Mass spec: base peak and molecular peak

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lotus0618
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Mass spec: base peak and molecular peak

Post by lotus0618 » Wed Jan 29, 2020 2:14 am

I jsut did some problems on the Mass spec and want some clarifications regarding the base peak and the molecular ion peak on the mass spec mentioned in the video

Base peak: is the peak that has the HIGHEST peak (could be higher than the molecular ion peak) -> this indicates that this atom is the most abundant. But abundant in what?

Molecular ion peak: is the peak found at the LARGEST m/z -> this indicates the molecular weight of a molecule

IS everything else correct?
NS_Tutor_Mathias
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Re: Mass spec: base peak and molecular peak

Post by NS_Tutor_Mathias » Wed Jan 29, 2020 3:11 am

Realize that the height of each peak is just percent abundance, and that the process of ionizing a molecule may fragment it in unintended ways. This can lead to smaller fragments that are more abundant than the molecular ion - the most abundant of which would be the base peak. Abundance in this context just means "out of all the fragments we generated, what percentage had what weight?".

The rest is pretty much right. Just don't forget the impact that isotopes of chlorine and bromine can have on mass spec readings, creating cases where your highest peak is actually M+2, not just M+.
lotus0618
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Re: Mass spec: base peak and molecular peak

Post by lotus0618 » Thu Jan 30, 2020 2:28 am

Oh, so the highest base peak at 40 m/z indicates the highest percentage of the fragments that have 40 microgram, while the molecular peak at 100 m/z indicates the MW of the molecule, but the fragments that have this weight is much lower in % compared to the highest base peak.

What is M+2 and M+? does M+ refer to the second isotope of a molecule and M+2 refers to, say a chlorine with 2 isotopes? please explain to me in a simple way.thanks
NS_Tutor_Mathias
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Re: Mass spec: base peak and molecular peak

Post by NS_Tutor_Mathias » Thu Jan 30, 2020 3:31 pm

The M+ peak is just another name for the molecular ion. A shorthand for "molecular cation" - since that is the ion you will conventionally be observing in mass spectrometry.

M+2 on the other hand is another molecular ion peak, two greater than that of the M+, due to the presence of a heavier isotope in a significant proportion of the sample. For instance, elemental chlorine appears as about 75% Cl35 and 25% Cl37. We can therefore expect to see an M+2 peak of about 1/3rd the size of the M+ peak. If we see this pattern, we can even infer the presence of a single chlorine atom from the mass spectrometry results alone!

For the MCAT, you are expected to know about this for the case of chlorine and bromine, including their natural abundances.


Edit: You wrote "micrograms" somewhere, but the units of measurement in mass-spectrometry are simply m/z (mass to charge) ratio. If you were to extrapolate to a unit of mass, you should probably consider the dalton as the standard unit of measurement.
lotus0618
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Re: Mass spec: base peak and molecular peak

Post by lotus0618 » Thu Jan 30, 2020 9:19 pm

I have a couple questions:
1) so M+2 always represents a heavier isotope?
2) Cl has 2 isotopes and is shown in 2 peaks (M+1 and M+2), so why do we see only fragments of M+1, not of M+2?
3) in regards to "infer the presence of a single chlorine atom from the mass pec result alone," isn't this always the case for mass spec? since each mass spec graph shows only fragments of one element.

Is there any good video on this that you know of? I try to maximize my time on practicing problems and little time on content review, so all I have been doing is watching Next time videos, khan academy and doing problems instead of reading Next step books.
NS_Tutor_Mathias
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Re: Mass spec: base peak and molecular peak

Post by NS_Tutor_Mathias » Thu Jan 30, 2020 9:48 pm

We would observe M+ (compound with one Cl35 atom) and M+2 (compound with one Cl37 atom).

We would not observe M+1 (because this would require Cl36, an extremely rare isotope). The number after "+" just indicates the number of amu above the "normal" weight of the molecular ion, meaning the most common molecular ion (which we just call M+).

If instead we analyzed a molecule with two chlorine atoms, we would see 3 peaks: M+, M+2 and M+4. Could you tell me which peak of the 3 should be tallest?
lotus0618
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Re: Mass spec: base peak and molecular peak

Post by lotus0618 » Thu Jan 30, 2020 10:35 pm

you cannot really tell which peak is the highest because this has to do with the abundance, how much of that molecular weight for an element. Unless you tell me the percentage of each peak, then i can tell you which one is the highest.

I honestly feel very hazy about the M+1, M+2. Its' hard for me to understand concepts like this via messages. is there any video you can recommend me?
NS_Tutor_Mathias
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Re: Mass spec: base peak and molecular peak

Post by NS_Tutor_Mathias » Thu Jan 30, 2020 11:00 pm

This might help a bit: https://youtu.be/8YKhiG25lcg?t=1212

It is tough to find something on this particular sub-subject of chlorine and bromine messing with mass spectrometry. Before you worry more about this and start watching videos, recall that we are worrying about these alternate peaks because all elements have myriad isotopes - but chlorine and bromine in particular have two similarly abundant isotopes, meaning the results that we get when performing mass spectrometry on chlorine- or bromine-containing compounds require a little bit of extra thinking.


As for the previous question:
A molecule with 2 chlorines should have an M+ peak, an M+2 peak and an M+4 peak. We can actually predict the heights of each peak, because we know the abundance of chlorine isotopes in nature (75% Cl35, 25% Cl37). For a compound with a single chlorine, the M+2 peak should be 1/3rd the size of the M+ peak. For two chlorines we have to do slightly more math, but we can worry about that later on. As long as you realize the M+ peak would be largest, the M+2 the next smallest and the M+4 the very smallest, all is good.
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