Skip to main content
SpringerLink
Log in

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

  • Protocol
  • First Online:
Proteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1550))

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 99.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  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):1885–95

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Erde J (2012) High throughput analysis of proteome perturbations induced by radiation, radiomitigators and chemotherapeutics. University of California, Los Angeles

    Google Scholar 

  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):1742–5

    Article  CAS  PubMed  Google Scholar 

  4. Wisniewski JR, Mann M (2009) Spin filter–based sample preparation for shotgun proteomics. Nat Methods 6(11):785–6

    Article  CAS  Google Scholar 

  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):307–9

    Article  CAS  PubMed  Google Scholar 

  6. Masuda T, Tomita M, Ishihama Y (2008 Feb) Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res 7(2):731–40

    Google Scholar 

  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):7698–703

    Article  CAS  PubMed  Google Scholar 

  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):2770–7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  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):2547–53

    Article  CAS  PubMed  Google Scholar 

  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):259–66

    Article  CAS  PubMed  Google Scholar 

  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):2705–13

    Article  CAS  PubMed  Google Scholar 

  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):135–7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Passivation of Amicon Microcon Concentrators for Improved Recovery (1999). Bedford, MA: Millipore Corporation, Technical Note PC1001EN00

    Google Scholar 

  14. Sebastiano R, Citterio A, Lapadula M, Righetti PG (2003) A new deuterated alkylating agent for quantitative proteomics. Rapid Commun Mass Spectrom 17(21):2380–6

    Article  CAS  PubMed  Google Scholar 

  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):2043–7

    Article  CAS  PubMed  Google Scholar 

  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. 207–17

    Google Scholar 

  17. Righetti PG (2006 Sep) Real and imaginary artefacts in proteome analysis via two-dimensional maps. J Chromatogr B 841(1–2):14–22

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA

    Jonathan Erde & Joseph A. Loo

  2. Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA

    Rachel R. Ogorzalek Loo & Joseph A. Loo

Authors
  1. Jonathan Erde
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rachel R. Ogorzalek Loo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Joseph A. Loo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Joseph A. Loo .

Editor information

Editors and Affiliations

  1. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

    Lucio Comai

  2. Keck School of Medicine, University of Southern California, Los Angeles, California, USA

    Jonathan E. Katz

  3. Stanford University, Palo Alto, California, USA

    Parag Mallick

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Erde, J., Loo, R.R.O., Loo, J.A. (2017). Improving Proteome Coverage and Sample Recovery with Enhanced FASP (eFASP) for Quantitative Proteomic Experiments. In: Comai, L., Katz, J., Mallick, P. (eds) Proteomics. Methods in Molecular Biology, vol 1550. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6747-6_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6747-6_2

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6745-2

  • Online ISBN: 978-1-4939-6747-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation