Analysis Of Complex Spectra Research Articles

Novel principal component analysis tool based on python for analysis of complex spectra of time-of-flight secondary ion mass spectrometry

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful surface analysis tool, which can simultaneously provide elemental, isotopic, and molecular information with part per million (ppm) sensitivity. However, each spectrum may be composed of hundreds of ion signals, which makes the spectra data complex. Principal component analysis (PCA) is a multivariate analysis technique that has been widely used to figure out the variances among samples in ToF-SIMS spectra data analysis and is showing great success in the explanation of complex ToF-SIMS spectra. So far, several software tools have been developed for PCA of ToF-SIMS spectra; however, none of them are freely available. Such a situation leads to some difficulties in extending applications of PCA to various research fields. More importantly, it has long been challenging for common researchers to understand PCA plots and extract chemical differences among samples. In this work, we developed a new and flexible software tool (named “advanced spectra pca toolbox”) based on python for PCA of complex ToF-SIMS spectra along with an easy-to-read manual. It can generate data analysis reports automatically to explain chemical differences among samples, allowing less experienced researchers to easily understand tricky PCA results. Moreover, it is expandable and compatible with artificial intelligence/machine learning functions. Pure goethite and different lignin adsorbed goethite samples were used as a model system to demonstrate our new software tool, proving that our software tool can be readily used in complex spectra data processing. Our new software tool is open-source, convenient, flexible, and expandable. We expect this open-source tool will benefit the ToF-SIMS community.

SpectraX: A Straightforward Tool for Principal Component Analysis-Based Spectral Analysis.

The analysis of complex spectra is an important component of direct/ambient mass spectrometry (MS) applications such as natural product screening. Unlike chromatography-based metabolomics or proteomics approaches, which rely on software and algorithms, the work of spectral screening is mostly performed manually in the initial stages of research and relies heavily on the experience of the analyst. As a result, throughput and spectral screening reliability are problematic when dealing with large amounts of data. Here, we present SpectraX, a MATLAB-based application, which can analyze MS spectra and quickly locate m/z features from them. Principal component analysis (PCA) is used to analyze the data set, and scoring plots are presented to help in understanding the clustering of data. The algorithm uses mass to charge (m/z) features to produce a list of potential natural products.

Deep-learning assisted fast orbital angular momentum complex spectrum analysis.

Analyzing the orbital angular momentum (OAM) distribution of a vortex beam is critical for OAM-based applications. Here, we propose a deep residual network (DRN) to model the relationship between characteristics of the multiplexed OAM beam and their complex spectrum. The favorable experimental results show that our proposal can obtain both the intensity and phase terms of multiplexed OAM beams, dubbed complex spectrum, with a wide range of OAM modes, varying in intensity, phase ratio, and mode intervals at high accuracy and real-time speed. Specifically, the root mean square error (RMSE) of intensity and phase spectrum is evaluated as 0.002 and 0.016, respectively, with a response time of only 0.020 s. To the best of our knowledge, this work opens a new sight for fast OAM complex spectrum analysis and paves the way for numerous advanced domains that need real-time OAM complex spectrum diagnostic like ultrahigh-dimensional OAM tailoring.

Picometer-scale optical vortex interferometer using azimuthal complex spectrum analysis.

An interferogram demodulation method based on azimuthal complex spectrum analysis is proposed for achieving picometer-scale accuracy with an optical vortex interferometer (OVI). The OVI uses conjugated p-radial-order Laguerre-Gaussian beams to produce a high-order petal-like interferogram. A camera with a multi-ring pattern written on its sensor is used to convert the interferogram into multiple azimuthal intensity profiles. A phase shift subjected to either uniform surface displacement or axisymmetric non-uniform surface deformation can be retrieved from the complex spectra of the azimuthal intensity profiles at the main frequency components. The experiment verified that the measurement error is 84 pm for a displacement of 10 nm and 0.359 nm for a deformation magnitude of 100 nm. The effect of surface misalignment on the measurement result is also discussed. The proposed method provides an effective and highly accurate method of interferogram demodulation for the OVI and extends the applicability of OVI from uniform surface displacement measurement to axisymmetric non-uniform surface deformation measurement.

Self-mode-locking in a high-power hybrid silicon nitride integrated laser.

Integrated mode-locked lasers are useful tools in microwave photonic applications as a local oscillator. In particular, hybrid integrated lasers could easily be integrated with passive processing circuits. In this Letter, we report on the self-mode-locking of a hybrid integrated laser comprising two indium phosphide gain sections and a silicon nitride feedback circuit that filters light using two ring resonators. The hybrid laser is shown to mode-lock and to have a mostly frequency-modulated field in the cavity using a stepped-heterodyne optical complex spectrum analysis. A mostly frequency modulated field output is good for high powers per line due to a more continuous emission, compared with mode-locked lasers using a saturable absorber; additionally, the filter limits the bandwidth of the comb, condensing the power to the fewer comb lines.

Identification of Poly-N-Acetyllactosamine-Carrying Glycoproteins from HL-60 Human Promyelocytic Leukemia Cells Using a Site-Specific Glycome Analysis Method, Glyco-RIDGE

To elucidate the relationship between the protein function and the diversity and heterogeneity of glycans conjugated to the protein, glycosylation sites, glycan variation, and glycan proportions at each site of the glycoprotein must be analyzed. Glycopeptide-based structural analysis technology using mass spectrometry has been developed; however, complicated analyses of complex spectra obtained by multistage fragmentation are necessary, and sensitivity and throughput of the analyses are low. Therefore, we developed a liquid chromatography/mass spectrometry (MS)-based glycopeptide analysis method to reveal the site-specific glycome (Glycan heterogeneity-based Relational IDentification of Glycopeptide signals on Elution profile, Glyco-RIDGE). This method used accurate masses and retention times of glycopeptides, without requiring MS2, and could be applied to complex mixtures. To increase the number of identified peptide, fractionation of sample glycopeptides for reduction of sample complexity is required. Therefore, in this study, glycopeptides were fractionated into four fractions by hydrophilic interaction chromatography, and each fraction was analyzed using the Glyco-RIDGE method. As a result, many glycopeptides having long glycans were enriched in the highest hydrophilic fraction. Based on the monosaccharide composition, these glycans were thought to be poly-N-acetyllactosamine (polylactosamine [pLN]), and 31 pLN-carrier proteins were identified in HL-60 cells. Gene ontology enrichment analysis revealed that pLN carriers included many molecules related to signal transduction, receptors, and cell adhesion. Thus, these findings provided important insights into the analysis of the glycoproteome using our novel Glyco-RIDGE method.Graphical ᅟ

Combining a Deconvolution and a Universal Library Search Algorithm for the Nontarget Analysis of Data-Independent Acquisition Mode Liquid Chromatography-High-Resolution Mass Spectrometry Results.

Nontarget analysis is considered one of the most comprehensive tools for the identification of unknown compounds in a complex sample analyzed via liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS). Due to the complexity of the data generated via LC-HRMS, the data-dependent acquisition mode, which produces the MS2 spectra of a limited number of the precursor ions, has been one of the most common approaches used during nontarget screening. However, data-independent acquisition mode produces highly complex spectra that require proper deconvolution and library search algorithms. We have developed a deconvolution algorithm and a universal library search algorithm (ULSA) for the analysis of complex spectra generated via data-independent acquisition. These algorithms were validated and tested using both semisynthetic and real environmental data. A total of 6000 randomly selected spectra from MassBank were introduced across the total ion chromatograms of 15 sludge extracts at three levels of background complexity for the validation of the algorithms via semisynthetic data. The deconvolution algorithm successfully extracted more than 60% of the added ions in the analytical signal for 95% of processed spectra (i.e., 3 complexity levels multiplied by 6000 spectra). The ULSA ranked the correct spectra among the top three for more than 95% of cases. We further tested the algorithms with 5 wastewater effluent extracts for 59 artificial unknown analytes (i.e., their presence or absence was confirmed via target analysis). These algorithms did not produce any cases of false identifications while correctly identifying ∼70% of the total inquiries. The implications, capabilities, and the limitations of both algorithms are further discussed.

Orbital angular momentum complex spectrum analyzer for vortex light based on the rotational Doppler effect

The ability to measure the orbital angular momentum (OAM) distribution of vortex light is essential for OAM applications. Although there have been many studies on the measurement of OAM modes, it is difficult to quantitatively and instantaneously measure the power distribution among different OAM modes, let alone measure the phase distribution among them. In this work, we propose an OAM complex spectrum analyzer that enables simultaneous measurements of the power and phase distributions of OAM modes by employing the rotational Doppler effect. The original OAM mode distribution is mapped to an electrical spectrum of beat signals using a photodetector. The power and phase distributions of superimposed OAM beams are successfully retrieved by analyzing the electrical spectrum. We also extend the measurement technique to other spatial modes, such as linear polarization modes. These results represent a new landmark in spatial mode analysis and show great potential for applications in OAM-based systems and optical communication systems with mode-division multiplexing.

