That's all we need!
It's bad enough trying to educate the bench scientists that using GUI apps gives you *an* answer just not necessarily *the* answer, but getting MS on board with their marketing machine is going to be disaster with a whole swathe of flawed results and conclusions. In order to get meaningful results you need to understand what the software is doing, but with MS it's going to be nothing more informative than a black box.
I do this full-time and it's all too common to have collaborators (not in the Nazi sense) come to you with data where there is some flaw in the experimental design or application. A nice shiny GUI will not be able to sort the wheat from the chaff in these instances and will lead scientists to incorrect conclusions.
Your everyday scientist cannot cope anymore with the shear volume of data these 'omic analyses are generating these days.
It is a major growth area and I can see why MS are wanting to get into it, but this has the potential to end really badly.... :(
BTW @sleepy each gene often produces multiple proteins and some don't produce any proteins at all, but are still have a function (e.g. ribosomal RNA). The one gene = one protein dogma is no longer true.