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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.

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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).

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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.

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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

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  1. Hin-Koon Woo
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Correspondence to Gary Siuzdak.

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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

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