Mass spectroscopy

[metherion]

So, I saw the thread out 'is there more to science than evolution debates', and I figured that hey, maybe we could use some more science talk that doesn't generally have much debate inherent in it.

So. One thing that I wind up using at my work is mass spectroscopy. I have had classes on it, and know the theory behind it, and I get how the m/z peaks work and what chunks they tend to represent.

I was hoping someone might be able to explain to me, though, what information can be gleaned from relative heights of peaks? I don't mean the whole A+1, A+2, A deal, I get that.

I mean things like… okay, I have a m/z peak at 29 with a relative abundance of 40, another at 43 with a relative abundance of 70, and one at 57 with a relative abundance of, say, 95. What can that tell me about my compound, given that all the little peaks around them from all the A+1 carbons are as they should be?

I can't give any specific examples from work as per my employment offer since it's all trade secrets and such, but if others have questions about how it works and how I use it, I'd love to talk about science in action.

Metherion

 

[Radagast]

I was hoping someone might be able to explain to me, though, what information can be gleaned from relative heights of peaks?

You mean, apart from the obvious isotopic composition?

Presumably, the peak heights tell us about the probabilities of certain fragments forming, which has got to be some vague kind of structural clue. Flicking through standard textbooks on Mass Spectroscopy, it seems to be complex, though.

For large molecules, like peptides, we presumably get clues about the relative abundances of particular components.

 

[metherion]

Yeah, it's quite a bit complex. I generally tend to work with a molecular weight of under 500, again, can't tell you more.

So, for instance, the 29/43/57 would be an alkane, since the peaks are 14 apart, and all are a multiple of 14 +1 for the CH3 on the end (so we'd have an ethyl fragment, a propyl fragment, and a butyl or isopropyl fragment). I would GUESS we could tell it's a butyl and not an isopropyl because if it were isopropyl I'd expect the ethyl fragment to be FAR smaller… I think. After all, breaking a CH3-CH-(CH3)2 into a CH3-CH2 would be near impossible, you'd get 2 CH3s and a CH3-CH, and those would be somewhat rare because both would need to break off, but it might happen. …I think.

That's part of why I started the topic

Metherion

 

[Radagast]

Yeah, it's quite a bit complex. I generally tend to work with a molecular weight of under 500, again, can't tell you more.

I must confess, I haven't thought about these kind of questions for 30 years, so I can't really help.

 

[pgp_protector]

No help on this end.
The only work with any form of spectrums I've used was when working with spectrum analyzer in the military doing Mux Repair.

 

[Michael]

While we're on this topic, I'm looking for some help isolating a 3.65 Kev emission signal from some element(s). This paper seems to relate that signal to Ca K-alpha emissions.

http://ietd.inflibnet.ac.in/bitstream/10603/3944/14/14_chapter%204.pdf

Are there any handy references that someone can site that list the various elements and their various valence shell emissions? I'm curious if any other elements emit in the 3.55-3.75 kev energy range.

 

[metherion]

Have you tried a recent edition of the CRC handbook? Mine is at work and they don't allow non-work related internet access, and now it smells too bad to take home. If there's a college library near you, they should have one.

edit: That online copy seemed to be for subscribers only. However, the physical books have many different colors of covers, but they all look something like this:

and are generally a few thousand pages thick.

Metherion

 

[Michael]

Have you tried a recent edition of the CRC handbook? Mine is at work and they don't allow non-work related internet access, and now it smells too bad to take home. If there's a college library near you, they should have one.

edit: That online copy seemed to be for subscribers only. However, the physical books have many different colors of covers, but they all look something like this:

and are generally a few thousand pages thick.

Metherion

Thanks for the suggestion. I can see that I'm eventually going to have reinvest in a good chemistry book again. I also ran across this link which contained the information I was looking for:

X-Ray Emission Lines

 

[MikeCarra]

So, I saw the thread out 'is there more to science than evolution debates', and I figured that hey, maybe we could use some more science talk that doesn't generally have much debate inherent in it.

