Skip to main content

Proteomic Profiling by Nanomaterials-Based Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for High-Resolution Data and Novel Protein Information Directly from Biological Samples

  • Protocol
Proteomic Profiling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1295))

Abstract

Qualitative and quantitative analyses of global proteome samples derived from biocomplex mixtures are very important to understand the cellular functions in cell biology. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)-based proteomics has recently become one of the most informative and attractive core technologies in proteomics. Particularly, nanomaterials-based MALDI mass spectrometric methods are quickly becoming a critical miniaturized bioanalytical tool for detecting and discerning proteins from biocomplex samples. These MALDI-developed strategies allow high-throughput identification of proteins from highly complex mixtures including accurate mass measurement of peptides derived from total proteome digests and peptides/proteins separations from various samples. The nanomaterials-integrated MALDI-MS technologies in protein arrays hold much promise for interrogating the diverse and immense proteome in cell biology. As a result, nanomaterials-assisted MALDI-MS-based proteomic workflow, including sample preparation, information on the local molecular composition, relative abundance and spatial distribution of peptides and proteins and their analysis, should make the technology more easily available to a broad community and turn it into a powerful methodology for bioanalysts.

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

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
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 219.99
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

Similar content being viewed by others

References

  1. Godovac-Zimmermann J, Brown LR (2001) Perspectives for mass spectrometry and functional proteomics. Mass Spectrom Rev 20:1–57

    Article  CAS  PubMed  Google Scholar 

  2. Chiang C-K, Chen W-T, Chang H-T (2011) Nanoparticle-based mass spectrometry for the analysis of biomolecules. Chem Soc Rev 40:1269–1281

    Article  CAS  PubMed  Google Scholar 

  3. Zhu Z-J, Rotello VM, Vachet RW (2009) Engineered nanoparticle surfaces for improved mass spectrometric analyses. Analyst 134:2183–2188

    Article  CAS  PubMed  Google Scholar 

  4. Kailasa SK, Cheng K-H, Wu H-F (2013) Semiconductor nanomaterials-based fluorescence spectroscopic and matrix-assisted laser desorption/ionization (MALDI) mass spectrometric approaches to proteome analysis. Materials 6:5763–5795

    Article  CAS  Google Scholar 

  5. Kailasa SK, Kiran K, Wu H-F (2008) Comparison of ZnS semiconductor nanoparticles capped with various functional groups as the matrix and affinity probes for rapid analysis of cyclodextrins and proteins in surface-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Chem 80:9681–9688

    Article  CAS  PubMed  Google Scholar 

  6. Kailasa SK, Wu H-F (2011) Semiconductor cadmium sulphide nanoparticles as matrices for peptides and as co-matrices for the analysis of large proteins in matrix-assisted laser desorption/ionization reflectron and linear time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 25:271–280

    Article  CAS  PubMed  Google Scholar 

  7. Chiang C-K, Yang Z, Lin Y-W, Chen W-T, Lin H-J, Chang H-T (2010) Detection of proteins and protein-ligand complexes using HgTe nanostructure matrixes in surface-assisted laser desorption/ionization mass spectrometry. Anal Chem 82:4543–4550

    Article  CAS  PubMed  Google Scholar 

  8. Kailasa SK, Wu H-F (2014) Recent developments in nanoparticle-based MALDI mass spectrometric analysis of phosphoproteomes. Microchim Acta 181:853–864

    Article  CAS  Google Scholar 

  9. Nesvizhskii AI, Aebersold R (2005) Interpretation of shotgun proteomic data. Mol Cell Proteomics 4(10):1419–1440

    Article  CAS  PubMed  Google Scholar 

  10. Zhang Y, Li L, Yang P, Lu H (2012) On-plate enrichment methods for MALDI-MS analysis in proteomics. Anal Methods 4:2622–2631

    Article  CAS  Google Scholar 

  11. Kailasa SK, Wu H-F (2014) Advances in nanomaterial-based microwaves and infrared wave-assisted tryptic digestion for ultrafast proteolysis and rapid detection by MALDI-MS. Comb Chem High Throughput Screen 17:68–79

