Duncan, Kyle

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    Mass spectrometry imaging methods for visualizing tumor heterogeneity
    (Elsevier, 2024-02-07) Duncan, Kyle D.; Pětrošová, Helena; Lum, Julian J.; Goodlett, David R.
    Profiling spatial distributions of lipids, metabolites, and proteins in tumors can reveal unique cellular microenvironments and provide molecular evidence for cancer cell dysfunction and proliferation. Mass spectrometry imaging (MSI) is a label-free technique that can be used to map biomolecules in tumors in situ. Here, we discuss current progress in applying MSI to uncover molecular heterogeneity in tumors. First, the analytical strategies to profile small molecules and proteins are outlined, and current methods for multimodal imaging to maximize biological information are highlighted. Second, we present and summarize biological insights obtained by MSI of tumor tissue. Finally, we discuss important considerations for designing MSI experiments and several current analytical challenges.
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    Ion-to-image, i2i, a mass spectrometry imaging data analysis platform for continuous ionization techniques
    (ACS Publications, 2023-07-28) Lillja, Johan; Duncan, Kyle D.; Lanekoff, Ingela
    Mass spectrometry imaging (MSI) techniques generate data that reveal spatial distributions of molecules on a surface with high sensitivity and selectivity. However, processing large volumes of mass spectrometry data into useful ion images is not trivial. Furthermore, data from MSI techniques using continuous ionization sources where data are acquired in line scans require different data handling strategies compared to data collected from pulsed ionization sources where data are acquired in grids. In addition, for continuous ionization sources, the pixel dimensions are influenced by the mass spectrometer duty cycle, which, in turn, can be controlled by the automatic gain control (AGC) for each spectrum (pixel). Currently, there is a lack of datahandling software for MSI data generated with continuous ionization sources and AGC. Here, we present ion-to-image (i2i), which is a MATLAB based application for MSI data acquired with continuous ionization sources, AGC, high resolution, and one or several scan filters. The source code and a compiled installer are available at https://github.com/LanekoffLab/i2i. The application includes both quantitative, targeted, and nontargeted data processing strategies and enables complex data sets to be processed in minutes. The i2i application has high flexibility for generating, processing, and exporting MSI data both from simple full scans and more complex scan functions interlacing MSn and SIM scan data sets, and we anticipate that it will become a valuable addition to the existing MSI software toolbox.
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    Membrane sampling separates naphthenic acids from biogenic dissolved organic matter for direct analysis by mass spectrometry
    (ACS Publications, 2022-03-01) Duncan, Kyle D.; Hawkes, Jeffrey A.; Berg, Mykelti; Clarijs, Bas; Gill, Chris G.; Bergquist, Jonas; Lanekoff, Ingela; Krogh, Erik T.
    Oil sands process waters can release toxic naphthenic acids (NAs) into aquatic environments. Analytical techniques for NAs are challenged by sample complexity and interference from naturally occurring dissolved organic matter (DOM). Herein, we report the use of a poly(dimethylsiloxane) (PDMS) polymer membrane for the on-line separation of NAs from DOM and use direct infusion electrospray ionization mass spectrometry to yield meaningful qualitative and quantitative information with minimal sample cleanup. We compare the composition of membrane-permeable species from natural waters fortified with a commercial NA mixture to those derived from weak anion exchange solid-phase extraction (SPE) using high-resolution mass spectrometry. The results show that SPE retains a wide range of carboxylic acids, including biogenic DOM, while permeation through PDMS was selective for petrogenic classically defined NAs (CnH2n+zO2). A series of model compounds (log Kow ∼1–7) were used to characterize the perm-selectivity and reveal the separation is based on hydrophobicity. This convenient sample cleanup method is selective for the O2 class of NAs and can be used prior to conventional analysis or as an on-line analytical strategy when coupled directly to mass spectrometry.
