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Automated Workflow for Large-Scale Selected Reaction Monitoring Experiments

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Author

  • Lars Malmstrom
  • Johan Malmström
  • Nathalie Selevsek
  • George Rosenberger
  • Ruedi Aebersold

Summary, in English

Targeted proteomics allows researchers to study proteins of interest without being drowned in data from other, less interesting proteins or from redundant or uninformative peptides. While the technique is mostly used for smaller, focused studies, there are several reasons to conduct larger targeted experiments. Automated, highly robust software becomes more important in such experiments. In addition, larger experiments are carried out over longer periods of time, requiring strategies to handle the sometimes large shift in retention time often observed. We present a complete proof-of-principle software stack that automates most aspects of selected reaction monitoring workflows, a targeted proteomics technology. The soft-ware allows experiments to be easily designed and carried out. The steps automated are the generation of assays, generation of mass spectrometry driver files and methods files, and the import. and analysis of the data. All data are normalized to a common retention time scale, the data are then scored using a novel score model, and the error is subsequently estimated. We also show that selected reaction monitoring can be used for label-free quantification. All data generated are stored in a relational database, and the growing resource further facilitates the design of new experiments. We apply the technology to a large-scale experiment studying how Streptococcus pyogenes remodels its proteome under stimulation of human plasma.

Publishing year

2012

Language

English

Pages

1644-1653

Publication/Series

Journal of Proteome Research

Volume

11

Issue

3

Document type

Journal article

Publisher

The American Chemical Society (ACS)

Topic

  • Immunology in the medical area

Keywords

  • discrete wavelet transform
  • selected reaction monitoring
  • mass spectrometry
  • targeted proteomics

Status

Published

Research group

  • Infection Medicine Proteomics

ISBN/ISSN/Other

  • ISSN: 1535-3893