What is emPAI ?
- Publication I (pdf): A short introduction (which appeared in Bioinformatics) to emPAI Calc.
- Publication II (pdf): Introduction to emPAI algorithm in proteomic data analysis with an emphasis on dynamic range and linearity.
emPAI (exponentially modified protein abundance index), developed by
Ishihama et al., is a measure to describe the protein composition in sample solutions. When the total protein amount in the sample is available, emPAI can be converted to the absolute amount of each protein in the sample. emPAI is derived from PAI, which is defined as the number of the observed peptides divided by the number of the observable peptides per protein. We recently found that log (PAI) had linear relationship to the protein amounts, and that emPAI, 10^(PAI)-1, was proportional to the protein amounts for whole cell lysate digested by trypsin. The accuracy of this method was within factor 5, similar or better than determination of abundance by protein staining. Since the emPAI index does not require further experimentation in protein identification experiments, it is suggested to use routinely in the reporting of proteomic results.
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