A proteome-wide technology for absolute quantification

Despite the success of methods for relative proteome quantification, scientists still need absolute quantitative data in some cases. Now, a new method for quantitative proteomic analysis has been developed by Ruedi Aebersold and colleagues at the Swiss Federal Institute of Technology Zurich, the University of Zurich, and the Institute for Systems Biology. Their approach measures the absolute quantity of a large portion of the proteome in genetically unaltered microorganisms.

Aebersold and colleagues combined three MS proteomic techniques: absolute quantification with isotope-labeled reference peptides, label-free quantification, and high-throughput LC/MS/MS proteome sequencing. The investigators applied their approach to Leptospira interrogans, a bacterium that causes leptospirosis. Aebersold and colleagues took advantage of the organism’s very thin cross section (100–180 nanometers) and validated the MS measurements by comparing them to single-cell analyses by cryoelectron tomography.

With their three-pronged MS strategy, the investigators generated an absolute protein abundance scale for 83% of the L. interrogans proteome from cells in different states. The approach also permitted the investigators to detect the proteomic reorganization when the bacteria were exposed to an antibiotic: the cells produced enormous amounts of a small number of proteins of unknown function that normally were not expressed. At the same time, the cells maintained a constant level of total cellular protein.

Aebersold and colleagues state that their new technique is fast and efficient and can be implemented in the future to analyze various biological systems of low and medium complexity. (Nature 2009, DOI 10.1038/nature08184)