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.