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

• Published in: Molecular & cellular proteomics Vol. 4; no. 9; pp. 1265 - 1272
• Main Authors: Ishihama, Yasushi, Oda, Yoshiya, Tabata, Tsuyoshi, Sato, Toshitaka, Nagasu, Takeshi, Rappsilber, Juri, Mann, Matthias
• Format: Journal Article
• Language: English
• Published: United States American Society for Biochemistry and Molecular Biology 01-09-2005
• Subjects: Animals; Cell Extracts; Cell Line, Tumor; Chromatography, Liquid; Clone Cells; Colonic Neoplasms - pathology; Gene Expression; Humans; Mass Spectrometry; Mice; Neuroblastoma - pathology; Peptides - chemistry; Proteins - analysis; Proteins - genetics; Proteomics; Sequence Analysis, Protein; Serum Albumin - analysis
• ISSN: 1535-9476; 1535-9484
• DOI: 10.1074/mcp.M500061-MCP200

To estimate absolute protein contents in complex mixtures, 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 obtained at different concentrations of serum albumin show a linear relationship
with the logarithm of protein concentration 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 10 PAI minus one, which is proportional to protein content in a protein mixture. For the 46 proteins in the whole lysate, the deviation
percentages of the emPAI-based abundances from the actual values were within 63% on average, similar or better than determination
of abundance by protein staining. emPAI was applied to comprehensive protein expression analysis and to a comparison study
between gene and protein expression in a human cancer cell line, HCT116. The values of emPAI are easily calculated and add
important quantitation information to proteomic experiments; therefore we suggest that they should be reported in large scale
proteomic identification projects.