XTract: Software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry

Thomas Walzthoeni, Lukasz A. Joachimiak, George Rosenberger, Hannes L. Röst, Lars Malmström, Alexander Leitner, Judith Frydman, Ruedi Aebersold

Research output: Contribution to journalArticle

44 Citations (Scopus)

Abstract

Chemical cross-linking in combination with mass spectrometry generates distance restraints of amino acid pairs in close proximity on the surface of native proteins and protein complexes. In this study we used quantitative mass spectrometry and chemical cross-linking to quantify differences in cross-linked peptides obtained from complexes in spatially discrete states. We describe a generic computational pipeline for quantitative cross-linking mass spectrometry consisting of modules for quantitative data extraction and statistical assessment of the obtained results. We used the method to detect conformational changes in two model systems: firefly luciferase and the bovine TRiC complex. Our method discovers and explains the structural heterogeneity of protein complexes using only sparse structural information.

Original languageEnglish (US)
Pages (from-to)1185-1190
Number of pages6
JournalNature methods
Volume12
Issue number12
DOIs
StatePublished - Dec 1 2015
Externally publishedYes

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Mass spectrometry
Mass Spectrometry
Software
Firefly Luciferases
Proteins
Membrane Proteins
Pipelines
Amino Acids
Peptides

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

XTract : Software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. / Walzthoeni, Thomas; Joachimiak, Lukasz A.; Rosenberger, George; Röst, Hannes L.; Malmström, Lars; Leitner, Alexander; Frydman, Judith; Aebersold, Ruedi.

In: Nature methods, Vol. 12, No. 12, 01.12.2015, p. 1185-1190.

Research output: Contribution to journalArticle

Walzthoeni, T, Joachimiak, LA, Rosenberger, G, Röst, HL, Malmström, L, Leitner, A, Frydman, J & Aebersold, R 2015, 'XTract: Software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry', Nature methods, vol. 12, no. 12, pp. 1185-1190. https://doi.org/10.1038/nmeth.3631
Walzthoeni, Thomas ; Joachimiak, Lukasz A. ; Rosenberger, George ; Röst, Hannes L. ; Malmström, Lars ; Leitner, Alexander ; Frydman, Judith ; Aebersold, Ruedi. / XTract : Software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. In: Nature methods. 2015 ; Vol. 12, No. 12. pp. 1185-1190.
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