Quantifying protein interaction dynamics by SWATH mass spectrometry: application to the 14-3-3 system
Open accessAbstract
Protein complexes and protein interaction networks are essential mediators of most biological functions. Complexes supporting transient functions such as signal transduction processes are frequently subject to dynamic remodeling. Currently, the majority of studies on the composition of protein complexes are carried out by affinity purification and mass spectrometry (AP-MS) and present a static view of the system. For a better understanding of inherently dynamic biological processes, methods to reliably quantify temporal changes of protein interaction networks are essential. Here we used affinity purification combined with sequential window acquisition of all theoretical spectra (AP-SWATH) mass spectrometry to study the dynamics of the 14-3-3β scaffold protein interactome after stimulation of the insulin-PI3K-AKT pathway. The consistent and reproducible quantification of 1,967 proteins across all stimulation time points provided insights into the 14-3-3β interactome and its dynamic changes following IGF1 stimulation. We therefore establish AP-SWATH as a tool to quantify dynamic changes in protein-complex interaction networks.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
SWATH-MS and related DIA approaches have achieved high intra-laboratory reproducibility in a variety of research questions.
“SWATH-MS and related DIA approaches have achieved a high degree of reproducibility in intra-laboratory studies in a variety of research questions such as interaction proteomics40, 41, plasma proteomics42, tissue proteomics43, microbial proteomics44, 45, pre-clinical toxicology9, analysis of genetic reference strains46, and many others.”
From Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry (2017) · cites this paper as [40]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
The citation lists haven’t been fetched yet
References 63 · Cited by 314
Research works printed but not linked: 1
- Glatter, T., Wepf, A., Aebersold, R. & Gstaiger, M. An integrated workflow for charting the human interaction proteome: insights into the PP2A system Mol Syst Biol 5, 237 (2009).
- Authors
- Collins, B. C., Gillet, L. C., Rosenberger, G., Röst, H. L., Vichalkovski, A., Gstaiger, M., & Aebersold, R.
- Affiliations
- ETH Zurich (CH)
- University of Zurich (CH)
- Corresponding author
- Aebersold, Ruedi
- ORCID
- Venue
- Nature Methods
- Published
- 2013-10-27
- Volume
- 10
- Issue
- 12
- Pages
- 1246-1253
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2086900521
- Cited by
- 314
- References
- 63
- Citations by year
- 2026: 4 · 2025: 10 · 2024: 9 · 2023: 18 · 2022: 12 · 2021: 21 · 2020: 32 · 2019: 25 · 2018: 32 · 2017: 37 · 2016: 38 · 2015: 52 · 2014: 22 · 2013: 2
- FWCI
- 17.04
- Type
- journal article
- Language
- en
- Open access
- green
- pure.qub.ac.uk
- Licence
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- Research Portal (Queen's University Belfast) (acceptedVersion, other-oa)
- Funders
- European Commission (233226)
- FP7 Ideas: European Research Council (233226)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › 14-3-3 protein interactions
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Keywords
- 14-3-3β, protein-protein interaction network, affinity purification, quantitative proteomics, signal transduction
- MeSH terms
- Mechanistic Target of Rapamycin Complex 1, Mechanistic Target of Rapamycin Complex 2, Chromatography, Affinity, Humans, Peptides, Protein Binding, Proteins, Mass Spectrometry, Time Factors, Signal Transduction, Gene Library, Computational Biology, Phosphatidylinositol 3-Kinases, Protein Interaction Mapping, Proteomics, Multiprotein Complexes, 14-3-3 Proteins, HEK293 Cells, TOR Serine-Threonine Kinases
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