Comparison of the equivalent width, the autocorrelation width, and the variance as figures of merit for XPS narrow scans

X-ray photoelectron spectroscopy (XPS) is widely used in surface and materials laboratories around the world. It is a near surface technique, providing detailed chemical information about samples in the form of survey and narrow scans. To extract the maximum amount of information about materials it is often necessary to peak fit XPS narrow scans. And while indispensable to XPS data analysis, even experienced practitioners can struggle with their peak fitting. In our previous publication, we introduced the equivalent width (EWXPS) as both a possible machine automated method, one that requires less expert judgment for characterizing XPS narrow scans, and as an approach that may be well suited for the analysis of complex spectra. The EWXPS figure of merit was applied to four different data sets. However, as previously noted, other width functions are also regularly employed for analyzing functions. Here we evaluate two other width functions for XPS narrow scan analysis: the autocorrelation width (AWXPS) and the variance (σXPS2). These widths were applied to the same four sets of spectra studied before: (a) four C 1s narrow scans of ozone-treated carbon nanotubes (CNTs) (EWXPS: ∼2.11–2.16eV, AWXPS: ∼3.9–4.1eV, σXPS2: ∼5.0–5.2eV, and a modified form of σXPS2, denoted σXPS2*: ∼6.3–6.8eV), (b) silicon wafers with different oxide thicknesses (EWXPS: ∼1.5–2.9eV, AWXPS: ∼2.28–4.9, and σXPS2: ∼0.7–4.9eV), (iii) hydrogen-terminated silicon surfaces, before and after modification with pentyl groups, and after annealing of the pentyl-terminated surface (EWXPS: ∼0.7–1.0eV, AWXPS: ∼1.2–1.6eV, and σXPS2: ∼0.12–0.19eV), and (iv) C 1s narrow scans from five different nanodiamond samples, three of which showed charging (EWXPS: ∼2.6–4.8eV, AWXPS: ∼3.8–6.9eV, and σXPS2: ∼1.6–4.2eV). All three of the width functions showed similar trends, except in the case of the C 1s spectra of the CNT samples, which were the most complex spectra evaluated, where σXPS2 showed poor correlation with the corresponding O/C ratios. Accordingly, we favor EWXPS and AWXPS. EWXPS is advantageous because it is conceptually simple, giving the most intuitive results. AWXPS has the advantage of not requiring the user to specify the height of the function at its maximum, which will be affected by noise. Because these functions are based on different mathematical operations/algorithms, best practices may involve the calculation of both widths for a set of narrow scans. The standard deviation, σXPS, i.e., the square root of the variance, was also examined. As expected, it gave results similar to σXPS2.

Vehicle-to-Vehicle Propagation Models With Large Vehicle Obstructions

Vehicle-to-vehicle (V2V) communication is an enabler for improved traffic safety and congestion control. As for any wireless system, the ultimate performance limit is determined by the propagation channel. A particular point of interest is the shadowing effect of large vehicles such as trucks and buses, as this might affect the communication range significantly. In this paper we present measurement results and model the propagation channel, in which a bus acts either as a shadowing object or as a relay between two passenger cars. The measurement setup is based on a Wireless Open-Access Research Platform (WARP) Field-Programmable Gate Array (FPGA) software radio as transmitter and a Tektronix RSA5106A real-time complex spectrum analyzer as receiver. We analyze the influence of the bus location and car separation distance on the path loss, shadowing, small-scale fading, delay spread, and cross correlation. The main effect of the bus is that it is acting as an obstruction creating an additional 15- to 20-dB attenuation and an increase in the root-mean-square delay spread by roughly 100 ns. A Nakagami distribution is found to well describe the statistics of the small-scale fading, by using Akaike's Information Criterion and the Kolmogorov-Smirnov test. The distance dependence of the path loss is analyzed and a stochastic model is developed.

