University of Western Ontario - Electronic Thesis and Dissertation Repository


Doctor of Philosophy




Dr. Robert H. Lipson

Delay of Publication



Nanostructured-Initiator Mass Spectrometry (NIMS), which uses ‘initiator’ molecules trapped within a nanostructured material to assist the release and ionization of intact molecules adsorbed on that material's surface upon laser or ion irradiation, is a new soft desorption/ ionization technique with several positive attributes including extraordinarily high detection sensitivities, relatively simple sample preparation protocols, and can be initiated using photon or ion irradiation sources. As result NIMS has a great deal of potential for the ready detection of small molecules from complex biofluids including metabolites, and for tissue imaging.

In the thesis, a variety of nanostructured materials including porous silicon (pSi), WO3 and TiO2 were fabricated with a home-made apparatus as substrates for NIMS. The benefit of pSi-based NIMS using BisF17 as an initiator over Desorption Ionization On Silicon (DIOS) and Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry (MS) was demonstrated by comparing the signal intensities of protonated polypeptide Dalargin, using the three techniques. A wide range of biological and pharmaceutical compounds were analyzed by NIMS that ionize in different ways to illustrate the versatility of this method.

Secondly, a fluorous-affinity NIMS chip was developed using a fluorous tag containing a 3-(perfluorooctyl)-propyl-1-maleimide moiety, to selectively capture peptides that contain cysteine residues. The fluorous tag was held to the NIMS chip by non-covalent fluorine-fluorine interactions. This methodology was utilized to effectively separate and enrich on-chip cysteine-containing peptides from mixtures, perform kinases (PKA and Abl) activity assays, as well as to quantitatively analyze enzymatic inhibition. It was shown that fluorous-affinity NIMS chips have the potential to be used as high throughput enzyme inhibitor screening methodology for drug discovery. Fluorous NIMS chips were also shown to be able to measure the enantiomeric excess (ee) of chiral analytes based on kinetic resolution.

An exploration of new micro/nanostructured substrates and laser sources for NIMS was also carried out using microstructured WO3 and porous TiO2, and the 532 nm output of a frequency-doubled Nd-YAG laser. It was shown that NIMS mass spectra of peptide (Dalargin) with good intensity could be obtained by these substrates and visible laser source using BisF17 as an initiator.

Lastly, the Surface-Assisted Laser Desorption Ionization (SALDI) mechanism was investigated by measuring the ion signal, I, as a function of laser fluence, F. Evidence is presented that shows that desorption is driven by a thermal process, and desorption activation energies were derived for pSi, WO3 and TiO2, respectively. A new ionization mode, Surface Assisted Multiphoton Ionization (SAMPI), is postulated that explains the observation of radical cations and the strong dependence of these ion signals on the position of laser focus relative to the substrate surface. The SAMPI mechanism which appears to be generic for all the porous SALDI substrates studied in this thesis, may prove to be useful for delivering biomolecules into the gas-phase for spectroscopy.