The quantitative and condition-dependent Escherichia coli proteome

Alexander Schmidt; Karl Kochanowski; Silke Vedelaar; Erik Ahrné; Benjamin Volkmer; Luciano Callipo; Kèvin Knoops; Manuel Bauer; Ruedi Aebersold; Matthias Heinemann

doi:10.1038/nbt.3418

The quantitative and condition-dependent Escherichia coli proteome

Alexander Schmidt^*
, Karl Kochanowski
, Silke Vedelaar
, Erik Ahrné
, Benjamin Volkmer
, Luciano Callipo
, Kèvin Knoops
, Manuel Bauer
, Ruedi Aebersold
, Matthias Heinemann

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

568 Citations (Scopus)

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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.

Original language	English
Pages (from-to)	104-110
Number of pages	7
Journal	Nature Biotechnology
Volume	34
Issue number	1
Early online date	7-Dec-2015
DOIs	https://doi.org/10.1038/nbt.3418
Publication status	Published - Jan-2016

Keywords

MASS-SPECTROMETRY
EVOLUTIONARY CONSERVATION
GENE-EXPRESSION
COG DATABASE
GROWTH-RATE
B-R
ACETYLATION
PROTEINS
REVEALS
RATES

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The quantitative and condition-dependent Escherichia coli proteomeFinal publisher's version, 1.89 MBLicence: Taverne

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Peer-reviewed dataset: The quantitative and condition-dependent Escherichia coli proteome
Schmidt, A. (Creator), Kochanowski, K. (Creator), Vedelaar, S. R. (Creator), Ahrne, E. (Creator), Volkmer, B. (Creator), Callipo, L. (Creator), Knoops, K. (Creator), Bauer, M. (Creator), Aebersold, R. (Creator) & Heinemann, M. (Creator), European Bioinformatics Institute (EMBL-EBI), 8-Dec-2015
DOI: 10.6019/PXD000498, https://www.ebi.ac.uk/pride/archive/projects/PXD000498
Dataset

Cite this

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AU - Vedelaar, Silke

AU - Ahrné, Erik

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AU - Callipo, Luciano

AU - Knoops, Kèvin

AU - Bauer, Manuel

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KW - PROTEINS

KW - REVEALS

KW - RATES

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The quantitative and condition-dependent Escherichia coli proteome

Abstract

Keywords

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Peer-reviewed dataset: The quantitative and condition-dependent Escherichia coli proteome

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