Unexplained Peaks Research Articles

Investigation of unexpected silane ions caused by gas-phase reactions in Orbitrap gas chromatography-mass spectrometry.

The mass spectra of compounds containing dimethyl (phenyl)silyl group (-SiMe2Ph) sometimes exhibit unusual ion peaks when measured using Orbitrap gas chromatography-mass spectrometry (GC-MS). This would complicate the mass spectra and may limit the matching of spectral data with preexisting resources for compound annotation. These peaks were identified as products from reactions with residual water. A series of dimethyl (phenyl)silyl compounds were dissolved in methanol and investigated using Orbitrap GC-MS. Certain ions reacted with residual water in the C-trap. The reaction was confirmed using accurate mass and elemental composition analysis via MS studies, and the active center of the reaction was determined using density functional theory (DFT) calculations. Two types of gas-phase reactions between gaseous water and cations from a series of silanes were identified. DFT calculations indicate that silicon (Si) acts as the active center for these gas-phase water reactions. Compounds with multiple Si atoms generate a larger number of additional ions, which would complicate the mass spectra. The mass spectra of vinylsilanes and alkylsilanes with -SiMe2Ph indicate that the conjugated group linked to -SiMe2Ph can affect the water adduction process. Silane ions could react with residual water in the C-trap of an Orbitrap mass spectrometer. The mass spectra of these compounds may exhibit unexplained peaks arising from gas-phase reactions. Although these reactions may decrease spectral matching scores for compound annotation, they offer opportunities for systematic investigations into the mechanistic and kinetic aspects of high-energy ion reactivity.

Low-Cost Methods for Improving Data Collection Speed in Microwave Bragg Diffraction

In many introductory physics classes, diffraction of light is introduced first, then more advanced diffraction topics such as x-ray diffraction, Bragg’s law, and crystallography are covered. Since using x-rays raises safety concerns and atomic spacing in a crystal is not easy to change, microwaves with macroscopic crystals have been used to study Bragg’s law in the undergraduate laboratory. A number of scientific supply companies, including PASCO and 3B Scientific, sell 10-GHz microwave optics systems. However, using these systems within the parameters of the manufacturer’s procedure for a Bragg diffraction lab poses some challenges. First, the receiver and transmitter must be manually positioned, making the data collection process slow. Second, the microwaves should be plane waves and the receiver should be located beyond the far-field limit. These 10-GHz microwave optics systems are low power, making them safe for lab use, but this limits the crystal size and working distance between the transmitter and receiver to under 1000 mm. The experimental setup suggested by the manufacturer separates the transmitter and receiver by about 10 wavelengths from the center of rotation. While the bells on the transmitter and receiver help with producing plane waves, it is expected that ideal conditions for Bragg’s law are not completely fulfilled. Indeed, the experiment guide warns of errors up to 15% and unexplained peaks in the data.

Surface energy budget at Curiosity through observations and column modeling

Diurnal ground surface temperatures (Tg) and the five major terms of the surface energy budget (SEB) are displayed from hourly Mars Science Laboratory observations and from column model simulations in four contrasting cases along the Curiosity traverse. Tg and the SEB terms are otherwise well simulated on regolith near the landing spot and on rocky Pahrump Hills, but the residual in observation-based SEB (~downwelling longwave radiation) shows unexplained peaks in the morning and evening and simultaneously model-Tg is too cold. Enhanced or diurnally variable crater dust does not help but diurnally variable soil thermal inertia (suggested by Fourier analysis of observed Tg) reduces both defects at both sites. Sand on the steep Namib dune is instead homogeneous, defects here being reduced by taking into account slope effects. Regolith at the 2018 dust storm site appears inhomogeneous, with the SEB terms and Tg relatively well simulated even in this case of extremely heavy dust load.

Unexplained spectral peaks in Earth tremor

Unexplained spectral peaks in Earth tremor

Impurity induced renormalized phonon spectrum of cuprate superconductors

The potential problem of anharmonic lattice vibrations in high-temperature superconductors (HTS) using the most suitable Born–Mayer–Huggins (BMH) potential has been taken up to investigate the renormalized phonon density of states (RPDOS). In order to develop the suitable results, the many body theory using quantum dynamical approach of Green’s function (GF) via an almost complete Hamiltonian (without using BCS type Hamiltonian) has been incorporated which includes harmonic electron and phonon Hamiltonian, electron–phonon interaction Hamiltonian, anharmonic and defect Hamiltonian. The derivation of anharmonic phonon GF for modified form of BMH potential enables to evaluate the renormalized and perturbed mode phonon frequencies of solids. The expressions obtained for the RPDOS can be resolved into diagonal and nondiagonal parts of which the nondiagonal part chiefly depends on impurities and disappears in pure crystals. A large number of new features are investigated in the light of this formulation followed by the numerical analysis for the energy spectrum of representative cuprate HTS YBa2Cu3O[Formula: see text]. The inclusion of defects, anharmonicities and electron–phonon interactions in the cuprate superconductors substantially modifies the scenario of RPDOS and reveals a large number of unexplained peaks in the spectrum.