Selected minor and trace elements from water bodies of western Paraguay

Minor and trace elements composition of bottom sediments from water bodies in Western Paraguay have been investigated by XRF techniques to determine their correlation as well as provenance. The analysis of complex spectra was performed by the AXIL software and the quantitative analysis by the QAES software. Analyzed trace elements were the refractory elements Rb, Sr, Y, Zr, Nb, Ba, La, Ce, Pr, Nd, Zr, y and other HFSE as Cr, Ni, Cu, together with Zn. Minor elements were Ti, Mn, Fe which are often to the above refractories related. According to their normalized spidergrams two sets of sediments can be differentiated. Those from Pilcomayo and Verde rivers as well as from km164-Wetland show light rare earth elements (LREE) enrichment, negative Nb and Ti anomalies and no spike at Zr. On the other hand, sediments from Confuso, Aguaray(Jehe), Negro and Montelindo rivers have spidergrams very alike, with strong negative anomalies at Nb, Nd and Ti whereas a positive at Zr. Further, in the former there is a strong correlation of Fe versus the refractory elements; such a correlation does not exist in the latter. The sediments from the Pilcomayo & Verde Rivers and from the km164-Wetland evolved as the sub-Andean/Andean metamorphic/sedimentary materials.

ChemInform Abstract: Liquid Crystals as Solvents in NMR Spectroscopy: Current Developments in Structure Determination

Nuclear Magnetic Resonance (NMR) spectroscopy of molecules aligned in liquid crystalline media provides information on molecular structure and order parameters. The partial alignment of the molecules in the anisotropic phase of the liquid crystals gives rise to residual intramolecular dipolar couplings which are dependent on the internuclear distances and therefore yield information on the geometry of molecules. The spectra of these aligned molecules become rapidly complex with the increase in the number of interacting spins and with decrease in the symmetry of the molecules. The spectra of these molecules are generally strongly coupled and are complex. Thus the first order analysis of the spectra as applicable to liquid state is generally not applicable and one should resort to numerical analysis using computers. In this report problems associated with the analyses of such complex spectra, methods developed to aid such analyses and the precision of the structural parameters derived are discussed. Use of mixed liquid crystals of opposite diamagnetic susceptibility anisotropies to extract information which is otherwise not possible to derive using single liquid crystals is highlighted. Current developments in the field with special emphasis on the discovery of a novel liquid crystal with low order parameter and the use of natural abundance deuterium NMR spectra of the probe molecules for the analyses of complex spectra are discussed.

Optical minimum-shift-keying transmitter based on a monolithically integrated quad Mach-Zehnder in-phase and quadrature modulator

We propose and demonstrate an optical minimum-shift-keying (MSK) transmitter using a single-quad Mach-Zehnder (MZ) in-phase and quadrature modulator, where four sub-Mach-Zehnder modulators are monolithically integrated on a main MZ superstructure. Using the proposed transmitter, a MSK signal at bit rate of B could be successfully generated by orthogonally superposing two low-speed (B/2) carrier-suppressed return-to-zero differential phase-shift-keying streams with a relative time offset, 1/B. MSK signals at bit rate of 20 and 80 Gbits/s were successfully generated using the proposed MSK transmitter. A continuous changed phase trajectory of the obtained MSK was confirmed using a complex spectrum analyzer. The filtering tolerance of the MSK was also characterized using a bandwidth-variable tunable filter.

An emergency response intercomparison exercise using a synthetically generated gamma-ray spectrum

Although high resolution gamma ray spectrometry serves as the primary analytical technique in emergency response situations, chances for laboratories to practice analysing the type of spectra that may be expected in the early phase of such a situation are limited. This problem is more acute for laboratories in countries that have no nuclear facilities. The analysis of synthetically generated spectra may serve as a useful surrogate for actual spectra; this paper reports the results of a multilateral intercomparison exercise conducted using such a spectrum. Results indicate that the laboratories involved appear to have no problems identifying radioactive isotopes that regularly appear in national and international intercomparisons or exercises. However, some problems are evident for isotopes that are less often encountered which may, however, occur during the early phases of a nuclear accident. Isotopes prone to true coincidence summation proved also to be difficult with regard to correction of activities in some cases. The synthesized spectrum constituted a useful means of comparative analysis of complex spectra multilaterally without the impracticalities of using a sample drawn from a reactor.

