Selective removal of interference signals for near-infrared spectra of biomedical samples by using region orthogonal signal correction

New approach for chemometrics algorithm named region orthogonal signal correction (ROSC) has been introduced to improve the predictive ability of PLS models for biomedical components in blood serum developed from their NIR spectra in the 1280-1849 nm region. Firstly, a moving window partial least squares regression (MWPLSR) method was employed to locate the region due to water as a region of interference signals and to find the informative regions of glucose, albumin, cholesterol and triglyceride from NIR spectra of bovine serum samples. Next, a novel chemometrics method named searching combination moving window partial least squares (SCMWPLS) was used to optimize those informative regions. Then, the specific regions that contained the information of water, glucose, albumin, cholesterol and triglyceride were obtained. When an interested component in the bovine serum solution, such as glucose, albumin, cholesterol or triglyceride is being an analyte, the other three interests and water are considered as the interference factors. Thus, new approach for ROSC has employed for each specific region of interference signal to calculate the orthogonal components to the concentrations of analyte that were removed specifically from the NIR spectra of bovine serum in the region of 1280-1849 nm and the highest interference signal for model of analyte will be revealed. The comparison of PLS results for glucose, albumin, cholesterol and triglyceride built by using the whole region of original spectra and those developed by using the optimized regions suggested by SCMWPLS of original spectra, spectra treated OSC for orthogonal components of 1-3 and spectra treated ROSC using selected removing the highest interference signals from the spectra for orthogonal components of 1-3 are reported. It has been found that new approach of ROSC to remove the highest interference signal located by SCMWPLS improves of the performance of PLS modeling, yielding the lower RMSECV and smaller number of PLS factors.     

Calibration model transfer for near-infrared spectra based on canonical correlation analysis

In order to solve the calibration transformation problem in near-infrared (NIR) spectroscopy, a method based on canonical correlation analysis (CCA) for calibration model transfer is developed in this work. Two real NIR data sets were tested. A comparative study between the proposed method and piecewise direct standardization (PDS) was conducted. It is shown that the transfer results obtained with the proposed method based on CCA were better than those obtained by PDS when the subset had sufficient samples.     

Removal of interference signals due to water from in vivo near-infrared (NIR) spectra of blood glucose by region orthogonal signal correction (ROSC).

A novel chemometric method, region orthogonal signal correction (ROSC), is proposed and applied to pretreat near-infrared (NIR) spectra of blood glucose measured in vivo. Water is the most serious interference component in such kinds of noninvasive measurements, because it shows very high absorbance in the spectra. In the present study, the spectra of blood glucose in the range of 1212 - 1889 nm are used, in which the absorption of water around 1440 nm is very high. ROSC aims at removing the interference signal due to water from the spectra by selecting a set of spectra with a special region of 1404 - 1454 nm that mainly contain information about the variation of the interference component, water, and calculating the orthogonal components to the concentrations of glucose that will be removed. The difference between ROSC and orthogonal signal correction (OSC) is that ROSC uses a special region of spectra for the estimation of scores and loading weights of orthogonal components to pretreat the spectra in other regions, while OSC only uses one fixed region of spectra to calculate loadings, scores and weights of OSC components and removes the OSC components in the same region. A clear advantage of ROSC is that it is more interpretable than OSC, because one can select a spectral region to remove the variation of a special component such as water. Another chemometric method, moving window partial least squares (MWPLSR), is also used to select informative regions of glucose from the NIR spectra of blood glucose measured in vivo, leading to improved PLS models. Results of the application of ROSC demonstrate that ROSC-pretreated spectra including the whole spectral region of 1212 - 1889 nm or an informative region of 1600- 1730 nm selected by MWPLSR provide very good performance of the PLS models. Especially, the later region yields a model with RMSECV of 15.8911 mg/dL for four PLS components. ROSC is a potential chemometric technique in the pretreatment of various spectra.     

Decomposition of mixtures' spectra by multivariate curve resolution of rapidly acquired TOCSY experiments

A method is presented that allows for retrieving 1D spectra of the individual components of a mixture from a sparsely acquired 2D‐TOCSY spectrum. The decomposition of the 2D‐TOCSY data into pure 1D traces is achieved using a non‐negative matrix factorization algorithm, also known as multivariate curve resolution analysis. Here, we show that the algorithm can be applied to data processed in the direct dimension only. Thus, our method can be applied to non‐linearly sampled experiments or data acquired with few indirect points. An example is shown for the spectra of a mixture of six amino acids, acquired in 15 min. Copyright © 2010 John Wiley & Sons, Ltd.     