Intricate Resonant Raman Response in Anisotropic ReS2.

The strong in-plane anisotropy of rhenium disulfide (ReS2) offers an additional physical parameter that can be tuned for advanced applications such as logic circuits, thin-film polarizers, and polarization-sensitive photodetectors. ReS2 also presents advantages for optoelectronics, as it is both a direct-gap semiconductor for few-layer thicknesses (unlike MoS2 or WS2) and stable in air (unlike black phosphorus). Raman spectroscopy is one of the most powerful characterization techniques to nondestructively and sensitively probe the fundamental photophysics of a 2D material. Here, we perform a thorough study of the resonant Raman response of the 18 first-order phonons in ReS2 at various layer thicknesses and crystal orientations. Remarkably, we discover that, as opposed to a general increase in intensity of all of the Raman modes at excitonic transitions, each of the 18 modes behave differently relative to each other as a function of laser excitation, layer thickness, and orientation in a manner that highlights the importance of electron-phonon coupling in ReS2. In addition, we correct an unrecognized error in the calculation of the optical interference enhancement of the Raman signal of transition metal dichalcogenides on SiO2/Si substrates that has propagated through various reports. For ReS2, this correction is critical to properly assessing the resonant Raman behavior. We also implemented a perturbation approach to calculate frequency-dependent Raman intensities based on first-principles and demonstrate that, despite the neglect of excitonic effects, useful trends in the Raman intensities of monolayer and bulk ReS2 at different laser energies can be accurately captured. Finally, the phonon dispersion calculated from first-principles is used to address the possible origins of unexplained peaks observed in the Raman spectra, such as infrared-active modes, defects, and second-order processes.

Resonance Raman effects in transition metal dichalcogenides

Raman spectroscopy is broadly used in the studies of transition metal dichalcogenides to determine the number of layers or other structural parameters. However, unlike the case of graphene, the Raman spectrum varies greatly depending on the excitation energy, and many unusual effects have been reported. The optical absorption spectrum has many features related to exciton states due to the strong coulomb interaction in these materials, and dramatic resonance effects occur when the excitation energy matches one of these exciton states. Several forbidden Raman modes and some unexplained peaks appear near resonance, and Davydov splitting of some Raman modes is observed. Furthermore, the polarization dependence of the some Raman modes also shows excitation energy dependence. In this review, recent progress in resonance Raman studies on transition metal dichalcogenides and some unresolved issues are reviewed. Copyright © 2017 John Wiley & Sons, Ltd.

Empirical Site Response and Comparison with Measured Site Conditions at ANSS Sites in the Vicinity of Reno, Nevada

We empirically evaluate spectral amplification relative to a nearby rock site at 18 Advanced National Seismic System strong‐motion stations within the basin containing the urban areas of Reno and Sparks, Nevada. The near‐surface site conditions have a strong effect on ground motion, which is clearly demonstrated through analysis of weak motion. The study uses multiple regional earthquake events of varying azimuth. Averages of these empirical amplifications, grouped by generalized geological formations (volcanic rock, Pliocene and early to mid‐Quaternary sediments, and younger Quaternary sedimentary sites), show dependence on the geology. However, when the stations are grouped according to V S 30 values, the mean amplifications are more distinct, indicating that V S 30 is a more useful predictor of amplification for the Reno–Sparks, Nevada, urban area. Spectral amplifications computed from ground motions of the local Mogul, Nevada, 2008 earthquake swarm ( M L 0.6–4.7; Anderson et al. , 2009) have similar spectral shapes for 8 of the 12 stations where comparisons could be made, but the absolute amplitudes are slightly inconsistent. Four stations show unexplained peaks in the amplitude spectral ratios from the mainshock ground motions. The comparisons verify that multiple regional ground motions can be used to obtain relative site‐response amplification functions for seismic‐hazard applications, but the discrepancies are a reminder that directional effects contribute uncertainty to the amplification functions. Online Material: Tables describing earthquakes recorded in the vicinity of Reno, Nevada, and figures of the Fourier spectral ratios (FSRs) and of the amplitude and basin depth relationships.