A Study of Brainwave Entrainment Based on EEG Brain Dynamics

The brain which is composed of more than 100 billion nerve cells is a sophisticated biochemical factory. For many years, neurologists, psychotherapists, researchers, and other health care professionals have studied the human brain. With the development of computer and information technology, it makes brain complex spectrum analysis to be possible and opens a highlight field for the study of brain science. In the present work, observation and exploring study of the activities of brain under brainwave music stimulus are systemically made by experimental and spectrum analysis technology. From our results, the power of the 10.5Hz brainwave appears in the experimental figures, it was proved that upper alpha band is entrained under the special brainwave music. According to the Mozart effect and the analysis of improving memory performance, the results confirm that upper alpha band is indeed related to the improvement of learning efficiency.

Complex Spectrum Analysis of Modulated Optical Signals Using Stimulated Brillouin Scattering

We introduce a novel method for the measurement of the spectral phase of modulated optical signals based on double-pump stimulated Brillouin scattering interaction and direct homodyne detection. This technique is combined with Brillouin high-resolution analysis to achieve a complete characterization of the complex optical spectrum. A 10-Gb/s nonreturn-to-zero signal with a 32-bit pattern modulated with an electroabsorption modulator is measured using this technique and its time-domain information (power and chirp) is obtained by inverse Fourier transform.

Using Cramer–Rao theory as spectrometer design tool aimed at quantitative complex-spectrum analysis

In this paper the use of the Cramer-Rao lower bound (CRLB) to aid in the design of diagnostic systems dealing with complex spectra is discussed. Specifically it is discussed how a priori knowledge, used to improve the estimation, can be included in the CRLB analysis. This provides improved predictions for the spectrometer characteristics that will lead to an optimal system.

Single-molecule PCR: an artifact-free PCR approach for the analysis of somatic mutations

A critical review of the clone-by-clone approach to the analysis of complex spectra of somatic mutations is presented. The study of a priori unknown somatic mutations requires painstaking analysis of complex mixtures of multiple mutant and non-mutant DNA molecules. If mutant fractions are sufficiently high, these mixtures can be dissected by the cloning of individual DNA molecules and scanning of the individual clones for mutations (e.g., by sequencing). Currently, the majority of such cloning is performed using PCR fragments. However, post-PCR cloning may result in various PCR artifacts – PCR errors and jumping PCR – and preferential amplification of certain mutations. This review argues that single-molecule PCR is a simple alternative that promises to evade the disadvantages inherent to post-PCR cloning and enhance mutational analysis in the future.

A new selective population transfer experiment using a double pulsed field gradient spin-echo.

A new pulse sequence is proposed for the determination of scalar coupling correlation in small- and medium-sized organic compounds. The method uses a combination of the double pulsed field gradient spin-echo (DPFGSE) and the selective population transfer (SPT) techniques and is shown to be useful in the analysis of complex spectra with many overlapped signals. The usefulness of this method in the structural elucidation of natural substances is demonstrated using strychnine and digitoxin as examples.

New applications of the genetic algorithm for the interpretation of high-resolution spectra

Rotationally resolved electronic spectroscopy yields a wealth of information on molecular structures in different electronic states. Unfortunately, for large molecules the spectra get rapidly very congested owing to close-lying vibronic bands, other isotopomers with similar zero-point energy shifts, or large-amplitude internal motions. A straightforward assignment of single rovibronic lines and, therefore, line position assigned fits are impossible. An alternative approach is unassigned fits of the spectra using genetic algorithms (GAs) with special cost functions for evaluation of the quality of the fit. This paper decribes the improvements we established on the GA method discussed before (J.A. Hageman, R. Wehrens, R. de Gelder, W.L. Meerts, and L.M.C. Buydens. J. Chem. Phys. 113, 7955 (2000)). In particular, we succeeded in obtaining a dramatic reduction in computing time that made it possible to apply the GA process in a large number of cases. A completely automated fit of a rotationally resolved laser-induced fluorescence spectrum without any prior knowledge of the molecular parameters can now be performed in less than 1 h. We demonstrate the power of the method on a number of typical examples such as very dense rovibronic spectra of van der Waals clusters and overlapping spectra due to different isotopomers. The discussed results demonstrate the extreme power of the GA in automated fitting and assigning of complex spectra. It opens the road to the analysis of complex spectra of biomolecules and their building blocks. Key words: high-resolution spectroscopy, genetic algorithm, biomolecules, structure, van der Waals clusters.