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Absolute quantification of microbial proteomes at different states by directed mass spectrometry

Schmidt, Alexander; Beck, Martin; Malmström, Johan LU ; Lam, Henry; Claassen, Manfred; Campbell, David and Aebersold, Ruedi (2011) In Molecular Systems Biology 7. p.510-510
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... (More)

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.

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author
publishing date
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Contribution to journal
publication status
published
keywords
Bacterial Proteins, Chromatography, Liquid, Cluster Analysis, Culture Media, Databases, Genetic, Down-Regulation, Gene Expression Profiling, Leptospira interrogans, Operon, Peptides, Proteome, Proteomics, Sequence Analysis, RNA, Tandem Mass Spectrometry, Up-Regulation, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't
in
Molecular Systems Biology
volume
7
pages
510 - 510
publisher
Nature Publishing Group
external identifiers
  • scopus:79960590826
ISSN
1744-4292
DOI
10.1038/msb.2011.37
language
English
LU publication?
no
id
c7f55ecb-44df-479e-b16f-99887bb20744
date added to LUP
2016-11-16 20:30:48
date last changed
2017-08-27 06:29:20
@article{c7f55ecb-44df-479e-b16f-99887bb20744,
  abstract     = {<p>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.</p>},
  author       = {Schmidt, Alexander and Beck, Martin and Malmström, Johan and Lam, Henry and Claassen, Manfred and Campbell, David and Aebersold, Ruedi},
  issn         = {1744-4292},
  keyword      = {Bacterial Proteins,Chromatography, Liquid,Cluster Analysis,Culture Media,Databases, Genetic,Down-Regulation,Gene Expression Profiling,Leptospira interrogans,Operon,Peptides,Proteome,Proteomics,Sequence Analysis, RNA,Tandem Mass Spectrometry,Up-Regulation,Journal Article,Research Support, N.I.H., Extramural,Research Support, Non-U.S. Gov't},
  language     = {eng},
  month        = {07},
  pages        = {510--510},
  publisher    = {Nature Publishing Group},
  series       = {Molecular Systems Biology},
  title        = {Absolute quantification of microbial proteomes at different states by directed mass spectrometry},
  url          = {http://dx.doi.org/10.1038/msb.2011.37},
  volume       = {7},
  year         = {2011},
}