Yes, you can use emPAI values to have an approximation of the quantitative analysis of proteins identified. This factor is already incorporated into proteomics softwares such as Mascot Software by Matrix Science:
This is a free software and you can use it to ID proteins and also to assess the relative abundance of each protein in the mixture, by comparing their emPAI values to each other.
You can also go for iBAQ values (Intensity based absolute quantification). And if you using Proteome Discoverer 2.2, you can use the Minora Feature detection node which gives you the differences in the abundance of proteins in the form of intensity.