LCMS is for non-volatile compounds especially for proteins while GCMS is for volatile compounds, mostly for organic compounds like bioactive metabolites. So, it depends on which type of compound you are looking for.

I think initially you can try on both LCMS and GCMS.But check with EI/CI or ESI/APCI which ionization technique u r going to use as GC-EI will fragment more.If u r good in interpretation then very useful, otherwise go for lc-ms

GC-MS include drug detection, fire investigation, environmental analysis, explosives investigation, and identification of unknown samples. GC-MS can also be used in airport security to detect substances in luggage or on human beings. Additionally, it can identify trace elements in materials that were previously thought to have disintegrated beyond identification.

GC-MS has been widely heralded as a "gold standard" for forensic substance identification because it is used to perform a specific test.

Where as-

(LC-MS, or alternatively HPLC-MS) is a powerful technique used for many applications which has very high sensitivity and selectivity. Generally its application is oriented towards the general detection and potential identification of chemicals in the presence of other chemicals (in a complex mixture) important to food, pharmaceutical, agrochemical and other industries. The limitations of LC-MS in urine analysis drug screening is that it often fails to distinguish between specific metabolites, in particular with hydrocodone and its metabolites. LC-MS urine analysis testing is used to detect specific categories of drugs. However, gas chromatography (GC-MS) should be used when detection of a specific drug and its metabolites is required.

Hence,

(GC-MS) would be best method for the characterization of a bioactive compound..........

It is important to know what kind of compounds

I've had the experience of working with phenolic bioactive compounds, i.e. antioxidants and we actually used LC-MS to characterize the molecular weight and structure of those purified phenolic compounds.

GC-MS can be used only for volatile substances. Though it has a tremendous application, it cannot be used for non-volatile compounds. An advantage of GC-MS is that we do not need to use standards for an accurate analysis; where as LC-MS needs standards for accurate determination. A large number of metabolites are non-volatile, so we cannot use GC-MS and need to depend on LC.

So, the instrument to analyze depends on the nature of your sample and availability of standards.

LC-MS

I have few mg of TLC purified compound from a microbial secondary metabolite. With this how can i check in both GC-MS and LC-MS. How can i identify my compound is volatile or not. Is there any methods?

I am not sure for your case but If compound is highly volatile then earlier i have observed some weight loss after keeping it for some period, even keeping it on weighing balance it was fluctuating.As you are saying it is pure, once check LC-MS.At least some information you will get, will show single peak in UV (for uv-active compd)and if ionized, get TIC and mass .If not then can try GC.

From the LC-MS we can characterize the non-volatile compounds. But GC-MS (for essential oil and some low mol.Wt compounds like natural product and synthetic compounds) is used to characterize the volatile compounds. Some of the bio active compounds like flavanoids, alkaloids etc..... are non-volatile, so LC-MS or LC-MS/MS is more suitable method to characterize the non-volatile bioactive compounds. Terpenoids and other volatile compounds are easily characterize by using GC-MS. Terpenoids also bioactive. So you can use both LC-MS/MS or LC-MS for characterizing the non volatile bioactive compounds and GC-MS is used to characterize the volatile compounds.

I am aggreed with Mr. Nandakishore Namboothiripad, and what he suggested is what i will also look for , nature or your compound either volatile or non volatile , and then select an appropriate method, also during my learnings i also had found that sonetimes derivatizing of volatile compound might get it phy. prop. changed and then you can switch over to GC/MS to LC/MS , now if your needed data is just for confirmation then which ever method you use will not be much compared.

Go through the literature, a lot you'll come to know.

Refer to papers whove used similar extraction procedures on related plants/extracts

Decide upon the class of bio-molecules narrowing down with some reasonable classification.

Once u have target(s), thru' literature itself, u'll know wot to do; whether u need to derivatize ur sample or simply GC or LC..

With too less the sample, u can only "TRY" GC-MS; as for LC, u need quiet some quantity for standardization n yeah, standards too

hai mr.muthamil. act i dn knw ans fr ur qustn. bt i need ur hlp. can u give d protocol for isolation of secondary metabolites especially actinomycetes.? [email protected]

If you have both LC-MS and GC-MS available, I'd try LC-MS fist, since it can get you some idea of the identity of your compound. Your LC-profile will show if it's very pure or very contaminated. The MS/MS capacity of your LC can fragment and perhaps help identify certain moieties. If you have a non-volatile compound you may still be able to do GC-MS after derivatisation by methylation or trimethylsililation, methods depend on whether it's carboxylic acids, hydorxyls, aldehyde or keto-groups that you need to alter.

i would try exactly opposite and try and develop GC first. In my opinion, it is easier and less time consumable compared to LC method development.

If you have couple of mg amount of the compound, and it is a metabolite (relatively small molecule), first I would try to get some structural information using 1H and 13C NMR, which are non-destructive structure investigation techniques, and you will get all amount back (but the solvent for NMR must be volatile). The NMR will give you most probably some information on the size of the compound (number of the carbon atoms in the molecule), and also some information on the polarity as well (showing the OH or NH2 groups if any).

Based on the information from from NMR you can decide between the gas and liquid phase. If the volatility allows the GC-MS is more informative as there are libraries with high number of compounds available. LC-MS will give the molecular weight, and if you are lucky, some fragmentation might give structural information.

All of the pieces of the puzzle together should give the result. Good luck!

I agree with Janos (NMR analysis idea). I can suggest, that you may also try FTIR or ATR-FTIR analysis of your sample.

You should do 1H and 13C NMR, FTIR, and HRMS in order to try to characterize your molecule.

Now that you have done TLC to purify the compound as a single spot, you should see the resolution in HPLC. I presume that you are considering certain possibilities of identity. See the lambda max of the pure compound and it will tell you whether to use LC MS or GC MS. Of course you need to see certain other properties like thermal stability etc. It may be so, that only MS might be the right option for you.

After confirmation of isolated fraction as a single compound by TLC and purification method by HPLC, you can send the sample to FT-IR, UV, Proton, C-13, 2D-NMR and Mass spectra (In case of new or known compound). But from the GC-MS (If your compound is volatile in nature) we can easily identify the compound matching with NIST library data (If your compound is a only known volatile compound). But in the case of LC-MS we can identify the non volatile compound with some difficult (But LC-MS do not have liberary match). But LC-MS/MS having Q-TOF system is very good compared to LC-MS.

Hello sir, probably you should not go for gc-ms , since if their are polar compounds in the mixture they will need to be derivatives before analysis. This will complicate the interpretation of fragmentation pattern.

So now, you have so many opinions to check for yourself. Only one thing that I would like to mention here is that, if you are not sure about what is MASS SPECTROSCOPY then do some study either using some standard books or using the internet. This will help you to select the right method for your need.

For volatile constituents gc-ms enough. For high polar compounds and non volatile lc-ms/ms preferable