Dataset

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

Schmidt, A. (Creator), Kochanowski, K. (Creator), Bonsing-Vedelaar, S. (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), 2015

Dataset

  • Alexander Schmidt (Creator)
  • Karl Kochanowski (Creator)
  • Silke Bonsing-Vedelaar (Creator)
  • Erik Ahrne (Creator)
  • Benjamin Volkmer (Creator)
  • Luciano Callipo (Creator)
  • Kèvin Knoops (Creator)
  • Manuel Bauer (Creator)
  • Ruedi Aebersold (Creator)
  • Matthias Heinemann (Creator)

Description

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.
SpeciesList: scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList: Oxidation; Acetyl; Carbamidomethyl
Instrument: LTQ Orbitrap Elite

Cell Type: permanent cell line cell
Instrument: LTQ Orbitrap Elite
Software: Mascot Parser 2.4.3.0, Mascot Server 2.4.1
Modification: Acetyl; Oxidation; Carbamidomethyl
Quantification: TIC
Experiment Type: Shotgun proteomics
Date made available2015
PublisherEuropean Bioinformatics Institute (EMBL-EBI)
Access to the dataset Open
Contact researchdata@rug.nl

    Keywords on Datasets

  • Escherichia coli, proteome, Absolute quantiifcation, iBAQ, mass spectreomtry, E. coli, NCBI TaxID: 562
Related Publications
  1. The quantitative and condition-dependent Escherichia coli proteome

    Schmidt, A., Kochanowski, K., Vedelaar, S., Ahrné, E., Volkmer, B., Callipo, L., Knoops, K., Bauer, M., Aebersold, R. & Heinemann, M., Jan-2016, In : Nature Biotechnology. 34, 1, p. 104-110 7 p.

    Research output: Contribution to journalArticleAcademicpeer-review

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Related Press / Media
  1. New massive dataset of bacterial proteins

    Matthias Heinemann & Kèvin Knoops

    08/12/2015

    1 item of media coverage

    Press/Media: Public Engagement ActivitiesPopular

  2. New massive dataset of bacterial proteins

    Matthias Heinemann & Kèvin Knoops

    07/12/2015

    1 item of media coverage

    Press/Media: Public Engagement ActivitiesPopular

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