So. One thing that I wind up using at my work is mass spectroscopy. I have had classes on it, and know the theory behind it, and I get how the m/z peaks work and what chunks they tend to represent.

I was hoping someone might be able to explain to me, though, what information can be gleaned from relative heights of peaks? I don't mean the whole A+1, A+2, A deal, I get that.

I mean things like… okay, I have a m/z peak at 29 with a relative abundance of 40, another at 43 with a relative abundance of 70, and one at 57 with a relative abundance of, say, 95. What can that tell me about my compound, given that all the little peaks around them from all the A+1 carbons are as they should be?

I can't give any specific examples from work as per my employment offer since it's all trade secrets and such, but if others have questions about how it works and how I use it, I'd love to talk about science in action.

Metherion

You want some debate? Well, I'm glad you posted this. My pastor says that the peak height is roughly proportional to how EVIL the fragment is. He said that there are people out there who want to teach our children that it is something else, but we insist on teaching the controversy.

Some "Spectroscopy-ists" (people who believe in a secular spectroscopy-only world) will tell you it has nothing to do with morality, but I contend that without morality involved how will one know they are doing GOOD spectroscopy.

Otherwise it's all just relative isn't it?

 

[Radagast]

 

[variant]

I mean things like… okay, I have a m/z peak at 29 with a relative abundance of 40, another at 43 with a relative abundance of 70, and one at 57 with a relative abundance of, say, 95. What can that tell me about my compound, given that all the little peaks around them from all the A+1 carbons are as they should be?

I'm honestly not understanding your question.

The relative abundance tells you how much of each specific breakdown product there is, so magnitude equals probability of that part of the molecule still existing in the detector.

For instance in a straight chain alkaline (which your chemical seems to be) the first bond to break will be the weakest so your biggest fragments will be those parts left over after the most likely bonds break.

Pentane:

(if I am remembering this right)

29 - Ch3-Ch2- (-Ch2-Ch2-Ch3)

43 - Ch3-Ch2-Ch2- (-Ch2-Ch3)

57 - Ch3-Ch2-Ch2-Ch2- (-Ch3)

72 - Ch3-Ch2-Ch2-Ch2-Ch3

So if you added the magnitude of the blue lines you can get the percent breakdown of each of the various products, telling you which bonds were strongest during breakup.

In pentane the bond on either side of the middle carbon is going to break off the most.

Yeah, it's quite a bit complex. I generally tend to work with a molecular weight of under 500, again, can't tell you more.

So, for instance, the 29/43/57 would be an alkane, since the peaks are 14 apart, and all are a multiple of 14 +1 for the CH3 on the end (so we'd have an ethyl fragment, a propyl fragment, and a butyl or isopropyl fragment). I would GUESS we could tell it's a butyl and not an isopropyl because if it were isopropyl I'd expect the ethyl fragment to be FAR smaller… I think. After all, breaking a CH3-CH-(CH3)2 into a CH3-CH2 would be near impossible, you'd get 2 CH3s and a CH3-CH, and those would be somewhat rare because both would need to break off, but it might happen. …I think.

That's part of why I started the topic

Metherion

Isopropaine will have a much larger peak at 44 ish (sources say 45 though?) since the fragment will be Ch3-ch2-Ch3 with a methane missing.

You would be looking at normal butane.

 

[Radagast]

So if you added the magnitude of the blue lines you can get the percent breakdown of each of the various products, telling you which bonds were strongest during breakup.

Presumably peak heights depend on both (1) the probability of a fragment forming through bonds breaking and (2) the probability of that fragment surviving without breaking up further.

I guess this means peak heights are difficult to interpret.

I did find this interesting article about peptide sequencing from peak spacings in the mass spec:

 

[variant]

Presumably peak heights depend on both (1) the probability of a fragment forming through bonds breaking and (2) the probability of that fragment surviving without breaking up further.

I guess this means peak heights are difficult to interpret.

Right, but this should give you some insight into the strength of each bond in particular.

I did find this interesting article about peptide sequencing from peak spacings in the mass spec:

The matrix assisted laser ionization mass spec technique would be a bit of a different animal.