Automated Workflow for Large-Scale Selected Reaction Monitoring Experiments

Research output: Contribution to journalArticle

Abstract

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.

Details

Authors
  • Lars Malmstrom
  • Johan Malmström
  • Nathalie Selevsek
  • George Rosenberger
  • Ruedi Aebersold
Organisations
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Immunology in the medical area

Keywords

  • discrete wavelet transform, selected reaction monitoring, mass spectrometry, targeted proteomics
Original languageEnglish
Pages (from-to)1644-1653
JournalJournal of Proteome Research
Volume11
Issue number3
Publication statusPublished - 2012
Publication categoryResearch
Peer-reviewedYes