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Best instrument for LC-MS metabolomics?

Best instrument for LC-MS metabolomics?
We\'re running short on capacity on our current UPLC-qTOF (Agilent 6540), so we\'re looking for an additional LC-MS for bacterial metabolomics.
Our primary requirements are robustness and up-time. We need an instrument which will be running as much as possible with low maintenance. Down-time and lost results are much more expensive to us than the instrument cost.
Any advice will be most welcome on:
qTOF vs. orbitrap or ?
UPLC vs. nanoLC
Specifications needed for instrument (resolution etc.?)
We will properly not rely on vendors software for analysis, but comments in this respect would also be appreciated.

Thanks

Best regards,
Morten Danielsen

Best instrument for LC-MS metabolomics?

Reply #1 –
Which is most important for you? Measuring amounts of metabolties or exact mass of metabolites?

Best instrument for LC-MS metabolomics?

Reply #2 –
The quantity of metabolites would be most important. Most metabolites will be known and we have our qTOF for exact mass if needed.

Best instrument for LC-MS metabolomics?

Reply #3 –
I am also in the same situation of selecting new instrument.

In may humble opinion, if one do untargeted type of analyses, then I would consider the following:
1) Due to software limitations and constraints, I think chromatographic peak shape is very important. Unfortunately I don\'t know which is better - UPLC or nanoLC. I am also not sure which would be more cost effective as nanoLC chips and hardware are expensive yet save you many litres of solvents......

2) Personally I do not see the advantages of freakishly high resolution instruments like Orbitraps for untargeted analyses. Chances are pretty good that the number of hits for a specific feature would be the same between the Orbitrap and previous generation QTOFs from Agilent, as the difference in accurate mass on the 3rd or 5th decimal would not limit you hits. So I would rather stick with TOFs but those which have some kind of in-source CID or similar - where fragment info can be collected in a different channel (which could be useful for ID).

3) That said, it will then all come down to how well the vendor\'s software is in deconvoluting the data as I do not think there is any non-commercial software available that can handle MSe or similar types of data (but I can be wrong).

I would actually like to see other people\'s thought on this (perhaps I am totally wrong).

Best instrument for LC-MS metabolomics?

Reply #4 –
If robustness is your primary concern, I would recommend a UPLC system over nanoLC although I will admit the gap between the two seems to be quickly narrowing. I have had very good experiences with Waters Acquity and Agilent 1200 and 1290 UPLC in particular in terms of their reliability. 

For what its worth, I have had much better luck with QTOF (Agilent and Bruker) compared to Orbitrap in terms of reliability and maintenance.