Synthesis, Characterization, and Photophysical Properties of Materials Obtained by Co-intercalation of Chromophores into Layered Double Hydroxides

A pair of chromophores with donor‐acceptor properties, coumarin‐3‐carboxylic acid (3‐CCA) and 9‐anthracene carboxylic acid (9‐ACA), have been successfully intercalated into the layered double hydroxide (LDH), [Zn_0.66Al_0.34(OH)₂](CO₃)_0.17·0.33H₂O by an ion‐exchange method. The obtained co‐intercalation compounds were characterized by X‐ray diffraction, FTIR spectral, thermogravimetry techniques and chemical composition. The guest molecular sizes and structures were investigated utilizing an ab initio (HF/6‐31G) method by G98w. These anions were steadily arranged between the metal hydroxide layers by their carboxylate functional groups interacting with the layer plane. The photophysical properties of the obtained compounds were studied by UV‐Vis absorption and fluorescence spectroscopy. These results indicate that the confinement of the pair of chromophores, 3‐CCA and 9‐ACA, within the interlayer region of the host is in favor of guest‐host interaction and guest‐guest interaction, and that the pair of chromophores, 3‐CCA and 9‐ACA can give rise to energy transfer processes because of the characteristics of their excited states.     

Nonadiabatic effects in the two-dimensional infrared spectra of peptides: application to alanine dipeptide

A method of simulating two-dimensional infrared spectra accounting for nonadiabatic effects is presented. The method is applied to the amide I modes of a dipeptide. The information necessary to construct the time-dependent Hamiltonian for the system is extracted from molecular dynamics simulations using a recently published ab initio-based model. It is shown that the linear absorption spectrum agrees with experiment only if the nonadiabatic effects are accounted for. The two-dimensional infrared spectrum is predicted for a range of mixing times. It is shown that population transfer between the amide I site vibrations affects the anisotropy at longer mixing times. It is also demonstrated that the population transfer can, to a good approximation, be extracted from the simulated spectra using a procedure that should also be applicable to experimental spectra.     

Simultaneous time resolution of the emission spectra of fluorescent proteins and zooxanthellar chlorophyll in reef-building corals

Light is absorbed by photosynthetic algal symbionts (i.e. zooxanthellae) and by chromophoric fluorescent proteins (FP) in reef‐building coral tissue. We used a streak‐camera spectrograph equipped with a pulsed, blue laser diode (50 ps, 405 nm) to simultaneously resolve the fluorescence spectra and kinetics for both the FP and the zooxanthellae. Shallow water (<9 m)–dwelling Acropora spp. and Plesiastrea versipora specimens were collected from Okinawa, Japan, and Sydney, Australia, respectively. The main FP emitted light in the blue, blue‐green and green emission regions with each species exhibiting distinct color morphs and spectra. All corals showed rapidly decaying species and reciprocal rises in greener emission components indicating Förster resonance energy transfer (FRET) between FP populations. The energy transfer modes were around 250 ps, and the main decay modes of the acceptor FP were typically 1900–2800 ps. All zooxanthellae emitted similar spectra and kinetics with peak emission (～683 nm) mainly from photosystem II (PSII) chlorophyll (chl) a. Compared with the FP, the PSII emission exhibited similar rise times but much faster decay times, typically around 640–760 ps. The fluorescence kinetics and excitation versus emission mapping indicated that the FP emission played only a minor role, if any, in chl excitation. We thus suggest the FP could only indirectly act to absorb, screen and scatter light to protect PSII and underlying and surrounding animal tissue from excess visible and UV light. We conclude that our time‐resolved spectral analysis and simulation revealed new FP emission components that would not be easily resolved at steady state because of their relatively rapid decays due to efficient FRET. We believe the methods show promise for future studies of coral bleaching and for potentially identifying FP species for use as genetic markers and FRET partners, like the related green FP from Aequorea spp.     

