title: The quantitative and condition-dependent Escherichia coli proteome.
abstract: Measuring precise concentrations of proteins can provide insights into biological processes. Here we use efficient protein extraction and sample fractionation, as well as state-of-the-art quantitative mass spectrometry techniques to generate a comprehensive, condition-dependent protein-abundance map for Escherichia coli. We measure cellular protein concentrations for 55% of predicted E. coli genes (>2,300 proteins) under 22 different experimental conditions and identify methylation and N-terminal protein acetylations previously not known to be prevalent in bacteria. We uncover system-wide proteome allocation, expression regulation and post-translational adaptations. These data provide a valuable resource for the systems biology and broader E. coli research communities.
authors.affiliation: Biozentrum, University of Basel, Basel, Switzerland.
authors.forename: Alexander
authors.initials: A
authors.lastname: Schmidt
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Karl
authors.initials: K
authors.lastname: Kochanowski
authors.affiliation: Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
authors.forename: Silke
authors.initials: S
authors.lastname: Vedelaar
authors.affiliation: Biozentrum, University of Basel, Basel, Switzerland.
authors.forename: Erik
authors.initials: E
authors.lastname: Ahrné
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Volkmer
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
authors.forename: Luciano
authors.initials: L
authors.lastname: Callipo
authors.affiliation: Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
authors.forename: Kèvin
authors.initials: K
authors.lastname: Knoops
authors.affiliation: Biozentrum, University of Basel, Basel, Switzerland.
authors.forename: Manuel
authors.initials: M
authors.lastname: Bauer
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.|Faculty of Science, University of Zurich, Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.|Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
authors.forename: Matthias
authors.identifier: http://orcid.org/0000-0002-5512-9077
authors.initials: M
authors.lastname: Heinemann
mesh_terms: D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D013058:Mass Spectrometry; D020543:Proteome
chemical_list: D029968:Escherichia coli Proteins; D020543:Proteome