, we're missing an electron. So that means one of these, one of basically, this entire molecule is going to have a net charge now. Okay? So the way we symbolize, in short, a molecular ion is we write capital M and then we write a positive and we write a radical. This is the same way to say that it's a radical cation because it has both positive character and it has a radical. You may also see in your textbook or in your homework that it's abbreviated as M+ radical to the side. It's the same thing. It's just a different way to draw it. But I like to draw them up and down. It takes less space. Alright? This is also, by the way, it's also called the parent ion. So if you hear parent ion, if you hear molecular ion, if you hear radical cation, these are all the same exact things. So you need to know your terminology. Alright, guys. So now we've ionized my sample, right? That's the ionization phase. What happens to the rest? You can see that there are other stages. It says deflection, detection, there's a magnet. What's going on? Well, guys, it turns out that only some of these fragments are going to be magnetically sensitive. Okay? It's the ones that are charged. So it turns out that fragment cations, whenever you get a cation produced by the ionization of this molecule, that's going to be deflected by the magnetic field. But not all cations are alike. It turns out that smaller ones are affected more than bigger ones. That means that this is just due to physics, due to inertia. Imagine a small ion, if it's moving through the tube, it's much easier to deflect it because it has very little inertia. Whereas a large ion, if it's very, very big, it's going to be more difficult to change its path. It's going to be more difficult to accelerate it and to deflect it. Okay? So what this does is it gives us the ability to detect where these radicals, I'm sorry, where these cations are hitting. If it doesn't deflect very much, I know it's really big and heavy. If it deflects a lot, then I know, okay, this thing's small. And that's exactly what happens here. It passes through a magnet where it gets deflected and I detect how much did it get deflected. Through this, I'm able to determine how big the mass is. What we actually get as a reading for a mass spectrometer is not exactly mass, but it's close. What it's called is the mass-to-charge ratio where your mass is equal to m and your charge is equal to z. Now, we just stated what kinds of charges are sensitive to the electromagnet? Positive charges. Okay? Cations. So what that means is that even though we're detecting the mass-to-charge ratio, MZ, really z is usually going to be equal to 1, Right? Because we said that the ones that are sensitive and getting detected are the cations. So that means that even though you're detecting mass over charge, what this really equals is mass over 1 because the charge is always 1 and any number over 1 is just itself. So what that means is that really this is just a fancy way to determine the molecular weight of your cationic fragments, the ones that are positively charged. Is that making sense so far? So now we've got the mass of your fragment. Now we just have to learn in terms of finishing this page, how are we going to read a mass spectrum if we're given one. So guys, here is the mass spectrum of our molecule. This is what we would get in the reading. And what we would see is that the radical cation here, remember that the radical cation only had an electron missing, so the radical cation is going to have the weight of the initial sample. Okay? So remember that the formula for this is CH₄ and if you were to approximate the weight of this molecule, carbon is equal to 12 and your H's, H₄ is equal to 4, so you should get 16. Okay? That's exactly what a mass spectrum says. It says that the largest peak, the base peak is my radical cation. Now you may be wondering, "Johnny, how can it have the same weight as it did originally if you knocked away an electron?" But keep in mind, guys, that electrons don't really count towards molecular weight because they're so tiny. They have such little mass that you can afford to knock it off and your molecules basically going to have the same mass. Okay? So really what we're doing is we're just measuring the weights of our radical cation here. This is what we would call our molecular ion. So that would be M plus radical. Okay? But now we see that there's these other peaks on our mass spectrum as well. There's one at 15. There's a smaller one at 14. What's going on there? Well, guys, these would be basically fragments. These would be cationic fragments that formed because these, this molecule is hit with very high energy electrons, so sometimes it's just going to knock off an electron and that's all that happens. But sometimes it's going to bust the molecule open. So the 15 would be what we call our M-minus-one. Okay? Because that's our molecular ion minus 1. But why is it minus 1? Well, that would be losing a hydrogen. That would be if I actually knocked off an entire hydrogen instead of just knocking off an electron, I would get 15. Okay? And what you can see is that, is this a common fragment? Absolutely. Notice that my M-minus-one peak is almost as tall as my molecular ion. Why is that? Well, because it's very easy for methane to knock off 1 hydrogen. Okay? But you can see that the more hydrogen you have to knock off, the less probable it is to get these signals and that's exactly what happens. So 14, that would be that I'm knocking off 2 hydrogens. This would be my M-minus-two. It's much more difficult to get that because you can see that the number is far, far lower. It just kind of makes common sense that the more atoms you have to knock off of this fragment, the less likely you're going to get it, the less you're going to detect it in your mass spectrum. Okay? Now, I just want to point out a few other things about how the axis work here. The x-axis is easy. Mass-to-charge, you guys already know that that really just stands for mass. Right? But I haven't talked about the y-axis yet which is the relative abundance. We're saying that there's 85 percent of one, a 100 percent of another. What does that mean? Well, guys, it doesn't mean, for example, it doesn't mean that 85 percent of the whole is made out of your m-minus-one. Well, all it means is that compared to your tallest peak, which my tallest peak here happens to be my radical cation, right, happens to be the molecular ion, compared to the tallest peak, which is the 100, I have 85 percent of my M-minus-one. So essentially, all this is saying is that if at the end of the day, I run my whole spectrum and I get a 100 of these molecules, I should expect to find 85 of these. Okay? So, it's just 85 percent as likely as the base peak. Now, that comes to another term. I keep using this term base peak.

