good reproducibility: advice needed

[pierre]

Dear All,

for a research project that will focus on disease diagnosis, we will have to analyze very large sample sets using non-targeted metabolomics. It will be particularly important to maintain reproducible metabolomics MS performance over many months or even years. This is crucial for the success of the project.

We have have still not determined the type of instrument that we will use and the methodology that we will follow to ensure good reproducibility. The two main criteria are (1) wide range and (2) excellent reproducibility. Can anyone here suggests a mass spectrometer and/or methodologies that will best fit our project? Also, does anyone have already tried to normalize MS data to compensate for day-to-day (I should say month-to-month...) variation?

Thank you in advance for any answers,
Pierre

[sneumann]

Hi,

check out http://www.nature.com/nprot/journal/v6/ ... 1.335.html

Yours,
Steffen

[hpbenton]

If I may also suggest some of the following papers which are good reproducibility papers. It may also be a good idea to do some identification of the biofluid that you're looking at so that you have some known ID-ed compounds. That way you can do some absolute quantification on them and see how they change over the years i.e. see if your method/relative quantification is changing. Recently I was involved in a large reproducibility study between different labs. While there were a lot of problems, the data was still very good in the end. One thing that the study did was to use the same batch of solvents and the same batch of columns. Might be worth trying to buy a single batch of solvents for the project.

(1) Baird, D. D.; Saldana, T. M.; Nepomnaschy, P. A.; Hoppin, J. A.; Longnecker, M. P.; Weinberg, C. R.; Wilcox, A. J. J Expos Sci Environ Epidemiol 2009, 20, 169–175.

(2) Zelena, E.; Dunn, W. B.; Broadhurst, D.; Francis-McIntyre, S.; Carroll, K.; Begley, P.; O'Hagan, S.; Knowles, J.; Halsall, A.; Wilson, I. D.; Kell, D. Anal. Chem. 2009, 81, 1357–1364.

(3) Gika, H. G.; Theodoridis, G. A.; Wingate, J. E.; Wilson, I. D. J Proteome Res 2007, 6, 3291–3303.