Absolute quantification of microbial proteomes at different states by directed mass spectrometry

Research output: Contribution to journalArticle


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.


  • Alexander Schmidt
  • Martin Beck
  • Johan Malmström
  • Henry Lam
  • Manfred Claassen
  • David Campbell
  • Ruedi Aebersold
External organisations
  • ETH Zürich
Research areas and keywords


  • Bacterial Proteins, Chromatography, Liquid, Cluster Analysis, Culture Media, Databases, Genetic, Down-Regulation, Gene Expression Profiling, Leptospira interrogans, Operon, Peptides, Proteome, Proteomics, Sequence Analysis, RNA, Tandem Mass Spectrometry, Up-Regulation, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't
Original languageEnglish
Pages (from-to)510
JournalMolecular Systems Biology
Publication statusPublished - 2011 Jul 19
Publication categoryResearch
Externally publishedYes