The minimum information about a proteomic experiments (MIAPE ) is supposed to mirror the effectiveness of MIAME in standardizing how proteomics based experiments is documented. In theory all the information about how an experiment is run should allow for independent researchers to repeat the experiment and get the same (or at least very similar) results. While I cannot attest to the accuracy of this approach for microarrays from a first hand experience I can talk about it from a proteomics perspective.

My general opinion of the MIAPE and MIAME are that they will serve as good references, but will likely not contribute to the general improvement of conducting high-dimensional biology. The number and type of obstacles present in running consecutive high-dimensional explorations have been discussed in several publications and, therefore, I think that rather than trying to create new tools to show us how complex the process is we need to reevaluate the aim and utility of the systems in general.

When I first started using proteomics and “systems biology” techniques I was floored at the lack of quality control and proper experimental planning that were present in the literature. To be sure the label of “fishing expeditions” was most appropriate. However, it was amazing how with the application of some traditional study design techniques (i.e. power analysis and pilot studies) one could quickly understand what types of data one could reasonably expect to get. Now here is where I like the general effect of MIAPE – to make scientist remember that even new techniques still require traditional scientific approaches in their use.

So now we get to the question of utility. The aim of these standardizations appear to be preludes to use in clinical diagnostic settings and here is where I think scientists are doing themselves and greater society a huge disservice. First, high-dimensional biology, because of its inherent complexity, does not belong outside the research lab at any time in the near future. Second, to what end do we really need to have multiple centers repeating the same results when it is difficult to do within the same center? Third, we must address the issue of resource allocation. Do we need to fund multiple efforts for these expensive undertakings, when at the end of the day the ability to analyze and interpret the results of these studies have no standardization?

While I understand that MIAME and MIAPE are being created to sort of stay ahead of the technology, I still think that by having these standards created we are actually giving too much power to the platforms themselves. We still need to develop better strategies for the validation of findings from small simple studies of high-dimensional data sets before we tackle problems as difficult as those of clinical diagnosis. Anyway, this is all to get to the point that there is nothing wrong with fishing. However, before you get on the boat you should understand what type of fish you want to catch and make sure you have the right equipment for catching it. And, as every angler knows, it is called fishing and not catching for a reason.