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Molecular Systems Biology
 Ruedi Aebersold

Absolute quantification of microbial proteomes at different states by directed mass spectrometry
Molecular Systems Biology 7: 510; published online 19 July 2011
Subject Categories:  proteomics; microbiology & pathogens
Keywords:  absolute quantification; directed mass spectrometry; Leptospira interrogans; microbiology;

Over the past decade, liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS) has evolved into the main proteome discovery technology. Up to several thousand proteins can now be reliably identified from a sample and the relative abundance of the identified proteins can be determined across samples. However, the remeasurement of substantially similar proteomes, for example those generated by perturbation experiments in systems biology, at high reproducibility and throughput remains challenging. Here, we apply a directed MS strategy to detect and quantify sets  of  pre-determined  peptides  in  tryptic  digests  of  cells  of  the  human  pathogen  Leptospira interrogans at 25 different states. We show that in a single LC–MS/MS experiment around 5000 peptides, covering 1680 L. interrogans proteins, can be consistently detected and their absolute expression  levels  estimated,  revealing  new  insights  about  the  proteome  changes  involved  in pathogenic progression and antibiotic defense of L. interrogans. This is the first study that describes the absolute quantitative behavior. of any proteome over multiple states, and represents the most comprehensive proteome abundance pattern comparison for any organism to date.




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