Interesting article on why NonLinear Dynamics doesn't use spectral counting

Spectral counting isn't my favorite thing in the world. It has its uses, for sure, but I have been lucky enough throughout my career to have access to first SILAC labeled strains and later to freezers full of reporter ion quantification reagents.

Here is an interesting blog post from NonLinear Dynamics regarding why they don't give you spectral counting numbers directly in their interface (though you can export the data out and do spectral counts in Excel or presumably a nice spectral counting interface like ProtMax.

I was interested to learn that Proteome Discoverer 2.0 actually added in a new column to every report that provides the exponentially modified protein abundance index (emPAI) for every protein in every separately generated output.  If you are going to do spectral counting, using the emPAI is generally a better way of doing it than what PD 1.4 offered with simply counting the PSMs.