How to Read a Mass Spectrum

So the base peak of the sample is simply going to be the tallest peak out of all of them. We always scale the base peak to be 100, so that means that we make our base peak 100 and then we compare everything else to that. Now in this case, my base peak happened to be my molecular ion, the radical. But this isn't always the case. Later on, when we talk about fragmentation, what we'll see is that sometimes the base peak is actually going to be one of the fragments because sometimes the fragments are more stable than the molecular ion themselves. So in this case, I gave you a simple situation where the base peak is actually equal to the molecular ion. But what we're going to see later on is that sometimes one of the smaller fragments is actually your base peak and your molecular ion is lower because it's more common that it fragments than that it doesn't. Does that make any sense? Awesome guys. So this is just an intro. Now what we're going to do is we're going to go more into fragmentation patterns, and we're going to talk about isotopes. By the way, I want to point out one thing, which is that notice that there is a tiny peak at 17 that I didn't talk about. How did that happen? Does that mean it has one extra hydrogen? We'll get there. That's its own kind of phenomenon. But for right now, just focus on 16 and below because that's what we can understand through the process of ionization. All right. So let's move on to the next video.

Here’s what students ask on this topic:

What is mass spectrometry and how does it work?

Mass spectrometry is an analytical technique used to determine the molecular weight of unknown samples. It works by ionizing the sample molecules using high-energy electrons in a process called electron impact ionization (EI). This creates a radical cation by dislodging an electron from the molecule. The mass spectrometer then deflects these cations in a magnetic field, allowing for the measurement of their mass-to-charge ratio (m/z). The resulting mass spectrum displays peaks that represent the molecular ion and its fragments, helping to identify the molecular structure.

What is a radical cation in mass spectrometry?

A radical cation in mass spectrometry is a molecule that has lost one electron due to electron impact ionization, resulting in a positively charged ion with an unpaired electron. This ion is represented as M⁺•, where M stands for the molecule, the superscript + indicates the positive charge, and the dot represents the unpaired electron. The radical cation is crucial for determining the molecular weight of the sample in mass spectrometry.

What is the base peak in a mass spectrum?

The base peak in a mass spectrum is the tallest peak, representing the most abundant ion detected. It is scaled to 100% relative abundance, and all other peaks are compared to it. The base peak can be the molecular ion or a fragment ion, depending on which ion is more stable and abundant. Understanding the base peak helps in interpreting the mass spectrum and identifying the molecular structure.

How is the mass-to-charge ratio (m/z) determined in mass spectrometry?

The mass-to-charge ratio (m/z) in mass spectrometry is determined by measuring how much the ionized fragments are deflected in a magnetic field. The deflection depends on the mass and charge of the ions. Since most ions detected are cations with a charge of +1, the m/z value often corresponds directly to the mass of the ion. This ratio helps in identifying the molecular weight and structure of the sample.

What are fragmentation patterns in mass spectrometry?

Fragmentation patterns in mass spectrometry refer to the way a molecule breaks apart into smaller ions when subjected to high-energy electrons. These patterns are represented by peaks in the mass spectrum, each corresponding to a fragment ion. The position and intensity of these peaks provide information about the structure and stability of the fragments, aiding in the identification of the original molecule.