Threshold Al KLL Auger spectra of oxidized aluminium foils

Threshold Al KLL Auger electron spectroscopy and K‐edge x‐ray absorption fine structure spectroscopy have been used to examine technical purity (99.5%) aluminium foil before and after chemical treatment that altered the thickness and degree of hydroxylation of the oxidized layer. Comprehensive surface chemical characterization was effected by means of monochromatized Al Kα‐excited photoelectron spectroscopy. Threshold Al KL_{2, 3}L_{2, 3} spectra were obtained for three of the foils investigated and these spectra were in broad agreement with those observed previously for pure Al foil. The relative intensities of the spectral components for two of the foils were clearly consistent with the previously proposed assignment of the resonantly enhanced Auger component, situated between those arising from the metal and Al(III) oxide, to a thin interfacial layer. The threshold Auger spectra from the aluminium foil bearing the thickest and most hydroxylated oxidized layer were not obviously consistent with the interfacial layer model but O K‐edge spectra revealed that this surface layer was fundamentally different from the others and could have had a greater interfacial surface area. Copyright © 2003 John Wiley & Sons, Ltd.     

Estimation of component spectra by the principal components method

The principal components method enables component spectra from pigment mixtures to be estimated by evaluating the eigenvectors of the second moment matrix. The components are linear combinations of these eivenvectors, but cannot be identified unambiguously. With the conditions of non-negativity of spectral values and of concentrations, this ambiguity can be limited; components spectra for 2 and 3 components were calculated earlier. In the present work, maximal dissimilarity of component spectra is assumed as a further condition. An algorithm based on linear programming is described; it enables any number of components to be estimated from eigenvectors of the second moment matrix with better reliability than previously.     

Interpretation of static secondary ion spectra

A model is presented in which electron impact (EI)/electronic excitation plays a pivotal role in the formation of secondary ions in the SIMS experiment, especially those originating from discrete molecular species. Positive ions are formed by electron loss whereas negative ions are formed by electron capture. Collisions of the new ions with the surface and with other species directly above the sample, along with metastable decay events, reduce the number of odd electron ions detected and produce the changes that make SIMS spectra so different from EI mass spectra. Primary support for this model is gathered from static SIMS spectra themselves, which can be rationalized to a large degree by assuming that the same rearrangement and fragmentation mechanisms that are invoked to explain EI mass spectra take place at the surface after kiloelectron‐volt ion impacts. The static secondary ion spectra of a variety of simple discrete molecular species, of simple hydrocarbons, of monofunctional organic species and of more complicated multifunctional organic species are analyzed in this way and the utility of this model is demonstrated. Copyright © 2004 John Wiley & Sons, Ltd.     

Calibration transfer of near‐IR partial least squares property models of fuels using virtual standards

Partial least squares (PLS) models of 10 important jet and diesel fuel properties were built using spectra from a master near‐IR dispersive instrument and then subsequently transferred to a secondary dispersive instrument via a novel calibration transfer method using virtual standards and a slope‐bias correction. Implementation of the transfer requires that only seven spectra of neat solvents be acquired on the master and secondary instruments. The spectra of the neat solvents are then used to digitally replicate spectra from the calibration set to generate virtual standards. Comparison of PLS predictions for the master and secondary instrument virtual standards provides a simple but effective slope‐bias correction for transfer. The transferred fuel properties include American Petroleum Institute gravity, % aromatics, cetane index, flashpoint, hydrogen content, % saturates, and distillation temperatures at 10%, 20%, 50%, and 90% volume recovered. Transfer error was lower than using either the pure solvents with a slope‐bias correction or than using a piecewise direct standardization calibration transfer using fuel spectra. Transfer error was higher than when using actual fuels to transfer the calibration. The use of virtual standards eliminates the need to maintain either complex fuel standards or the master instrument for future instrument calibration transfers. Copyright © 2011 John Wiley & Sons, Ltd.     

13C‐NMR detection of STD spectra

We have investigated the use of ¹³C for the detection of saturation transfer difference (STD) NMR spectra. By detecting the STD spectrum in the ¹³C channel it is possible to eliminate the residual water signal in the STD‐NMR spectrum. We have employed an INEPT transfer in order to shift the magnetization from the proton channel to ¹³C. As a sample system to check our method we have used human serum albumin and phenylalanine. We have shown that such a transfer can be accomplished and gives reasonable signal intensities. Copyright © 2009 John Wiley & Sons, Ltd.     