First-principles calculations of phonons and Raman spectra in monoclinicCsSnCl3

Density functional perturbation theory is used to calculate the phonons at the zone center for monoclinic ${\mathrm{CsSnCl}}_{3}$. We report the calculated normal mode frequencies classified according to irreducible representations for both infrared-active and Raman-active modes. We also report the dielectric constants and Born-effective charges and investigate the anisotropy of the nonanalyticities near the zone center. The first-principles calculated Raman-active phonon frequencies and simulated Raman spectra are compared with experimental results from literature. We find that aside from the first-order allowed Raman modes of ${A}_{g}$ and ${B}_{g}$ symmetries, forbidden LO Raman modes appear prominently in the measured spectra. Several of these modes are close to or coincide with allowed modes and alter their intensity, while others appear as separate otherwise unexplained peaks. With this interpretation, good agreement is obtained with experimental mode frequencies to within a few ${\mathrm{cm}}^{\ensuremath{-}1}$.

Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques.

BackgroundMass spectrometry-based proteomics experiments generate spectra that are rich in information. Often only a fraction of this information is used for peptide/protein identification, whereas a significant proportion of the peaks in a spectrum remain unexplained. In this paper we explore how a specific class of data mining techniques termed “frequent itemset mining” can be employed to discover patterns in the unassigned data, and how such patterns can help us interpret the origin of the unexpected/unexplained peaks.ResultsFirst a model is proposed that describes the origin of the observed peaks in a mass spectrum. For this purpose we use the classical correlative database search algorithm. Peaks that support a positive identification of the spectrum are termed explained peaks. Next, frequent itemset mining techniques are introduced to infer which unexplained peaks are associated in a spectrum. The method is validated on two types of experimental proteomic data. First, peptide mass fingerprint data is analyzed to explain the unassigned peaks in a full scan mass spectrum. Interestingly, a large numbers of experimental spectra reveals several highly frequent unexplained masses, and pattern mining on these frequent masses demonstrates that subsets of these peaks frequently co-occur. Further evaluation shows that several of these co-occurring peaks indeed have a known common origin, and other patterns are promising hypothesis generators for further analysis. Second, the proposed methodology is validated on tandem mass spectrometral data using a public spectral library, where associations within the mass differences of unassigned peaks and peptide modifications are explored. The investigation of the found patterns illustrates that meaningful patterns can be discovered that can be explained by features of the employed technology and found modifications.ConclusionsThis simple approach offers opportunities to monitor accumulating unexplained mass spectrometry data for emerging new patterns, with possible applications for the development of mass exclusion lists, for the refinement of quality control strategies and for a further interpretation of unexplained spectral peaks in mass spectrometry and tandem mass spectrometry.Electronic supplementary materialThe online version of this article (doi:10.1186/s12953-014-0054-1) contains supplementary material, which is available to authorized users.

Unexpected peaks in tandem mass spectra due to reaction of product ions with residual water in mass spectrometer collision cells.

Certain product ions in electrospray ionization tandem mass spectrometry are found to react with residual water in the collision cell. This reaction often leads to the formation of ions that cannot be formed directly from the precursor ions, and this complicates the mass spectra and may distort MRM (multiple reaction monitoring) results. Various drugs, pesticides, metabolites, and other compounds were dissolved in acetonitrile/water/formic acid and studied by electrospray ionization mass spectrometry to record their MS(2) and MS(n) spectra in several mass spectrometers (QqQ, QTOF, IT, and Orbitrap HCD). Certain product ions were found to react with residual water in collision cells. The reaction was confirmed by MS(n) studies and the rate of reaction was determined in the IT instrument using zero collision energy and variable activation times. Examples of product ions reacting with water include phenyl and certain substituted phenyl cations, benzoyl-type cations formed from protonated folic acid and similar compounds by loss of the glutamate moiety, product ions formed from protonated cyclic siloxanes by loss of methane, product ions formed from organic phosphates, and certain negative ions. The reactions of product ions with residual water varied greatly in their rate constant and in the extent of reaction (due to isomerization). Various types of product ions react with residual water in mass spectrometer collision cells. As a result, tandem mass spectra may contain unexplained peaks and MRM results may be distorted by the occurrence of such reactions. These often unavoidable reactions must be taken into account when annotating peaks in tandem mass spectra and when interpreting MRM results. Published in 2014. This article is a U.S. Government work and is in the public domain in the USA.

