The optimal exponent base for emPAI is 6.5

Andrzej Kudlicki

Research output: Contribution to journalArticle

4 Scopus citations

Abstract

Exponentially Modified Protein Abundance Index (emPAI) is an established method of estimating protein abundances from peptide counts in a single LC-MS/MS experiment. EmPAI is defined as 10 PAI minus one, where PAI (Protein Abundance Index) denotes the ratio of observed to observable peptides. EmPAI was first proposed by Ishihama et al [1] who found that PAI is approximately proportional to the logarithm of absolute protein concentration. I define emPAI65 = 6.5 PAI-1 and show that it performs significantly better than emPAI, while it is equally easy to compute. The higher accuracy of emPAI65 is demonstrated by analyzing three data sets, including the one used in the original study [1]. I conclude that emPAI65 ought to be used instead of the original emPAI for protein quantitation.

Original languageEnglish (US)
Article numbere32339
JournalPloS one
Volume7
Issue number3
DOIs
StatePublished - Mar 5 2012

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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