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Sample Preparation for Proteomics Analysis: Filter-Aided Sample Preparation (FASP) and Single-Pot Solid-Phase Sample Preparation (SP3)

  • Ka Wan LiEmail author
Protocol
Part of the Neuromethods book series (NM, volume 146)

Abstract

The success of a proteomics experiment critically depends on the correct execution of the sample preparation. Gel-based sample preparation is a well-proven method widely used in qualitative and quantitative proteomics. Recently, sample preparation in a single vessel has gained popularity because of the ease to perform, the possibility for large-scale analysis, and the potential to improve sensitivity. In this chapter I describe two sample preparation protocols, filter-aided sample preparation (FASP) and single-pot solid-phase sample preparation (SP3).

Keywords

Sample preparation FASP SP3 Proteomics 

References

  1. 1.
    Chen N, Pandya NJ, Koopmans F, Castelo-Szekelv V, van der Schors RC, Smit AB, Li KW (2014) Interaction proteomics reveals brain region-specific AMPA receptor complexes. J Proteome Res 13:5695–5706CrossRefGoogle Scholar
  2. 2.
    Sielaff M, Kuharev J, Bohn T, Hahlbrock J, Bopp T, Tenzer S, Distler U (2017) Evaluation of FASP, SP3, and iST protocols for proteomic sample preparation in the low microgram range. J Proteome Res 16:4060–4072CrossRefGoogle Scholar
  3. 3.
    Wisniewski JR, Zougman A, Nagaraj N, Mann M (2009) Universal sample preparation method for proteome analysis. Nat Methods 6:359–362CrossRefGoogle Scholar
  4. 4.
    Hughes CS, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J (2014) Ultrasensitive proteome analysis using paramagnetic bead technology. Mol Syst Biol 10:757CrossRefGoogle Scholar
  5. 5.
    Moggridge S, Sorensen PH, Morin GB, Hughes CS (2018) Extending the compatibility of the SP3 paramagnetic bead processing approach for proteomics. J Proteome Res 17:1730–1740CrossRefGoogle Scholar
  6. 6.
    Kulak NA, Pichler G, Paron I, Nagaraj N, Mann M (2014) Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods 11:319–324CrossRefGoogle Scholar
  7. 7.
    Taoka M, Fujii M, Tsuchiya M, Uekita T, Ichimura T (2017) A sensitive microbead-based organic media-assisted method for proteomics sample preparation from dilute and denaturing solutions. ACS Appl Mater Interfaces 9:42661–42667CrossRefGoogle Scholar
  8. 8.
    Ludwig KR, Schroll MM, Hummon AB (2018) Comparison of in-solution, FASP, and S-trap based digestion methods for bottom-up proteomic studies. J Proteome Res 17(7):2480–2490CrossRefGoogle Scholar
  9. 9.
    Zougman A, Selby PJ, Banks RE (2014) Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis. Proteomics 14:1006–1000CrossRefGoogle Scholar
  10. 10.
    Yu Y, Bekele S, Pieper R (2017) Quick 96FASP for high throughput quantitative proteome analysis. J Proteome 166:1–7CrossRefGoogle Scholar
  11. 11.
    Pandya NJ, Klaassen RV, van der Schors RC, Slotman JA, Houtsmuller A, Smit AB, Li KW (2016) Group 1 metabotropic glutamate receptors 1 and 5 form a protein complex in mouse hippocampus and cortex. Proteomics 16:2698–2705CrossRefGoogle Scholar
  12. 12.
    Gonzalez-Lozano MA, Koopmans F, Paliukhovich I, Smit AB, Li KW (2019) A fast and economical sample preparation protocol for interaction proteomics analysis. Proteomics:e1900027Google Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam NeuroscienceVrije Universiteit AmsterdamAmsterdamThe Netherlands

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