Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Protocol
  • Published:

Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis

Nature Protocols volume 3, pages 1341–1349 (2008)Cite this article

Abstract

Nanostructure-initiator mass spectrometry (NIMS) is a new surface-based MS technique that uses a nanostructured surface to trap liquid ('initiator') compounds. Analyte materials adsorbed onto this 'clathrate' surface are subsequently released by laser irradiation for mass analysis. In this protocol, we describe the preparation of NIMS surfaces capable of producing low background and high-sensitivity mass spectrometric measurement using the initiator compound BisF17. Examples of analytes that adsorb to this surface are small molecules, drugs, lipids, carbohydrates and peptides. Typically, NIMS is used to analyze samples ranging from simple analytical standards and proteolytic digests to more complex samples such as tissues, cells and biofluids. Critical experimental considerations of NIMS are described. Specifically, NIMS sensitivity is examined as a function of pre-etch cleaning treatment, etching current density, etching time, initiator composition, sample concentration, sample deposition method and laser fluence. Typically, NIMS surface preparation can be completed in less than 2 h. Subsequent sample preparation requires 1–5 min, depending on sample deposition method. Mass spectrometric data acquisition typically takes 1–30 s per sample.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Schematic diagram showing the dimensions of the etching chamber.
Figure 2: Procedures for preparing an NIMS chip.
Figure 3: Comparison of NIMS performance prepared with and without Piranha solution cleaning before electrochemical HF etching.
Figure 4: Mass spectra obtained for propafenone (5 fmol) with NIMS surface prepared with different etching time.
Figure 5: Comparison of NIMS activity using different initiators for carbohydrates analysis.
Figure 6: Effect of sample application methods and sample concentrations on NIMS performance.
Figure 7: A comparison of laser energy required to desorb/ionize tetrapeptide MRFA (50 fmol) and des-Arg9-bradykinin (25 fmol) on NIMS and MALDI.
Figure 8: Laser fluence dependence of NIMS performance for different analytes: morphine (5 fmol), 1-palmitoyl-sn-glycero-3-phosphocholine (10 fmol) and peptide KVPQVSTPTLVEVSR (200 amol).

Similar content being viewed by others

References

  1. Peterson, D.S. Matrix-free methods for laser desorption/ionization mass spectrometry. Mass Spectrom. Rev. 26, 19–34 (2007).

    Article  CAS  PubMed  Google Scholar 

  2. Wei, J., Buriak, J.M. & Siuzdak, G. Desorption-ionization mass spectrometry on porous silicon. Nature 399, 243–246 (1999).

    Article  CAS  PubMed  Google Scholar 

  3. Nayak, R. & Knapp, D.R. Effects of thin-film structural parameters on laser desorption/ionization from porous alumina. Anal. Chem. 79, 4950–4956 (2007).

    Article  CAS  PubMed  Google Scholar 

  4. Wada, Y., Yanagishita, T. & Masuda, H. Ordered porous alumina geometries and surface metals for surface-assisted laser desorption/ionization of biomolecules: possible mechanistic implications of metal surface melting. Anal. Chem. 79, 9122–9127 (2007).

    Article  CAS  PubMed  Google Scholar 

  5. Wen, X.J., Dagan, S. & Wysocki, V.H. Small-molecule analysis with silicon-nanoparticle-assisted laser desorption/ionization mass spectrometry. Anal. Chem. 79, 434–444 (2007).

    Article  CAS  PubMed  Google Scholar 

  6. McLean, J.A., Stumpo, K.A. & Russell, D.H. Size-selected (2–10 nm) gold nanoparticles for matrix assisted laser desorption ionization of peptides. J. Am. Chem. Soc. 127, 5304–5305 (2005).

    Article  CAS  PubMed  Google Scholar 

  7. Seino, T. et al. Matrix-free laser desorption/ionization-mass spectrometry using self-assembled germanium nanodots. Anal. Chem. 79, 4827–4832 (2007).

    Article  CAS  PubMed  Google Scholar 

  8. Go, E.P. et al. Desorption/ionization on silicon nanowires. Anal. Chem. 77, 1641–1646 (2005).

    Article  CAS  PubMed  Google Scholar 

  9. Xu, S.Y. et al. Carbon nanotubes as assisted matrix for laser desorption/ionization time-of-flight mass spectrometry. Anal. Chem. 75, 6191–6195 (2003).

    Article  CAS  PubMed  Google Scholar 

  10. Ren, S.F., Zhang, L., Cheng, Z.H. & Guo, Y.L. Immobilized carbon nanotubes as matrix for MALDI-TOF-MS analysis: Applications to neutral small carbohydrates. J. Am. Soc. Mass Spectrom. 16, 333–339 (2005).

    Article  CAS  PubMed  Google Scholar 

  11. Northen, T.R. et al. Clathrate nanostructures for mass spectrometry. Nature 449, 1033 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This project was funded by DOE GTL Grants (MAGGIE and GeneMAP). This work was supported by the US Department of Energy Office of Science under contract no. DE-AC02-05CH11231 through the Genomics: GTL Research Program.

Author information

Authors and Affiliations

  1. Department of Molecular Biology, Scripps Center for Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, 92037, California, USA

    Hin-Koon Woo, Trent R Northen, Oscar Yanes & Gary Siuzdak

  2. Department of Genome Stability, Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, 94720, California, USA

    Trent R Northen

Authors
  1. Hin-Koon Woo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Trent R Northen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Oscar Yanes
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gary Siuzdak
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gary Siuzdak.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Woo, HK., Northen, T., Yanes, O. et al. Nanostructure-initiator mass spectrometry: a protocol for preparing and applying NIMS surfaces for high-sensitivity mass analysis. Nat Protoc 3, 1341–1349 (2008). https://doi.org/10.1038/nprot.2008.110

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nprot.2008.110

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing