title: Absolute quantification of microbial proteomes at different states by directed mass spectrometry.
abstract: 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.
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli-Str. 16, Zurich, Switzerland. alex.schmidt@unibas.ch
authors.forename: Alexander
authors.initials: A
authors.lastname: Schmidt
authors.forename: Martin
authors.initials: M
authors.lastname: Beck
authors.forename: Johan
authors.initials: J
authors.lastname: Malmström
authors.forename: Henry
authors.initials: H
authors.lastname: Lam
authors.forename: Manfred
authors.initials: M
authors.lastname: Claassen
authors.forename: David
authors.initials: D
authors.lastname: Campbell
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis*; D002853:Chromatography, Liquid; D016000:Cluster Analysis; D003470:Culture Media; D030541:Databases, Genetic; D015536:Down-Regulation; D020869:Gene Expression Profiling; D007921:Leptospira interrogans / Q000378:metabolism*; D009876:Operon; D010455:Peptides / Q000032:analysis; D020543:Proteome / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D017423:Sequence Analysis, RNA; D053719:Tandem Mass Spectrometry / Q000379:methods*; D015854:Up-Regulation
chemical_list: D001426:Bacterial Proteins; D003470:Culture Media; D010455:Peptides; D020543:Proteome