Proteomics pp 11-18 | Cite as

Improving Proteome Coverage and Sample Recovery with Enhanced FASP (eFASP) for Quantitative Proteomic Experiments

  • Jonathan Erde
  • Rachel R. Ogorzalek Loo
  • Joseph A. LooEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1550)


Enhanced Filter Aided Sample Preparation (eFASP) incorporates plastics passivation and digestion-enhancing surfactants into the traditional FASP workflow to reduce sample loss and increase hydrophobic protein representation in qualitative and quantitative proteomics experiments. Resulting protein digests are free of contaminants and can be analyzed directly by LC-MS.

Key words

Enhanced filter aided sample preparation Quantitative proteomics Detergent Ammonium deoxycholate 


  1. 1.
    Erde J, Loo RRO, Loo JA (2014) Enhanced FASP (eFASP) to increase proteome coverage and sample recovery for quantitative proteomic experiments. J Proteome Res 13(4):1885–95CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Erde J (2012) High throughput analysis of proteome perturbations induced by radiation, radiomitigators and chemotherapeutics. University of California, Los AngelesGoogle Scholar
  3. 3.
    Manza LL, Stamer SL, Ham A-JL, Codreanu SG, Liebler DC (2005) Sample preparation and digestion for proteomic analyses using spin filters. Proteomics 5(7):1742–5CrossRefPubMedGoogle Scholar
  4. 4.
    Wisniewski JR, Mann M (2009) Spin filter–based sample preparation for shotgun proteomics. Nat Methods 6(11):785–6CrossRefGoogle Scholar
  5. 5.
    Wisniewski JR, Zielinska DF, Mann M (2011) Comparison of ultrafiltration units for proteomic and N-glycoproteomic analysis by the filter-aided sample preparation method. Anal Biochem 410(2):307–9CrossRefPubMedGoogle Scholar
  6. 6.
    Masuda T, Tomita M, Ishihama Y (2008 Feb) Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res 7(2):731–40Google Scholar
  7. 7.
    Masuda T, Sugiyama N, Tomita M, Ishihama Y (2011) Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines. Anal Chem 83(20):7698–703CrossRefPubMedGoogle Scholar
  8. 8.
    Masuda T, Saito N, Tomita M, Ishihama Y (2009) Unbiased quantitation of escherichia coli membrane proteome using phase transfer surfactants. Mol Cell Proteomics 8(12):2770–7CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Zhou J, Zhou T, Cao R, Liu Z, Shen J, Chen P et al (2006) Evaluation of the application of sodium deoxycholate to proteomic analysis of rat hippocampal plasma membrane. J Proteome Res 5(10):2547–53CrossRefPubMedGoogle Scholar
  10. 10.
    Lin Y, Zhou J, Bi D, Chen P, Wang X, Liang S (2008) Sodium-deoxycholate-assisted tryptic digestion and identification of proteolytically resistant proteins. Anal Biochem 377(2):259–66CrossRefPubMedGoogle Scholar
  11. 11.
    Lin Y, Liu Y, Li J, Zhao Y, He Q, Han W et al (2010) Evaluation and optimization of removal of an acid-insoluble surfactant for shotgun analysis of membrane proteome. Electrophoresis 31(16):2705–13CrossRefPubMedGoogle Scholar
  12. 12.
    Yeung Y-G, Nieves E, Angeletti RH, Stanley ER (2008) Removal of detergents from protein digests for mass spectrometry analysis. Anal Biochem 382(2):135–7CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Passivation of Amicon Microcon Concentrators for Improved Recovery (1999). Bedford, MA: Millipore Corporation, Technical Note PC1001EN00Google Scholar
  14. 14.
    Sebastiano R, Citterio A, Lapadula M, Righetti PG (2003) A new deuterated alkylating agent for quantitative proteomics. Rapid Commun Mass Spectrom 17(21):2380–6CrossRefPubMedGoogle Scholar
  15. 15.
    Bai F, Liu S, Witzmann FA (2005) A “de-streaking” method for two-dimensional electrophoresis using the reducing agent tris(2-carboxyethyl)-phosphine hydrochloride and alkylating agent vinylpyridine. Proteomics 5(8):2043–7CrossRefPubMedGoogle Scholar
  16. 16.
    Liu S, Bai F, Witzmann F (2006) Destreaking strategies for two-dimensional electrophoresis. In: Separation methods in proteomics. Eds.: Smejkal GB, Lazarev A, CRC Press/Taylor & Francis, Boca Raton, pp. 207–17Google Scholar
  17. 17.
    Righetti PG (2006 Sep) Real and imaginary artefacts in proteome analysis via two-dimensional maps. J Chromatogr B 841(1–2):14–22Google Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Jonathan Erde
    • 1
  • Rachel R. Ogorzalek Loo
    • 2
  • Joseph A. Loo
    • 1
    • 2
    Email author
  1. 1.Department of Chemistry and BiochemistryUniversity of California-Los AngelesLos AngelesUSA
  2. 2.Department of Biological ChemistryUniversity of California-Los AngelesLos AngelesUSA

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