hSWATH: Unlocking SWATH's Full Potential for an Untargeted Histone Perspective
Laura De Clerck1, Sander Willems1, Roberta Noberini2
1ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium.
Journal of Proteome Research
|August 21, 2019
Summary
We developed a new mass spectrometry workflow (hSWATH) for analyzing histone post-translational modifications (hPTMs). This method enables untargeted identification and quantification of hPTMs, advancing histone research in cancer cell lines.
Area of Science:
- Proteomics
- Epigenetics
- Mass Spectrometry
Background:
- Mass spectrometry (MS) is crucial for analyzing histone post-translational modifications (hPTMs).
- Histone analysis using MS requires specialized workflows distinct from traditional methods.
- Untargeted approaches are vital for novel discovery in hPTM research.
Purpose of the Study:
- To present a comprehensive SWATH workflow tailored for untargeted histone analysis (hSWATH).
- To validate the hSWATH workflow using a controlled deacetylation experiment.
- To apply hSWATH for investigating differential responses to HDAC inhibition in breast cancer cell lines.
Main Methods:
- Development of the histone-specific SWATH (hSWATH) workflow.
- Technical validation using time-lapse deacetylation of histone extracts with HDAC1.
- Application in a biological context to study breast cancer cell lines.
Main Results:
- The hSWATH workflow accurately identified and quantified hPTMs.
- Validation demonstrated the expected decrease in acetylated peptides.
- Differential responses to HDAC inhibition were observed across different breast cancer cell lines.
Conclusions:
- The hSWATH workflow is a robust tool for untargeted hPTM analysis.
- This method facilitates discovery-driven research in epigenetics.
- hSWATH provides insights into epigenetic regulation in cancer.
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