Image and Spectral Processing for ToF-SIMS Analysis of Biological Materials

Graham, Daniel J.; Castner, David G.

doi:10.5702/massspectrometry.s0014

Cited by 16 publications

(21 citation statements)

References 53 publications

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“…Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a widely used imaging mass spectrometry technique, and it offers surface chemical analysis and chemical imaging with nanoscale details in various materials. [10][11][12][13][14] Compared to other imaging mass spectrometry techniques, such as desorption electrospray ionization and matrix-assisted laser desorption ionization, ToF-SIMS uses high energy primary ions or ion clusters (i.e., Bi 3 + , Au 3 + , and C 60 ) and offers the highest lateral resolution in the submicrometer range. 15,16 Previously, ToF-SIMS has been used to analyze biological materials, extracellular polymeric substance (EPS) of bacteria and microalgae, including protein, lipid, amino acid, and many organic molecules.…”

Section: Introductionmentioning

confidence: 99%

Peak selection matters in principal component analysis: A case study of syntrophic microbes

et al. 2019

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In situ liquid time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique to study surface characterization of living biofilms in hydrated conditions. However, ToF-SIMS data analysis is still a great challenge in complicated bacterial biofilms, because many interference peaks from the medium may result in inaccurate interpretation. In this study, two syntrophic Geobacter populations are investigated using in situ liquid ToF-SIMS to reveal the biofilm surface changes between them due to direct interspecies electron transfer. By comparing spectral principal component analysis (PCA) results of all peaks and selected peaks, the authors find that spectral peak overlay is an effective strategy to reduce the matrix effect in handling complex ToF-SIMS data. Additionally, the spectral PCA results of high intensity and high resolution data obtained from liquid ToF-SIMS are compared. Selected peaks, amino acid peaks, and water cluster peaks spectral PCA produce nice separation among samples in both high intensity and high resolution data sets. However, the high resolution data show better separation between coculture planktonic and coculture aggregates, confirming that the higher mass accuracy is useful in the analysis of microbial samples. In conclusion, the results show that peak selection is critical for acquiring effective microbial information and interpretation of syntrophic Geobacter using spectral data from in situ liquid ToF-SIMS.

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Section: Introductionmentioning

confidence: 99%

Peak selection matters in principal component analysis: A case study of syntrophic microbes

et al. 2019

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“…Peak lists for all 173 XPS spectra-composed of S, C, Ti, O, and Na-were imported into a series of scripts written by NESAC/BIO for MATLAB (MathWorks, Inc., Natick, MA). 33,34 Although data normalization is often performed prior to PCA, XPS compositions are in the form of atomic percentages and therefore already normalized. The data were, however, square-root transformed and mean centered to be consistent with the ANOVA procedure and to ensure that variance within the data set was due to differences in sample variances rather than in sample means.…”

Section: H Data Analysismentioning

confidence: 99%

Experimental design and analysis of activators regenerated by electron transfer-atom transfer radical polymerization experimental conditions for grafting sodium styrene sulfonate from titanium substrates

Foster

Johansson

Tom

et al. 2015

Journal of Vacuum Science &Amp; Technology A: Vacuum, Surfaces, and Films

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A 2 4 factorial design was used to optimize the activators regenerated by electron transfer-atom transfer radical polymerization (ARGET-ATRP) grafting of sodium styrene sulfonate (NaSS) films from trichlorosilane/10-undecen-1-yl 2-bromo-2-methylpropionate (ester ClSi) functionalized titanium substrates. The process variables explored were: (1) ATRP initiator surface functionalization reaction time; (2) grafting reaction time; (3) CuBr 2 concentration; and (4) reducing agent (vitamin C) concentration. All samples were characterized using x-ray photoelectron spectroscopy (XPS). Two statistical methods were used to analyze the results: (1) analysis of variance with a ¼ 0:05, using average ffiffiffiffi ffi Ti p XPS atomic percent as the response; and (2) principal component analysis using a peak list compiled from all the XPS composition results. Through this analysis combined with follow-up studies, the following conclusions are reached: (1) ATRP-initiator surface functionalization reaction times have no discernable effect on NaSS film quality; (2) minimum ( 24 h for this system) grafting reaction times should be used on titanium substrates since NaSS film quality decreased and variability increased with increasing reaction times; (3) minimum ( 0.5 mg cm À2 for this system) CuBr 2 concentrations should be used to graft thicker NaSS films; and (4) no deleterious effects were detected with increasing vitamin C concentration. V C

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“…Five characteristic FA peaks (m/z 199, 213, 227, 241, and 255, corresponding to C12, C13, C14, C15, and C16 FAs) were used in image PCA. 27 Images representing each PC were reconstructed from the score matrix using the red, green, and blue (RGB) color scale.…”

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confidence: 99%

Two-dimensional and three-dimensional dynamic imaging of live biofilms in a microchannel by time-of-flight secondary ion mass spectrometry

et al. 2015

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A vacuum compatible microfluidic reactor, SALVI (System for Analysis at the Liquid Vacuum Interface), was employed for in situ chemical imaging of live biofilms using time-of-flight secondary ion mass spectrometry (ToF-SIMS). Depth profiling by sputtering materials in sequential layers resulted in live biofilm spatial chemical mapping. Two-dimensional (2D) images were reconstructed to report the first three-dimensional images of hydrated biofilm elucidating spatial and chemical heterogeneity. 2D image principal component analysis was conducted among biofilms at different locations in the microchannel. Our approach directly visualized spatial and chemical heterogeneity within the living biofilm by dynamic liquid ToF-SIMS.

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Image and Spectral Processing for ToF-SIMS Analysis of Biological Materials

Cited by 16 publications

References 53 publications

Peak selection matters in principal component analysis: A case study of syntrophic microbes

Peak selection matters in principal component analysis: A case study of syntrophic microbes

Experimental design and analysis of activators regenerated by electron transfer-atom transfer radical polymerization experimental conditions for grafting sodium styrene sulfonate from titanium substrates

Two-dimensional and three-dimensional dynamic imaging of live biofilms in a microchannel by time-of-flight secondary ion mass spectrometry

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