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Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics

  • Sophie Moggridge
    Sophie Moggridge
    Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
    Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 3E6, Canada
  • Poul H. Sorensen
    Poul H. Sorensen
    Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia V5Z 1L3, Canada
  • Gregg B. Morin*
    Gregg B. Morin
    Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
    Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
    *E-mail: [email protected]
  • , and 
  • Christopher S. Hughes
    Christopher S. Hughes
    Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
Cite this: J. Proteome Res. 2018, 17, 4, 1730–1740
Publication Date (Web):March 22, 2018
https://doi.org/10.1021/acs.jproteome.7b00913
Copyright © 2018 American Chemical Society

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    Abstract

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    The diversity in protein and peptide biochemistry necessitates robust protocols and reagents for efficiently handling and enriching these molecules prior to analysis with mass spectrometry (MS) or other techniques. Further exploration of the paramagnetic bead-based approach, single-pot solid-phase-enhanced sample preparation (SP3), is carried out toward updating and extending previously described conditions and experimental workflows. The SP3 approach was tested in a wide range of experimental scenarios, including (1) binding solvents (acetonitrile, ethanol, isopropanol, acetone), (2) binding pH (acidic vs neutral), (3) solvent/lysate ratios (50–200%, v/v), (4) mixing and rinsing conditions (on-rack vs off-rack rinsing), (5) Enrichment of nondenatured proteins, and (6) capture of individual proteins from noncomplex mixtures. These results highlight the robust handling of proteins in a broad set of scenarios while also enabling the development of a modified SP3 workflow that offers extended compatibility. The modified SP3 approach is used in quantitative in-depth proteome analyses to compare it with commercial paramagnetic bead-based HILIC methods (MagReSyn) and across multiple binding conditions (e.g., pH and solvent during binding). Together, these data reveal the extensive quantitative coverage of the proteome possible with SP3 independent of the binding approach utilized. The results further establish the utility of SP3 for the unbiased handling of peptides and proteins for proteomic applications.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jproteome.7b00913.

    • Figures S-1 and S-2. Handling of protein mixtures with SP3 using a variety of solvents. Figures S-3–S-6. Processing of proteins using SP3 with modified mixing and rinsing approaches. Figures S-7 and S-8. Measurement of reproducibility between SP3 batches and technical replicates. Figure S-9. Processing of nondenatured proteins with SP3. Figure S-10. Processing of noncomplex protein mixtures with SP3. Figure S-11. Identifications overlap in the in-depth proteome analysis of samples processed with SP3. (PDF)

    • Tables S-1 and S-2. Whole-proteome analysis of SP3 in comparison with MagReSyn and across different processing conditions. (XLSX)

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