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  • Review Article
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Analysis of protein complexes using mass spectrometry

Nature Reviews Molecular Cell Biology volume 8, pages 645–654 (2007)Cite this article

Key Points

  • In this article, we review the current status of affinity purification and mass spectrometry (AP–MS) and its promise for better understanding protein complexes, complex structure and the dynamics of complex formation.

  • We describe the general AP–MS strategy, with an emphasis on generic approaches (flag-tag, tandem AP) and how AP–MS of multiple components (that is, high-density AP–MS) can help to reveal the true composition of protein complexes.

  • Recent high-throughput studies with flag-tagging or tandem AP significantly improved our understanding of protein–protein interactions in yeast.

  • AP–MS can be combined with classical biochemical purification approaches to reveal complex composition and to resolve the problem of mutually exclusive complexes co-precipitating with the same tagged protein.

  • Crosslinkers can contribute to AP–MS strategies by stabilizing weak or transient protein interactions and by revealing details concerning complex organization and interacting surfaces.

  • Stoichiometry of protein complexes can be obtained using intact-complex mass measurement and absolute quantitative proteomics tools.

  • Quantitative proteomics approaches can help to decipher the dynamics of protein-complex formation.

Abstract

The versatile combination of affinity purification and mass spectrometry (AP–MS) has recently been applied to the detailed characterization of many protein complexes and large protein-interaction networks. The combination of AP–MS with other techniques, such as biochemical fractionation, intact mass measurement and chemical crosslinking, can help to decipher the supramolecular organization of protein complexes. AP–MS can also be combined with quantitative proteomics approaches to better understand the dynamics of protein–complex assembly.

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Figure 1: General overview of an affinity purification and mass spectrometry experiment.
Figure 2: High-density data acquisition to elucidate complex composition.
Figure 3: Incorporation of stable isotopes into proteins.
Figure 4: Isobaric tags to elucidate complex formation dynamics.

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Acknowledgements

Funding was provided in part by the Terry Fox Foundation to A.-C.G., the Canada Institutes of Health Research to B.R. and the National Heart, Lung, and Blood Institute, National Institute of Health contract N01-HV-28179 to R.A. A.-C.G. and B.R. are recipients of Canada Research Chairs, Canadian Foundation for Innovation and Ontario Research Fund grants.

Author information

Authors and Affiliations

  1. Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave, Room 992A, Toronto, M5G 1X5, Ontario, Canada

    Anne-Claude Gingras

  2. Department of Medical & Molecular Genetics and Graduate Department of Molecular & Medical Genetics, University of Toronto, Toronto, Canada

    Anne-Claude Gingras

  3. Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, ETH Hönggerberg HPT E 78, Zürich, CH-8093, Switzerland

    Matthias Gstaiger & Ruedi Aebersold

  4. Competence Center for Systems Physiology and Metabolic Diseases, Zurich, Switzerland

    Matthias Gstaiger & Ruedi Aebersold

  5. University Health Network, Ontario Cancer Institute and McLaughlin Centre for Molecular Medicine, 101 College St, MaRS TMDT 9-805, Toronto, M5G 1L7, Ontario, Canada

    Brian Raught

  6. Department of Medical Biophysics, University of Toronto, Toronto, Canada

    Brian Raught

  7. Institute for Systems Biology, 1441 N. 34th St, Seattle, Washington, 98103, USA

    Ruedi Aebersold

  8. Faculty of Science, University of Zurich, Switzerland

    Ruedi Aebersold

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  1. Anne-Claude Gingras
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Correspondence to Anne-Claude Gingras.

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Glossary

Interactomes

Global networks of interactions (proteinprotein interactions in this article).

Yeast two-hybrid

A genetic technique that detects binary interactions between protein pairs.

Flag tag

A short amino-acid sequence (usually 811 amino acids) that is recognized by monoclonal antibodies and is used to tag proteins for detection and purification.

Tandem affinity purification (TAP) tag

A recombinant fusion tag formed of two moieties, used sequentially for protein purification. The original version consists of the immunoglobulin G (IgG)-binding portion of Staphylococcus aureus protein A (distal tag) and the calmodulin-binding peptide (proximal tag); these tags are separated by a tobacco etch virus protease cleavage site.

Electrospray ionization

(ESI). One of two common techniques (see MALDI) used in mass spectrometry to ionize large, non-volatile molecules (such as peptides). ESI charges analytes directly from the liquid phase and is easily coupled with reversed-phase high-pressure liquid chromatography.

Matrix-assisted laser desorption/ionization

(MALDI). One of two common techniques (see ESI) used in mass spectrometry to ionize large, non-volatile molecules (such as peptides). MALDI ionizes molecules through laser excitation of a matrix in which the molecules are embedded.

Graph-clustering algorithm

Proteinprotein interactions are often represented in a graph format, in which individual proteins are depicted as circles (nodes) and the observed associations are depicted as lines (edges) that link the nodes.

Socio-affinity index

Measure of the propensity of proteins to form partnerships. This index represents the log odds of the number of times particular proteins are observed together in a tandem affinity purification, as compared to what would be expected for their individual frequency of detection in the data set.

Tobacco etch virus protease

Specific endopeptidase that recognizes the linear epitope EXXYXQG/S, in which X is any amino acid (although some preferences are observed).

Gel filtration

A chromatographic method (also called size-exclusion chromatography) that separates proteins or protein complexes on the basis of their size (or hydrodynamic volume).

Density gradient

Centrifugation-based separation technique that often uses sucrose or glycerol density gradients to separate components on the basis of their density. It is applicable to protein complexes, organelles and intact cells.

Selective precipitation

Common enrichment procedure (also known as salting out) that most often uses increasing concentrations of ammonium sulphate to alter the solubility of proteins and cause their precipitation. It is usually used in the early steps of a biochemical fractionation protocol.

Ion-exchange chromatography

A frequently used separation technique for peptides, proteins and protein complexes that exploits the charge properties of the molecules to be fractionated.

Free-flow electrophoresis

(FFE). Separation procedure that fractionates the sample (ranging in size from small molecules, including peptides, to objects of cellular dimension) on the basis of the isoelectric point (or electrophoretic mobility). FFE operates continuously in the absence of a solid support.

Blue native gel electrophoresis

A native gel-based approach that efficiently separates protein complexes. It can be used alone or in combination with a denaturing second dimension.

Spacer arm length

Spacer arm length refers to the distance between two reactive groups in a bifunctional crosslinker. The spacer arm length defines the maximal distance between the two crosslinked moieties.

Isobaric tags for relative and absolute quantification

A type of chemical labelling for quantitative proteomics in which isobaric tags are added to the N terminus of every peptide (and to the lysine -amine).

Stable-isotope labelling with amino acids in cell culture

A type of metabolic labelling for quantitative proteomics in which heavy isotopic versions of one or more amino acids are used in the culture medium to replace their normal (light) isotopic counterparts.

Isotope-coded affinity tags

(ICAT). A chemical labelling reagent used for quantitative proteomics. The current version of ICAT consists of an acid-cleavable biotin-labelled tag that reacts with cysteine groups on proteins. Isotopically heavy (13C9) and light (12C9) variants are commercially available.

DNA-repair syndrome trichothiodystrophy group A

Trichothiodystrophy is a human syndrome characterized by brittle hair and nails, ichthyotic skin, and developmental and mental retardation. Photosensitivity is observed in roughly half of the patients and has been linked to defects in nucleotide-excision repair.

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Gingras, AC., Gstaiger, M., Raught, B. et al. Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol 8, 645–654 (2007). https://doi.org/10.1038/nrm2208

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