    Article  CAS  PubMed  Google Scholar 

  12. Kailasa SK, Mehta VN, Wu H-F (2014) Recent developments of liquid-phase microextraction techniques directly combined with ESI- and MALDI-mass spectrometric techniques for organic and biomolecule assays. RSC Adv 4:16188–16205

    Article  CAS  Google Scholar 

  13. Nuhua AA, Basheera C, Saad B (2011) Liquid-phase and dispersive liquid–liquid microextraction techniques with derivatization: recent applications in bioanalysis. J Chromatogr B 879:1180–1188

    Article  Google Scholar 

  14. Kailasa SK, Wu H-F (2012) Functionalized quantum dots with dopamine dithiocarbamate as the matrix for the quantification of efavirenz in human plasma and as affinity probes for rapid identification of microwave tryptic digested proteins in MALDI-TOF-MS. J Proteomics 75:2924–2933

    Article  CAS  PubMed  Google Scholar 

  15. Kailasa SK, Wu H-F (2012) One-pot synthesis of dopamine dithiocarbamate functionalized gold nanoparticles for quantitative analysis of small molecules and phosphopeptides in SALDI- and MALDI-MS. Analyst 137:1629–1638

    Article  CAS  PubMed  Google Scholar 

  16. Shastri L, Kailasa SK, Wu H-F (2010) Nanoparticle-single drop microextraction as multifunctional and sensitive nanoprobes: binary matrix approach for gold nanoparticles modified with (4-mercaptophenyliminomethyl)-2-methoxyphenol for peptide and protein analysis in MALDI-TOF MS. Talanta 81:1176–1182

    Article  CAS  PubMed  Google Scholar 

  17. Ke Y, Kailasa SK, Wu H-F, Chen Z-Y (2010) High resolution detection of high mass proteins up to 80,000 Da via multifunctional CdS quantum dots in laser desorption/ionization mass spectrometry. Talanta 83:178–184

    Article  CAS  PubMed  Google Scholar 

  18. Kailasa SK, Wu H-F (2010) Surface modified silver selinide nanoparticles as extracting probes to improve peptide/protein detection via nanoparticles-based liquid phase microextraction coupled with MALDI mass spectrometry. Talanta 83:527–534

    Article  CAS  PubMed  Google Scholar 

  19. Kailasa SK, Wu H-F (2013) Surface modified BaTiO3 nanoparticles as the matrix for phospholipids and as extracting probes for LLME of hydrophobic proteins in Escherichia coli by MALDI–MS. Talanta 114:283–290

    Article  CAS  PubMed  Google Scholar 

  20. Kailasa SK, Wu H-F (2010) Interference free detection for small molecules: probing the Mn2+-doped effect and cysteine capped effect on the ZnS nanoparticles for coccidiostats and peptide analysis in SALDI-TOF MS. Analyst 135:1115–1123

    Article  CAS  PubMed  Google Scholar 

  21. Kailasa SK, Wu H-F (2012) Rapid enrichment of phosphopeptides by BaTiO3 nanoparticles after microwave-assisted tryptic digest of phosphoproteins, and their identification by MALDI-MS. Microchim Acta 179:83–90

    Article  CAS  Google Scholar 

  22. Chen W-T, Chiang C-K, Lee C-H, Chang H-T (2012) Using surface-assist laser desorption/ionization mass spectrometry to detect proteins and protein–protein complexes. Anal Chem 84:1924–1930

    Article  CAS  PubMed  Google Scholar 

  23. López-Ferrer D, Cańas B, Vázquez J, Lodeiro C, Rial-Otero R, Moura I, Capelo JL (2006) Sample treatment for protein identification by mass spectrometry-based techniques. TrAC Trend Anal Chem 25:996–1005

    Article  Google Scholar 

Download references

Acknowledgement

The authors greatly acknowledge Elsevier, Royal Chemical Society, Springer, and American Chemical Society for giving copyright permission to reuse figures and some of the text for this chapter.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hui-Fen Wu .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Kailasa, S.K., Wu, HF. (2015). Proteomic Profiling by Nanomaterials-Based Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for High-Resolution Data and Novel Protein Information Directly from Biological Samples. In: Posch, A. (eds) Proteomic Profiling. Methods in Molecular Biology, vol 1295. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2550-6_34

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-2550-6_34

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-2549-0

  • Online ISBN: 978-1-4939-2550-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics