Protein Enrichment and Sample Cleanup
In bottom-up proteomics, effective protein enrichment and sample cleanup are essential for obtaining reliable and reproducible mass spectrometry (MS) results. These steps remove unwanted contaminants such as salts, detergents, and lipids while enriching target proteins or peptides—ultimately improving detection sensitivity.
One widely used method is Single-Pot, Solid-Phase–enhanced Sample Preparation (SP3®). This method has become a cornerstone in the proteomics community due to its robustness and simplicity. Our Magnetic Proteomics Sample Prep (MPSP) kit leverages the principles of the SP3 workflow, offering a highly efficient, magnetic bead-based solution for sample cleanup and enrichment.
Other commonly used techniques include Protein Aggregation Capture (PAC), Solid-Phase Extraction (SPE), ultrafiltration, immunoaffinity capture, and co-immunoprecipitation. A well-optimized sample preparation workflow, particularly those following SP3-like strategies, can enhance digestion efficiency, reduce background noise, and improve proteome coverage for accurate protein identification and quantification.
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What is Protein Enrichment and Sample Cleanup?
Successful mass spectrometry (MS)-based proteomics depends on robust protein enrichment and sample cleanup strategies. These steps refine complex biological samples by eliminating interfering substances, such as detergents, denaturants, and salts, and by selectively concentrating proteins or peptides for downstream analysis.
Common techniques—such as precipitation, filtration, chromatography-based purification and affinity enrichment—streamline bottom-up workflows, enhancing digestion efficiency and boosting peptide recovery. Optimizing these processes reduces variability and increases proteome depth, enabling you to uncover meaningful biological insights with higher confidence.
Among these techniques, workflows based on SP3 methodology have become favored for their scalability and compatibility with automation. Our MPSP (Magnetic Proteomics Sample Prep) kit builds on this approach by integrating optimized magnetic bead chemistry tailored for consistent performance across diverse sample types and input amounts. This helps streamline preparation while maintaining high recovery and reproducibility.
SP3 is a trademark of EMBL, Germany. Promega’s MPSP kit is based on the SP3 method but is not affiliated with or endorsed by EMBL.
