Journal
MOLECULAR SYSTEMS BIOLOGY
Volume 7, Issue -, Pages -Publisher
WILEY
DOI: 10.1038/msb.2011.37
Keywords
absolute quantification; directed mass spectrometry; Leptospira interrogans; microbiology; proteomics
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Funding
- ETH Zurich
- Swiss National Science Foundation [31000-10767]
- National Heart, Lung and Blood Institute
- National Institutions of Health [N01-HV-28179]
- SystemsX.ch
- Swiss initiative for systems biology
- European Research Council [ERC-2008-AdG 233226]
- Swedish Society of Medical Research (SSMF)
- European Molecular Biology Organization
- European Commission
- Competence Center for Systems Physiology and Metabolic Diseases
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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. Molecular Systems Biology 7: 510; published online 19 July 2011; doi:10.1038/msb.2011.37
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