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Visual proteomics of the human pathogen Leptospira interrogans

Beck, Martin; Malmström, Johan A LU ; Lange, Vinzenz; Schmidt, Alexander; Deutsch, Eric W. and Aebersold, Ruedi (2009) In Nature Methods 6(11). p.23-817
Abstract

Systems biology conceptualizes biological systems as dynamic networks of interacting elements, whereby functionally important properties are thought to emerge from the structure of such networks. Owing to the ubiquitous role of complexes of interacting proteins in biological systems, their subunit composition and temporal and spatial arrangement within the cell are of particular interest. 'Visual proteomics' attempts to localize individual macromolecular complexes inside of intact cells by template matching reference structures into cryo-electron tomograms. Here we combined quantitative mass spectrometry and cryo-electron tomography to detect, count and localize specific protein complexes in the cytoplasm of the human pathogen... (More)

Systems biology conceptualizes biological systems as dynamic networks of interacting elements, whereby functionally important properties are thought to emerge from the structure of such networks. Owing to the ubiquitous role of complexes of interacting proteins in biological systems, their subunit composition and temporal and spatial arrangement within the cell are of particular interest. 'Visual proteomics' attempts to localize individual macromolecular complexes inside of intact cells by template matching reference structures into cryo-electron tomograms. Here we combined quantitative mass spectrometry and cryo-electron tomography to detect, count and localize specific protein complexes in the cytoplasm of the human pathogen Leptospira interrogans. We describe a scoring function for visual proteomics and assess its performance and accuracy under realistic conditions. We discuss current and general limitations of the approach, as well as expected improvements in the future.

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Contribution to journal
publication status
published
keywords
Bacterial Proteins, Chromatography, Liquid, Ciprofloxacin, Computer Simulation, Cryoelectron Microscopy, Electron Microscope Tomography, Leptospira interrogans, Proteome, Proteomics, Stress, Physiological, Tandem Mass Spectrometry, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't
in
Nature Methods
volume
6
issue
11
pages
7 pages
publisher
Nature Publishing Group
external identifiers
  • scopus:70350709997
ISSN
1548-7105
DOI
10.1038/nmeth.1390
language
English
LU publication?
no
id
a547ca80-02fa-4585-b683-a06317c494c2
date added to LUP
2017-09-04 17:20:18
date last changed
2017-10-22 05:35:30
@article{a547ca80-02fa-4585-b683-a06317c494c2,
  abstract     = {<p>Systems biology conceptualizes biological systems as dynamic networks of interacting elements, whereby functionally important properties are thought to emerge from the structure of such networks. Owing to the ubiquitous role of complexes of interacting proteins in biological systems, their subunit composition and temporal and spatial arrangement within the cell are of particular interest. 'Visual proteomics' attempts to localize individual macromolecular complexes inside of intact cells by template matching reference structures into cryo-electron tomograms. Here we combined quantitative mass spectrometry and cryo-electron tomography to detect, count and localize specific protein complexes in the cytoplasm of the human pathogen Leptospira interrogans. We describe a scoring function for visual proteomics and assess its performance and accuracy under realistic conditions. We discuss current and general limitations of the approach, as well as expected improvements in the future.</p>},
  author       = {Beck, Martin and Malmström, Johan A and Lange, Vinzenz and Schmidt, Alexander and Deutsch, Eric W. and Aebersold, Ruedi},
  issn         = {1548-7105},
  keyword      = {Bacterial Proteins,Chromatography, Liquid,Ciprofloxacin,Computer Simulation,Cryoelectron Microscopy,Electron Microscope Tomography,Leptospira interrogans,Proteome,Proteomics,Stress, Physiological,Tandem Mass Spectrometry,Journal Article,Research Support, N.I.H., Extramural,Research Support, Non-U.S. Gov't},
  language     = {eng},
  number       = {11},
  pages        = {23--817},
  publisher    = {Nature Publishing Group},
  series       = {Nature Methods},
  title        = {Visual proteomics of the human pathogen Leptospira interrogans},
  url          = {http://dx.doi.org/10.1038/nmeth.1390},
  volume       = {6},
  year         = {2009},
}