emPAI Calc--for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry.

emPAI Calc is an open-source web application for the estimation of protein abundance. It uses the correlation between the number of identified peptides and protein abundance in mass spectrometry-based proteomic experiments. The program is the first implementation of our previously reported emPAI algorithm; it calculates the emPAI from the protein identification results obtained by database search engines such as Mascot.