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Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring

Lange, Vinzenz; Malmstroem, Johan A.; Didion, John; King, Nichole L.; Johansson, Björn LU ; Schaefer, Juliane; Rameseder, Jonathan; Wong, Chee-Hong; Deutsch, Eric W. and Brusniak, Mi-Youn, et al. (2008) In Molecular & Cellular Proteomics 7(8). p.1489-1500
Abstract
In many studies, particularly in the field of systems biology, it is essential that identical protein sets are precisely quantified in multiple samples such as those representing differentially perturbed cell states. The high degree of reproducibility required for such experiments has not been achieved by classical mass spectrometry-based proteomics methods. In this study we describe the implementation of a targeted quantitative approach by which predetermined protein sets are first identified and subsequently quantified at high sensitivity reliably in multiple samples. This approach consists of three steps. First, the proteome is extensively mapped out by multidimensional fractionation and tandem mass spectrometry, and the data generated... (More)
In many studies, particularly in the field of systems biology, it is essential that identical protein sets are precisely quantified in multiple samples such as those representing differentially perturbed cell states. The high degree of reproducibility required for such experiments has not been achieved by classical mass spectrometry-based proteomics methods. In this study we describe the implementation of a targeted quantitative approach by which predetermined protein sets are first identified and subsequently quantified at high sensitivity reliably in multiple samples. This approach consists of three steps. First, the proteome is extensively mapped out by multidimensional fractionation and tandem mass spectrometry, and the data generated are assembled in the PeptideAtlas database. Second, based on this proteome map, peptides uniquely identifying the proteins of interest, proteotypic peptides, are selected, and multiple reaction monitoring (MRM) transitions are established and validated by MS2 spectrum acquisition. This process of peptide selection, transition selection, and validation is supported by a suite of software tools, TIQAM (Targeted Identification for Quantitative Analysis by MRM), described in this study. Third, the selected target protein set is quantified in multiple samples by MRM. Applying this approach we were able to reliably quantify low abundance virulence factors from cultures of the human pathogen Streptococcus pyogenes exposed to increasing amounts of plasma. The resulting quantitative protein patterns enabled us to clearly define the subset of virulence proteins that is regulated upon plasma exposure. (Less)
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publication status
published
subject
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Molecular & Cellular Proteomics
volume
7
issue
8
pages
1489 - 1500
publisher
American Society for Biochemistry and Molecular Biology
external identifiers
  • wos:000258283400007
  • scopus:43049090085
ISSN
1535-9484
DOI
10.1074/mcp.M800032-MCP200
language
English
LU publication?
yes
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8e09fc73-14bc-40fd-8f1d-71c0905b0724 (old id 1253339)
date added to LUP
2008-10-31 07:56:26
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2017-09-10 03:40:00
@article{8e09fc73-14bc-40fd-8f1d-71c0905b0724,
  abstract     = {In many studies, particularly in the field of systems biology, it is essential that identical protein sets are precisely quantified in multiple samples such as those representing differentially perturbed cell states. The high degree of reproducibility required for such experiments has not been achieved by classical mass spectrometry-based proteomics methods. In this study we describe the implementation of a targeted quantitative approach by which predetermined protein sets are first identified and subsequently quantified at high sensitivity reliably in multiple samples. This approach consists of three steps. First, the proteome is extensively mapped out by multidimensional fractionation and tandem mass spectrometry, and the data generated are assembled in the PeptideAtlas database. Second, based on this proteome map, peptides uniquely identifying the proteins of interest, proteotypic peptides, are selected, and multiple reaction monitoring (MRM) transitions are established and validated by MS2 spectrum acquisition. This process of peptide selection, transition selection, and validation is supported by a suite of software tools, TIQAM (Targeted Identification for Quantitative Analysis by MRM), described in this study. Third, the selected target protein set is quantified in multiple samples by MRM. Applying this approach we were able to reliably quantify low abundance virulence factors from cultures of the human pathogen Streptococcus pyogenes exposed to increasing amounts of plasma. The resulting quantitative protein patterns enabled us to clearly define the subset of virulence proteins that is regulated upon plasma exposure.},
  author       = {Lange, Vinzenz and Malmstroem, Johan A. and Didion, John and King, Nichole L. and Johansson, Björn and Schaefer, Juliane and Rameseder, Jonathan and Wong, Chee-Hong and Deutsch, Eric W. and Brusniak, Mi-Youn and Buehlmann, Peter and Björck, Lars and Domon, Bruno and Aebersold, Ruedi},
  issn         = {1535-9484},
  language     = {eng},
  number       = {8},
  pages        = {1489--1500},
  publisher    = {American Society for Biochemistry and Molecular Biology},
  series       = {Molecular & Cellular Proteomics},
  title        = {Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring},
  url          = {http://dx.doi.org/10.1074/mcp.M800032-MCP200},
  volume       = {7},
  year         = {2008},
}