Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number

To estimate absolute protein contents in complex mix-tures, we previously defined a protein abundance index (PAI) as the number of observed peptides divided by the number of observable peptides per protein (Rappsilber, J., Ryder, U., Lamond, A. I., and Mann, M. (2002) Large-scale proteomic analysis of the human spliceosome. Genome. Res. 12, 1231–1245). Here we report that PAI values ob-tained at different concentrations of serum albumin show a linear relationship with the logarithm of protein concen-tration in LC-MS/MS experiments. This was also the case for 46 proteins in a mouse whole cell lysate. For absolute quantitation, PAI was converted to exponentially modified PAI (emPAI), equal to 10PAI minus one, which is propor-tional to protein content in a protein mixture. For the 46 proteins in the whole lysate, the deviation percentages o