MS or MS/MS?; single quad or triple quad?
As a newbie, I find it puzzling with the many different configurations a GC-mass spectrometer can possess (for metabolites identification and profiling).
I would appreciate it a lot if you could please enlighten me on a few questions below:
1. Is the same concept in LC-MS/MS proteomics transferrable to the field of GC-MS or GC-MS/MS based metabolomics? E.g., GC-MS/MS allows one to achieve additional structural confirmation, while triple quad allows one to perform targeted analysis of selected metabolites, etc.
2. Would you mind sharing with me the system you are using for routine metabolites identification and profiling, preferably with a “all-in-one functionality”?
- (e.g. Would a triple quadrupole GC-MS/MS system the most applicable to process a much broader types of metabolites, and could fulfill the needs for most diverse scenarios of metabolomics experiments)? Just like the latest QTOF or Orbitrap mass spec which allows one to do protein/peptide quantification, quantitation; discovery, as well as certain level of targeted (MRM) analysis on the same instrument.
If there is one such "comprehensive" GC mass spec, it would be a useful starting point for me to focus, consolidate, and read more on the literature related to its applications.
Appreciate your advice. Thank you very much.
You are looking at the wrong platform. GC is nearly useless for protein measurements. You can't easily get proteins through a GC column. If you need additional structural information from your LC-MS/MS you are better off getting or building a direct EI interface (see Browner et. al., Georgia Tech). Just bear in mind that proteins fragment extensively; the data you obtain may not be interpretable.
To repeat, GC-MS will not work for metabolomics. You can't chromatograph proteins on a GC. You need either CE or LC.
Lipids you can chromatograph; depending upon the lipid and your choice of injectors. You might have to derivatize them. In general, MS/MS is always preferred over MS since you have significant improvement in noise levels. You can always run a MS in a single quad mode or dual scan (survey) mode.
Hello Kay! We did a profiling on rice metabolites using GCMS/MS (triple quad), see link. For GCMSMS, it will definitely be dependent on what metabolites you are looking at. In the initial phase, you need to identify the compounds first. In the second phase, you will tell the MS what to look for. Hope this and the link may be able to enlighten some of your queries. :)
Hi
I have publications regarding metabolomic by GCMS (but it is not too new publications), maybe you have not yet those articles
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