Mass spec studio for integrative structural biology

Martial Rey, Vladimir Sarpe, Kyle M Burns, Joshua Buse, Charles A H Baker, Marc van Dijk, Linda Wordeman, Alexandre M J J Bonvin, David C Schriemer

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS and tandem MS (MS(2)) data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-MS(2) and data-independent HX-MS(2). The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions.

Original languageEnglish
Pages (from-to)1538-48
Number of pages11
JournalStructure
Volume22
Issue number10
DOIs
Publication statusPublished - 2014
Externally publishedYes

Keywords

  • Binding Sites
  • Deuterium
  • Hydrogen
  • Macrolides
  • Mass Spectrometry
  • Models, Molecular
  • Molecular Docking Simulation
  • Protein Conformation
  • Proteomics
  • Software
  • Tandem Mass Spectrometry
  • Tubulin
  • Journal Article
  • Research Support, Non-U.S. Gov't

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