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Topic: GC-MS of biological samples?  (Read 3335 times)

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Offline Omega Glory

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GC-MS of biological samples?
« on: April 08, 2013, 11:25:18 PM »
I am sadly unfamiliar with the use of GC-MS for biological samples. GC-MS itself, I'm well-acquainted with -- but the procedures required when you're dealing with things of a biological nature, not so much.

I have a passing familiarity with the use of restriction enzymes for digestions, soft ionization modes for the analysis of proteins, etc... but that isn't really what I'm interested in.

Rather, I'm interested in analyzing a sample whose matrix contains large biological structures. The sample contains not only the small molecules that I'm interested in determining, but also whole cells. I'd really appreciate if someone could explain to me the work-up involved in analyzing something like this via liquid injection. I imagine a plant cell, or a clump of plant cells, wouldn't be easy to volatilize in the injection port -- and even then it would probably just gum up the head of the column. What is required for this sort of analysis? Can the cells be centrifuged out, or something else?

Offline Arkcon

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Re: GC-MS of biological samples?
« Reply #1 on: April 09, 2013, 09:18:30 AM »
Yes.  The GC (or LC) will not be able to handle whole cells, or fragments of whole cells.  Also, some things, like portions of cell membranes, or complete organelles are too complex a mixture to be easily fractionated on the GC -- even if we ignore the fact that they're often not very volatile.  And furthermore, will rapidly clog the skimmer cone (substitute the name your MS manufacturer uses for that part) with stuff that failed to ionize because it was just too large.  You will have to look up procedures similar to what you're looking to to to determine some method of clean-up. 

Now, analyzing proteins, oligonucleotides and lipids on MS is done.  But they have to be in a dispersed solution, often the output of an LC.  There are deconvolution algorithms, which back calculate from the fragmentation the parent ion (which generally never appears for large biomolecules) and also user-built databases that can use the fragmentation data to predict structure changes in large biomolecules.  But those applications are specialized, and a vendor can help you with that.

I don't know if you want to be able to do both, at the same time, on the same instrument.  But that may be too tall of an order to be practical.  Or maybe not possible.
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Offline Omega Glory

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Re: GC-MS of biological samples?
« Reply #2 on: April 09, 2013, 12:44:59 PM »
I don't really care so much about the analysis of oligonucleotides and other things that occur inside the cell -- I'm more interested in the non-cellular components.

I will continue to search for an optimal method of separating out the cellular fraction from the rest. Unless someone knows of a better way?

Offline JGK

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Re: GC-MS of biological samples?
« Reply #3 on: April 09, 2013, 03:00:08 PM »
To be honest If GC was the appropriate technique for what you are wanting to do there would be a plethora of literature on the subject.

Some heavier less volatile classes of material can be derivatised for GC. However, LC-MS is the easier option for the non volatile. Classes of material.
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Online Babcock_Hall

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Re: GC-MS of biological samples?
« Reply #4 on: April 09, 2013, 04:03:24 PM »
Can you be more specific about the type of molecule in which you are interested?

Offline sschoe2

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Re: GC-MS of biological samples?
« Reply #5 on: April 29, 2013, 04:37:40 PM »
For GC/MS you are only going to see volitile compounds like small alcohols, aldehydes,  terpenoids. For them you can do liquid liquid extraction with water and methylene chloride, isopentane, or ethyl acetate.

Another great way is Head Space SPME though it requires some fairly expensive equipment. You just seal it in a 22ml headspace container and sample with the fiber @ ~50deg C and then inject it into the GC injector (with an appropriate liner).

We need to know what kind of compounds in particular you are interested in.
You can look at the lipid content using the fatty acid methyl ester procedure (that is better done using a flame ionization detector), you can see amino acids if you derivitize with ethyl or propyl chloroformate (except arginine it doesn't derivitize), you can see nucleotides or sugars if you silyate the sample with say BSTFA + TMCS.

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