Ab initio study of electronic spectra of merocyanine 540 and its photoproducts

Molecular structures of three derivatives of merocyanine 540 (MC 540) were studied using the density functional method in conjunction with the 6‐31G*, 6‐31G**, and 6‐311G** basis sets. The excited states were calculated using the configuration interaction method involving singly excited configurations (CIS). The predicted transition energies and oscillator strength agree well with the experimental UV adsorption spectra of the studied systems. The existence of two stable conformers of merocyanine explain the experimentally observed dependence of the UV spectra upon the change of concentration of added salts. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Multiisotopic modeling of fragmentation ion patterns in mass spectra of organometallic and coordination compounds

Investigation of hardly interpretable complex patterns can lead to an explanation of details of fragmentation and, therefore, the identification of ion clusters can be a significant procedure of mass spectra interpretation. The modeling presented remains a simple tool for mass spectra interpretation and determination of parameters of complex cluster components. Good adjustment of model to experimental data suggests that such components must be considered in the pattern interpretation; approach results in the model fits within a 1% precision for the cluster of two or more components. Applications of the Multiisotopic Modeling of Fragmentation Ion Patterns (MMFIP method) are presented for bis(dibutyldithiophosphate)‐zinc(II)‐[(C₄H₉O)₂PS₂]₂Zn, 1′,1‴‐dibenzylbiferrocene‐C₃₄H₃₀Fe₂ and 1,1′,2,2′,3,3′‐hexachloroferrocene‐C₁₀H₄Cl₆Fe as examples. It seems that the isotopic cluster modeling based on the least squares method can be a helpful aid for determination of the complex pattern components. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 354–365, 2001     

Comparison and improvement of commonly applied statistical approaches for identification of plant species from IR spectra

Fourier transform infrared spectroscopy (FTIR) has been studied many times in the context of identification of plant, fungal and bacterial species. Infrared spectra are commonly analyzed using multivariate statistical methods such as cluster analysis (CA), principal component analysis (PCA), partial least squares analysis (PLS) and discriminant analysis (DA). In this study, a univariate statistical method for analysis of variance (ANOVA) was used to reduce the number of variables before applying the multivariate methods. Analyzing variables using ANOVA or a combination of ANOVA with CA produced better results. Here, experiments were carried out by performing ANOVA using the first derivative of the spectra instead of the original spectra or its second derivative because using the first‐derivative variables led to improved distinction between species. Different results were obtained by applying different validation methods. The leave‐one‐out validation method gave higher results than the validation‐with‐training and validation sample sets, thus indicating the non‐objectivity of the leave‐one‐out validation method. Copyright © 2010 John Wiley & Sons, Ltd.     

Model-independent structure and resonant X-ray spectra of intermediate smectic phases

It is shown that the orientational structure of intermediate smectic phases can be determined using the symmetry properties of the general free energy with arbitrary orientational coupling between smectic layers, without addressing a particular model. The structure of three- and four-layer intermediate phases, obtained in this way, corresponds to experimental data. The same method enables one to predict the structure of intermediate phases with periodicity of five and six layers, which have not been observed experimentally so far. The resonant X-ray spectra of the five- and six-layer intermediate phases with predicted structure have also been calculated. These spectra are characterized by a number of features which enable one to distinguish five-layer and six-layer intermediate phases from phases with smaller periods.     

Explicit–implicit mapping approach to nonlinear blind separation of sparse nonnegative dependent sources from a single mixture: pure component extraction from nonlinear mixture mass spectra

The nonlinear, nonnegative single‐mixture blind source separation problem consists of decomposing observed nonlinearly mixed multicomponent signal into nonnegative dependent component (source) signals. The problem is difficult and is a special case of the underdetermined blind source separation problem. However, it is practically relevant for the contemporary metabolic profiling of biological samples when only one sample is available for acquiring mass spectra; afterwards, the pure components are extracted. Herein, we present a method for the blind separation of nonnegative dependent sources from a single, nonlinear mixture. First, an explicit feature map is used to map a single mixture into a pseudo multi‐mixture. Second, an empirical kernel map is used for implicit mapping of a pseudo multi‐mixture into a high‐dimensional reproducible kernel Hilbert space. Under sparse probabilistic conditions that were previously imposed on sources, the single‐mixture nonlinear problem is converted into an equivalent linear, multiple‐mixture problem that consists of the original sources and their higher‐order monomials. These monomials are suppressed by robust principal component analysis and hard, soft, and trimmed thresholding. Sparseness‐constrained nonnegative matrix factorizations in reproducible kernel Hilbert space yield sets of separated components. Afterwards, separated components are annotated with the pure components from the library using the maximal correlation criterion. The proposed method is depicted with a numerical example that is related to the extraction of eight dependent components from one nonlinear mixture. The method is further demonstrated on three nonlinear chemical reactions of peptide synthesis in which 25, 19, and 28 dependent analytes are extracted from one nonlinear mixture mass spectra. The goal application of the proposed method is, in combination with other separation techniques, mass spectrometry‐based non‐targeted metabolic profiling, such as biomarker identification studies. Copyright © 2015 John Wiley & Sons, Ltd.     