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    [Post-print] Direct analysis of naphthenic acids in constructed wetland samples by condensed phase membrane introduction mass spectrometry 
    (Elsevier, 2020-05-10) Duncan, Kyle D.; Richards, Larissa C.; Monaghan, Joseph; Simair, Monique C.; Ajaero, Chukwuemeka; Peru, Kerry M.; Friesen, Vanessa; McMartin, Dena W.; Headley, John V.; Gill, Chris G.; Krogh, Erik T.
    The application of direct mass spectrometry techniques to the analysis of complex samples has a number of advantages including reduced sample handling, higher sample throughput, in situ process monitoring, and the potential for adaptation to on-site analysis. We report the application of a semi-permeable capillary hollow fibre membrane probe (immersed directly into an aqueous sample) coupled to a triple quadrupole mass spectrometer by a continuously flowing methanol acceptor phase for the rapid analysis of naphthenic acids with unit mass resolution. The intensity of the naphthenic acid-associated peaks in the mass spectrum are normalized to an internal standard in the acceptor phase for quantitation and the relative abundance of the peaks in the mass spectrum are employed to monitor compositional changes in the naphthenic acid mixture using principle component analysis. We demonstrate the direct analysis of a synthetic oil sands process-affected water for classical naphthenic acids (CnH2n+zO2) as they are attenuated through constructed wetlands containing sedge (Carex aquatilis), cattail (Typha latifolia), or bulrush (Schoenoplectus acutus). Quantitative results for on-line membrane sampling compare favourably to those obtained by solid-phase extraction high-resolution mass spectrometry. Additionally, chemometric analysis of the mass spectra indicates a clear discrimination between naphthenic acid-influenced and natural background waters. Furthermore, the compositional changes within complex naphthenic acid mixtures track closely with the degree of attenuation. Overall, the technique is successful in following changes in both the concentration and composition of naphthenic acids from synthetic oil sands process-affected waters, with the potential for high throughput screening and environmental forensics.
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    [Pre-print] Direct analysis of naphthenic acids in constructed wetland samples by condensed phase membrane introduction mass spectrometry
    (Elsevier, 2020-05-10) Duncan, Kyle D.; Richards, Larissa C.; Monaghan, Joseph; Simair, Monique C.; Ajaero, Chukwuemeka; Peru, Kerry M.; Friesen, Vanessa; McMartin, Dena W.; Headley, John V.; Gill, Chris G.; Krogh, Erik T.
    The application of direct mass spectrometry techniques to the analysis of complex samples has a number of advantages including reduced sample handling, higher sample throughput, in situ process monitoring, and the potential for adaptation to on-site analysis. We report the application of a semi-permeable capillary hollow fibre membrane probe (immersed directly into an aqueous sample) coupled to a triple quadrupole mass spectrometer by a continuously flowing methanol acceptor phase for the rapid analysis of naphthenic acids with unit mass resolution. The intensity of the naphthenic acid-associated peaks in the mass spectrum are normalized to an internal standard in the acceptor phase for quantitation and the relative abundance of the peaks in the mass spectrum are employed to monitor compositional changes in the naphthenic acid mixture using principle component analysis. We demonstrate the direct analysis of a synthetic oil sands process-affected water for classical naphthenic acids (CnH2n+zO2) as they are attenuated through constructed wetlands containing sedge (Carex aquatilis), cattail (Typha latifolia), or bulrush (Schoenoplectus acutus). Quantitative results for on-line membrane sampling compare favourably to those obtained by solid-phase extraction high-resolution mass spectrometry. Additionally, chemometric analysis of the mass spectra indicates a clear discrimination between naphthenic acid-influenced and natural background waters. Furthermore, the compositional changes within complex naphthenic acid mixtures track closely with the degree of attenuation. Overall, the technique is successful in following changes in both the concentration and composition of naphthenic acids from synthetic oil sands process-affected waters, with the potential for high throughput screening and environmental forensics.