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Application of SWATH Proteomics to Mouse Biology
Yibo Wu1, Evan G Williams1, Ruedi Aebersold1,2
1Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
Current Protocols in Mouse Biology
|June 20, 2017
Summary
This study presents standard protocols for preparing tissue samples for SWATH-MS analysis, enabling biologists to reliably quantify proteomes. These methods facilitate high-throughput proteomic measurements for physiological and cell biology insights.
Area of Science:
- Biochemistry
- Molecular Biology
- Proteomics
Background:
- The proteome offers unique physiological and cell biology insights beyond genomics and transcriptomics due to complex transcriptome-proteome relationships.
- Mass spectrometry (MS)-based proteomics, particularly SWATH-MS, has advanced for reliable use by non-specialist biologists.
Purpose of the Study:
- To provide standard protocols for preparing tissue samples for SWATH-MS analysis.
- To enable high-throughput processing of tissue samples (≥5 mg) for proteomic analysis.
Main Methods:
- Standardized protocols for tissue sample preparation for SWATH-MS.
- High-throughput processing capabilities for up to 48 samples per day (144 per week).
- Data acquisition protocols for SWATH-MS.
Main Results:
- Protocols are designed for samples with ≥5 mg of tissue.
- An experienced user can process 48 samples daily, with 1.5 hr machine time per sample.
- Suitable for biologists without specialized mass spectrometry expertise.
Conclusions:
- Standardized SWATH-MS protocols facilitate reliable proteomic measurements in biological research.
- These methods enhance the accessibility of high-throughput quantitative proteomics for diverse biological studies.