Calculation of polymer blend compositions from Raman spectra: A new method based on parameter estimation techniques

A simple method to determine polymer blend compositions from their Raman spectra is presented. The method is based on expanding linearly the experimentally measured Raman spectrum of the blend, in terms of Raman spectra of pure components. A smooth function has also been included in the linear expansion to take into account the fluorescence interference, inherent to Raman spectroscopy. The coefficients of the linear expansion that give the best fit to the experimentally measured Raman spectrum of the blend are found by using a standard method of parameter estimation (Marquardt–Levenberg). These coefficients are directly related to the blend composition via a simple calibration procedure. Unlike standard methods of processing Raman spectra as deconvolution and curve‐fitting—which use Gaussian and/or Lorentzian functions to approximate the spectrum bands—the proposed method does not require either baseline correction or previous knowledge of peak parameters. Also, this method requires less CPU time than deconvolution and curve‐fitting procedures, and it is easy to automate. The proposed method has been applied to blends made out of two polymers: Polystyrene (PS) and poly(phenylene oxide) (PPO), to test its precision and consistency. Excellent agreement was found between calculated and expected blend compositions. Also, the reconstructed spectra agree very well with the experimentally measured blend spectra. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1013–1023, 2000     

Standardless spectrochemical analysis and direct simulations of time-resolved vibronic spectra of polyatomic molecules, isomers and mixtures

The efficient method for calculation of dynamical time-resolved vibronic spectra of polyatomic molecules is proposed. It allows to perform direct real-time computer simulations of such spectra for models of complex compounds, isomers and multicomponent mixtures with quantum beats and non-radiative vibrational relaxation taken into account. The examples of calculated spectra show the ways of how to search and select optimal experimental conditions and retrieve the most informative data for solution of inverse spectral problems in different situations. The new method of standardless analysis based on time-resolved vibronic spectroscopy has been developed and its main ideas are presented here. This method is able to solve quantitative and qualitative spectrochemical problems for individual substances and multicomponent mixtures (even for species with similar optical properties) with the use of experimentally measured relative intensities of dynamical spectra only. The algorithms of how to perform analysis in various experimental conditions are proposed.     

A binary matrix for improved detection of phosphopeptides in matrix‐assisted laser desorption/ionization mass spectrometry

Application of matrix‐assisted laser‐desorption/ionization mass spectrometry (MALDI MS) to analysis and characterization of phosphopeptides in peptide mixtures may have a limitation, because of the lower ionizing efficiency of phosphopeptides than nonphosphorylated peptides in MALDI MS. In this work, a binary matrix that consists of two conventional matrices of 3‐hydroxypicolinic acid (3‐HPA) and α‐cyano‐4‐hydroxycinnamic acid (CCA) was tested for phosphopeptide analysis. 3‐HPA and CCA were found to be hot matrices, and 3‐HPA not as good as CCA and 2,5‐dihydroxybenzoic acid (DHB) for peptide analysis. However, the presence of 3‐HPA in the CCA solution with a volume ratio of 1:1 could significantly enhance ion signals for phosphopeptides in both positive‐ion and negative‐ion detection modes compared with the use of pure CCA or DHB, the most common phosphopeptide matrices. Higher signal intensities of phosphopeptides could be obtained with lower laser power using the binary matrix. Neutral loss of the phosphate group (?80 Da) and phosphoric acid (?98 Da) from the phosphorylated‐residue‐containing peptide ions with the binary matrix was decreased compared with CCA alone. In addition, since the crystal shape prepared with the binary matrix was more homogeneous than that prepared with DHB, searching for ‘sweet’ spots can be avoided. The sensitivity to detect singly or doubly phosphorylated peptides in peptide mixtures was higher than that obtained with pure CCA and as good as that obtained using DHB. We also used the binary matrix to detect the in‐solution tryptic digest of the crude casein extracted from commercially available low fat milk sample, and found six phosphopeptides to match the digestion products of casein, based on mass‐to‐charge values and LIFT TOF‐TOF spectra. Copyright © 2009 John Wiley & Sons, Ltd.