Chemical clustering and visualization applied to macromolecular crystallography

Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and the insertion and correct placement of a sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient appears to be robust in this application and coupled with hierarchical clustering and the overlay of crystallization outcome reveals information of biological relevance. While tested with a single example the potential applications appear promising.

Comparing chemistry to outcome: the development of a chemical distance metric, coupled with clustering and hierarchal visualization applied to macromolecular crystallography.

Many bioscience fields employ high-throughput methods to screen multiple biochemical conditions. The analysis of these becomes tedious without a degree of automation. Crystallization, a rate limiting step in biological X-ray crystallography, is one of these fields. Screening of multiple potential crystallization conditions (cocktails) is the most effective method of probing a proteins phase diagram and guiding crystallization but the interpretation of results can be time-consuming. To aid this empirical approach a cocktail distance coefficient was developed to quantitatively compare macromolecule crystallization conditions and outcome. These coefficients were evaluated against an existing similarity metric developed for crystallization, the C6 metric, using both virtual crystallization screens and by comparison of two related 1,536-cocktail high-throughput crystallization screens. Hierarchical clustering was employed to visualize one of these screens and the crystallization results from an exopolyphosphatase-related protein from Bacteroides fragilis, (BfR192) overlaid on this clustering. This demonstrated a strong correlation between certain chemically related clusters and crystal lead conditions. While this analysis was not used to guide the initial crystallization optimization, it led to the re-evaluation of unexplained peaks in the electron density map of the protein and to the insertion and correct placement of sodium, potassium and phosphate atoms in the structure. With these in place, the resulting structure of the putative active site demonstrated features consistent with active sites of other phosphatases which are involved in binding the phosphoryl moieties of nucleotide triphosphates. The new distance coefficient, CDcoeff, appears to be robust in this application, and coupled with hierarchical clustering and the overlay of crystallization outcome, reveals information of biological relevance. While tested with a single example the potential applications related to crystallography appear promising and the distance coefficient, clustering, and hierarchal visualization of results undoubtedly have applications in wider fields.

Building and Searching Tandem Mass Spectral Libraries for Peptide Identification

Spectral library searching is an emerging approach in peptide identifications from tandem mass spectra, a critical step in proteomic data analysis. Conceptually, the premise of this approach is that the tandem MS fragmentation pattern of a peptide under some fixed conditions is a reproducible fingerprint of that peptide, such that unknown spectra acquired under the same conditions can be identified by spectral matching. In actual practice, a spectral library is first meticulously compiled from a large collection of previously observed and identified tandem MS spectra, usually obtained from shotgun proteomics experiments of complex mixtures. Then, a query spectrum is then identified by spectral matching using recently developed spectral search engines. This review discusses the basic principles of the two pillars of this approach: spectral library construction, and spectral library searching. An overview of the software tools available for these two tasks, as well as a high-level description of the underlying algorithms, will be given. Finally, several new methods that utilize spectral libraries for peptide identification in ways other than straightforward spectral matching will also be described.

Interpretation of the 4f-5d Excitation Spectra of Eu 3+ and Tb 3+ Doped in Crystals

The structure of the low-temperature 4f N →4f N−1 5d excitation spectra of Eu 3+ and Tb 3+ doped in crystals LiYF 4, YPO 4 and CaF 2 measured by van Pieterson et al. in 2002 was analyzed and assigned based on the simple model proposed by Duan and co-workers in the last few years. Some complemental discussion on effects of J-mixing on the f-d transition intensities for Eu 3+ due to the f-electron crystal-field interaction H cf( f), which was ignored in the simple model, was presented. Some previously unexplained peaks for Tb 3+ were interpreted to be spin-forbidden transitions to higher 5d crystal-field levels, or assigned to be f→d excitations with the core 4f 7 excited from 8S to 6P, 6I and 6D, respectively. It is shown that the main structure of 4f-5d excitation spectra of Eu 3+ and Tb 3+ can be well interpreted with the simple model.

