What is all this about labeling and signal integration can’t you just count the peptides?

Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein Yasushi Ishihama, Yoshiya Oda, Tsuyoshi Tabata, Toshitaka Sato, Takeshi Nagasu, Juri Rappsilber, and Matthias Mann Molecular & Cellular Proteomics 4:1265-1272, 2005.

A technique is presented that can be used to calculated protein concentrations from the results of database search engines such as Mascot or SEQUEST. Thus it is possible to apply this approach to previously measured datasets and in cases where isotopes or labeling are not practical.

emPAI = 10^PAI - 1

The PAI is defined as the number of peptides observed divided by the number of peptides observable.
PAI can be used to estimate the relative proteins. emPAI can be used to predict the absolute concentration.


“At present, it is not clear why the logarithm of protein concentration correlates with the number of observed peptides, and in any case this relationship is likely to be due to a combination of processes and probably holds only approximately.”

In many ways this paper demonstrates the field of proteomic’s craving for simple quantition. Proteomics is quickly graduating from qualitative to quantitative analyis. On thing that makes it hard for me to take this technique seriously is the numerous reports demonstrating abysmal peptide identification reproducibility. I am concerned that the number of observed peptides in a complex proteome is influenced by the tandem MS ion selection, digestion and ion suppression.
Essentially this technique builds the quantitation on the reproducibility of the identification. I do not mean to imply that I do not believe the results that are presented, but I do wonder if a critical part of implementing this technique in a real world sample has been glossed over and I have not been observant enough to identify it.

One aspect of the presented experiment that might be key to the application of this technique is that the experiment was run such that there was a high coverage of the peptides. In the data presented proteins had as many as 31 peptides identifies.

Regardless of my doubts their data is impressive. In conclusion if tandem MS reproducibility, digestion and ion suppression can be controlled this might be a great option for quantitation.