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Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline

Nature Protocols volume 9, pages 120–137 (2014)Cite this article

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Abstract

Chemical cross-linking in combination with LC-MS/MS (XL-MS) is an emerging technology to obtain low-resolution structural (distance) restraints of proteins and protein complexes. These restraints can also be used to characterize protein complexes by integrative modeling of the XL-MS data, either in combination with other types of structural information or by themselves, to establish spatial relationships of subunits in protein complexes. Here we present a protocol that has been successfully used to generate XL-MS data from a multitude of native proteins and protein complexes. It includes the experimental steps for performing the cross-linking reaction using disuccinimidyl suberate (a homobifunctional, lysine-reactive cross-linking reagent), the enrichment of cross-linked peptides by peptide size-exclusion chromatography (SEC; to remove smaller, non-cross-linked peptides), instructions for tandem MS analysis and the analysis of MS data via the open-source computational software pipeline xQuest and xProphet (available from http://proteomics.ethz.ch). Once established, this robust protocol should take ∼4 d to complete, and it is generally applicable to purified proteins and protein complexes.

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Figure 1: Typical workflow of an XL-MS experiment.
Figure 2: Workflow of the xQuest/xProphet software pipeline for the identification and statistical validation of cross-linked peptides from XL-MS experiments.
Figure 3: Examples of typical SEC chromatograms.
Figure 4: Simulated monitoring of the cross-linking reaction by SDS-PAGE by using a hypothetical trimeric complex.

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Acknowledgements

We thank M. Bonvin, M. Faini and F. Stengel for critical reading of the manuscript. This work was supported by the European Union 7th Framework project PROSPECTS (Proteomics Specification in Space and Time, grant no. HEALTH-F4-2008-201648) and by the European Research Council Advanced Grant Proteomics v3.0 (grant no. 233226) of the European Union to R.A.

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Author notes

  1. Alexander Leitner and Thomas Walzthoeni: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland

    Alexander Leitner, Thomas Walzthoeni & Ruedi Aebersold

  2. PhD Program in Molecular Life Sciences, University of Zurich–ETH Zurich, Zurich, Switzerland

    Thomas Walzthoeni

  3. Faculty of Science, University of Zurich, Zurich, Switzerland

    Ruedi Aebersold

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  1. Alexander Leitner
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Contributions

A.L., T.W. and R.A. designed research. A.L. and T.W. performed the experiments and analyzed the data. A.L., T.W. and R.A. wrote and edited the manuscript.

Corresponding authors

Correspondence to Alexander Leitner or Ruedi Aebersold.

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Integrated supplementary information

Supplementary Figure 1 xQuest/xProphet results manager.

The results manager is used as the central program for organizing and exploring xQuest/xProphet search results. Detailed documentation can be found following the link “How to use” (A). Different options are available to display and organize the individual search results (B). Individual experiments and definition files can be accessed from the table that displays the experiments (C). Experiments can be explored in the results viewer by clicking on “view” (D and Supplementary Figure 2).

Supplementary Figure 2 xQuest/xProphet results viewer.

Multiple filter and export options are available in the upper menu panel of the results viewer (A). If an xProphet analysis was performed, the filters that were used for the analysis are automatically loaded. Search results of the individual spectra are displayed in the table (B). For further inspection of the search results the “view” link can be used to open the spectrum viewer and display the spectrum of the identification (C and Supplementary Figure 3).

Supplementary Figure 3 xQuest spectrum viewer.

An example spectrum for a cross-linked peptide is depicted. Different filter options are displayed at the top of the window (A), which are initially loaded automatically from the xQuest definition file that was used for the search. The experimental spectrum (B) and the corresponding cross-link sequence (C) are shown below, whereby matched ions are indicated by diamonds in the spectrum, and as tick marks on the cross-link sequence. Spectrum (D) displays the matched ions that correspond to the individual peptides of a cross-link, indicated by the different colors, blue and yellow, for the alpha- and beta-peptide, respectively. (E) shows the table with the matched fragment-ion masses. Color coding in B and E: green indicates a common fragment ion, red indicates a cross-linker containing fragment ion.

Supplementary Figure 4 Example of an MS/MS spectrum from an mzXML file.

Tags and attributes used by the xQuest/xProphet pipeline are highlighted in yellow.

Supplementary Figure 5 Example of the LC-MS/MS analysis of two SEC fractions.

(A) and (B) show total ion chromatograms of fractions 1 and 2 highlighted in Figure 3b. Peptides from the higher molecular weight fraction 1 tend to be more hydrophobic so they elute slightly later under identical chromatographic conditions than peptides from fraction 2. (C) Two-dimensional plot (mass-to-charge vs. retention time) of the run shown in B. Only a small retention time (20-30 min) and m/z window (700-1100) is shown for clarity. Signals highlighted by asterisks on their right side correspond to peptides carrying a cross-linker modification. The difference in m/z space is 12/z for DSS-d0/d12. Due to the slight change in hydrophobicity, peptides with the heavy version of the cross-linker elute slightly (typically a few seconds) before the light form. xQuest allows the definition of a time window that is considered for pairing MS/MS spectra for the light and heavy forms. Even in this small window, more than 30 high-abundant pairs are clearly visible, and many more low-abundance pairs exist.

Supplementary information

Supplementary Figure 1

xQuest/xProphet results manager.. (PDF 170 kb)

Supplementary Figure 2

xQuest/xProphet results viewer. (PDF 683 kb)

Supplementary Figure 3

xQuest spectrum viewer. (PDF 172 kb)

Supplementary Figure 4

Example of an MS/MS spectrum from an mzXML file. (PDF 84 kb)

Supplementary Figure 5

Example of the LC-MS/MS analysis of two SEC fractions. (PDF 126 kb)

Supplementary Manual

User manual for the xQuest/xProphet virtual machine. (PDF 378 kb)

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Leitner, A., Walzthoeni, T. & Aebersold, R. Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nat Protoc 9, 120–137 (2014). https://doi.org/10.1038/nprot.2013.168

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