Anomalous drag coupling between a thin superconducting film and a two-dimensional electron gas caused by radio frequency interference

We studied a bilayer system consisting of a two-dimensional electron gas in a $\mathrm{Ga}\mathrm{As}∕\mathrm{Al}\mathrm{Ga}\mathrm{As}$ heterostructure and a thin superconducting Al film. Drag measurements were made by passing current through the two-dimensional electron gas layer and measuring the voltage induced in the superconducting layer. Unexplained peaks in drag voltage near the transition region were seen in previous similar experiments. We also detected a draglike voltage peak in the transition region. The signal is found to be nonintrinsic and due to radio frequency interference. The extremely nonlinear impedance of the Al in the transition region allows the interference to couple in this manner. We show a simplified analysis of the measurement system that reproduces the main features of our results.

A circulation description of a rip current neck

This paper considers wave-driven rip currents from a circulation-vorticity point of view. A highly simplified description of rip currents using continuous generation of point vortices at fixed locations is found to have a wide range of applicability around the rip neck. Rip scaling becomes straightforward, and is seen to collapse to a single form. Numerical experiments with this simplified system have the ability to predict well startup transients including previously unexplained peaks, and frequency-dependent effects of wave groups on rip currents. Quantitative mean currents in the rip neck are represented moderately well by this theory.

A theory of patterns of passby noise

Some people say they are annoyed by traffic noise. There is rather a lot of evidence to show that where traffic noise is louder, more people say they are annoyed by it. On the basis of this sort of evidence, there is a consensus that road traffic noise causes annoyance, but some studies have detected unexplained peaks of annoyance in quieter places, or a plateau of annoyance in high noise. Such anomalies may especially affect those sensitive to noise. The pattern of alternation of passby noise and background traffic noise explains the positioning in soundspace of anomalies variously reported at 60 dB(A) L eq , 4000 NV and 1800 NHV. Such anomalies occur where there are regular or rapidly alternating patterns of passby noise.

Longitudinal Optical Vibrations in Glasses: GeO2and SiO2

We show that longitudinal optical (LO) vibrational modes account for several previously unexplained peaks in the Raman spectra of vitreous Ge${\mathrm{O}}_{2}$ and Si${\mathrm{O}}_{2}$. Identification of LO modes in these and other glasses reduces the complexity of the spectra that must be explained by simple structural models. It also follows that long-range (Coulomb) forces should be included in complete theories of the vibrational properties of many glasses.

Heat capacity of hexagonal tungsten bronzes

The heat capacity of four hexagonal tungsten bronzes (${\mathrm{K}}_{x}\mathrm{W}{\mathrm{O}}_{3}, {\mathrm{Rb}}_{x}\mathrm{W}{\mathrm{O}}_{3}, {\mathrm{Cs}}_{x}\mathrm{W}{\mathrm{O}}_{3}, \mathrm{and} {\mathrm{Tl}}_{x}\mathrm{W}{\mathrm{O}}_{3}$), W${\mathrm{O}}_{3}$, and cubic ${\mathrm{Na}}_{x}\mathrm{W}{\mathrm{O}}_{3}$ have been measured from 1 to 55 K. The excess heat capacity reported by King et al. for ${\mathrm{Rb}}_{x}\mathrm{W}{\mathrm{O}}_{3}$ and attributed to an Einstein mode is also present in ${\mathrm{K}}_{x}\mathrm{W}{\mathrm{O}}_{3}$, ${\mathrm{Cs}}_{x}\mathrm{W}{\mathrm{O}}_{3}$, and ${\mathrm{Tl}}_{x}\mathrm{W}{\mathrm{O}}_{3}$. The values of $x$ determined from the excess heat capacity agree reasonably well with the nominal composition having $x=0.33$. The Einstein temperatures ${\ensuremath{\Theta}}_{E}$ for the metal ions vibrating in the channels formed by the six-membered rings of W${\mathrm{O}}_{6}$ octahedra were found to be 58 K for Rb, 70 K for Cs, and 38 K for Tl. Two unexplained peaks in the heat capacity of ${\mathrm{K}}_{x}\mathrm{W}{\mathrm{O}}_{3}$ near 20 K precluded an accurate determination of ${\ensuremath{\Theta}}_{E}$ for this tungsten bronze, but ${\ensuremath{\Theta}}_{E}$ is estimated to be between 60 and 90 K. The magnitudes of the Einstein temperatures can be understood in terms of the masses and ionic radii of the metal ions. All four hexagonal tungsten bronzes are superconductors. Measurements of the heat capacity with a magnetic field showed ${\mathrm{Rb}}_{x}\mathrm{W}{\mathrm{O}}_{3}$ to be a type-I superconductor, but ${\mathrm{K}}_{x}\mathrm{W}{\mathrm{O}}_{3}$ to be a type-II superconductor.