I would like to ask whether the MS library is able to identify the compounds in a crude extract? Or still have to go through purification before sending to the MS to identify?
If you want to send this for LC-MS, a purified sample has the highest chance of a positive identification. It's better if your samples are dissolved in water, methanol, or acetonitrile .
Make sure your samples do not contain any kind of additives such as:
Alkali salts and non-volatile buffers, Polyethylene glycol (PEGS), plastics and plasticizers,detergents, in particular, Tween , Triton, NP-40 and SDS.
Additives such as carbohydrates, glycerol, EDTA, Urea, GnHCl because them compete for the ionization.
Use volatile buffers (ammonium salts), for positive ion mode use formic, acetic acid, TFA and volatile bases for negative ion mode (triethyamine, ammonium hydroxide)
On a more general note: whichever method you use (GC/MS? LC-MS? Ionization by EI? CI? ESI? APCI? APPI?), you will only ever get a subset of the answers. No single MS method will give yuo an unbiased report of all different kinds of compounds. Therefore you need to specify an analytical question - what is it that you want to look at? Low polarity (>GC/MS) vs. High polarity (>LC/MS)? Small organic compounds, lipids, peptides, carbohydrates? This is the question you need to answer first, and the choice of purification protocol completely depends on this.
Hi, Candace -
Robero and Christof together have highlighted most of the issues with metabolite identification (and to some extent good analytical practice), i.e., the simple answer to the question -' Will a library identify all the compounds in a crude extract?' - is 'no'.
Roberto notes many of the technical issues; basically - the cleaner your sample, the better your data and the longer your mass spectrometer will survive before you lose sensitivity and have to clean the source (or he optics). The longer your columns will last. There are also dynamic-range considerations, i.e., low-abundance analytes in the presence of very-high-abundance components of a mixture. If at all possible, crude extracts should rarely be injected into the mass spec.
Christof summarizes the experimental strategic and tactitcal questions that should be addressed before going to the instrument.
In addition, it may not be the best idea to depend too heavily on a library.
It would be helpful if you could answer some of the questions raised by Roberto and Cristof. What are you extracting, and with what solvents? Are you using GC/MS or LC/MS? (Or LC/MS/MS?) Are you looking for differences between different samples or at different time-points; or both? Qualitative analyses or quantitative analyses?
Hi, I'm using GCMS. Thank you very much for the information. I try to fractionate my samples to get a more purified compounds before subjected into the GCMS.
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