Critical Evaluation of Spectral Resolution Enhancement Methods for Raman Hyperspectra

Overlapping peaks in Raman spectra complicate the presentation, interpretation, and analyses of complex samples. This is particularly problematic for methods dependent on sparsity such as multivariate curve resolution and other spectral demixing as well as for two-dimensional correlation spectroscopy (2D-COS), multisource correlation analysis, and principal component analysis. Though software-based resolution enhancement methods can be used to counter such problems, their performances often differ, thereby rendering some more suitable than others for specific tasks. Furthermore, there is a need for automated methods to apply to large numbers of varied hyperspectral data sets containing multiple overlapping peaks, and thus methods ideally suitable for diverse tasks. To investigate these issues, we implemented three novel resolution enhancement methods based on pseudospectra, over-deconvolution, and peak fitting to evaluate them along with three extant methods: node narrowing, blind deconvolution, and the general-purpose peak fitting program Fityk. We first applied the methods to varied synthetic spectra, each consisting of nine overlapping Voigt profile peaks. Improved spectral resolution was evaluated based on several criteria including the separation of overlapping peaks and the preservation of true peak intensities in resolution-enhanced spectra. We then investigated the efficacy of these methods to improve the resolution of measured Raman spectra. High resolution spectra of glucose acquired with a narrow spectrometer slit were compared to ones using a wide slit that degraded the spectral resolution. We also determined the effects of the different resolution enhancement methods on 2D-COS and on chemical contrast image generation from mammalian cell spectra. We conclude with a discussion of the particular benefits, drawbacks, and potential of these methods. Our efforts provided insight into the need for effective resolution enhancement approaches, the feasibility of these methods for automation, the nature of the problems currently limiting their use, and in particular those aspects that need improvement.

Application of the method of differential scanning calorimetry in the study of the properties of oilseeds

The method of differential scanning calorimetry (DSC) is used to characterize the thermophysical properties during melting of samples of milk thistle oil of various geographic origins, seeds and meal. The world experience in applying the DSC method on the study of milk thistle oils is generalized. The temperature measurement program is described. It is shown that, despite the general similarity of the curve profiles of the melting DSC, there are differences in the profiles due to genotypic and phenotypic factors - variety and growing location. The DSC curves of freshly squeezed oil distinguish from the DSC curves after 6 months storage of the oil due to oxidative deterioration and the formation of more refractory partially oxidized triacylglycerols. This fact is relevant to determining the capabilities of the DSC method in controlling the freshness of vegetable oils. The peaks amplitudes in the DSC curves of fresh oil are higher than those of oils that has been stored at room temperature for six months. Double differentiation of the melting curves makes it possible to reveal the temperatures of phase transitions in the case of overlapping endothermic peaks, the establishment of which is difficult without double differentiation. Using the «Netzsch Peak Separation» software to divide the peaks in the melting curves allows at once to estimate the areas of overlapping peaks and increase the informativeness of the DSC data. Thermal analysis of milk thistle seeds and meal reveals that the meal contains a residual amount of oil, in which the proportion of triunsaturated fats is overestimated in comparison to seeds, indicating that triunsaturated fats are more difficult to extract from oil by cold pressing.

The Effect of Oxidation Temperature on the (1000–1300) Cm−1 Band in FT-IR Spectra of Silicon Oxide Synthesized by Thermal Oxidation of Silicon Wafers

In this work, silicon wafers were thermal treated in air at temperatures varied in the range 800–1200°C. The annealed samples were investigated using FTIR, X-ray diffraction, FTIR and optical reflection spectroscopy. The effect of annealing temperature on the (1000–1300) cm− 1 band in FT-IR spectra of the prepared samples was investigated. The results showed that thermal oxidation at temperatures less than 1200°C leads to enhance the phenomenon of the splitting of longitudinal optical and transverse optical stretching motions. This phenomenon was verified by observing the appearance of two overlapping peaks in the region (1000–1300) cm− 1 in FT-IR spectra. The results also showed that the splitting process leads to the formation of defects in the crystal structure of silicon, which in turn leads to the formation of silicon nanoparticles.

Separation of Chromatographic Co-Eluted Compounds by Clustering and by Functional Data Analysis

Peak overlapping is a common problem in chromatography, mainly in the case of complex biological mixtures, i.e., metabolites. Due to the existence of the phenomenon of co-elution of different compounds with similar chromatographic properties, peak separation becomes challenging. In this paper, two computational methods of separating peaks, applied, for the first time, to large chromatographic datasets, are described, compared, and experimentally validated. The methods lead from raw observations to data that can form inputs for statistical analysis. First, in both methods, data are normalized by the mass of sample, the baseline is removed, retention time alignment is conducted, and detection of peaks is performed. Then, in the first method, clustering is used to separate overlapping peaks, whereas in the second method, functional principal component analysis (FPCA) is applied for the same purpose. Simulated data and experimental results are used as examples to present both methods and to compare them. Real data were obtained in a study of metabolomic changes in barley (Hordeum vulgare) leaves under drought stress. The results suggest that both methods are suitable for separation of overlapping peaks, but the additional advantage of the FPCA is the possibility to assess the variability of individual compounds present within the same peaks of different chromatograms.

MCR-ALS with Sample Insertion Constraint to Enhance the Sensitivity of Surface-Enhanced Raman Scattering Detection

The multivariate curve resolution-alternative least square (MCR-ALS) algorithm was modified with sample insertion constraint to deconvolute the overlapping peaks in SERS spectra. The developed method was evaluated by the spectral...

Cloning and in silico analysis revealed a genetic variation in osmotin-encoding genes in an Indonesian local cacao cultivar

Theobroma cacao L. is an important Indonesian estate crop, which suffers from biotic and abiotic stresses. TcOSM, which encodes osmotin as a response to pathogens and environmental stresses, is, therefore, a focus of interest in this research, aiming to characterize TcOSM in an Indonesian local cacao cultivar. Bioinformatics queries for putative TcOSM were performed against the reference genome of a Criollo-type cacao cultivar. Based on nucleotide sequence determination, our results revealed two genes, TcOSM1 and TcOSM2, which have the highest similarity (≥ 90\%) to the cacao reference genes. Heterozygosity was detected in the TcOSM1-encoding gene, which contained two overlapping peaks in Sanger-sequencing chromatograms. One of the alleles resulted from a single nucleotide change (G to A), leading to a same-sense mutation that did not substitute corresponding alanine residue. Homology modeling using Phyre2 and structural alignment (superimposition) was conducted to examine the influence of genetic variations in TcOSM sequences upon the global protein structures. The result showed no significant changes (RMSD ≤ 0.206 Å, TM-score > 0.5) in tertiary protein structures. Altogether, this research succeeded in characterizing TcOSM while providing a fundamental study for future cacao biotechnology endeavors.