Assignment Of Spectra Research Articles

GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis.

Identification evaluation and result dissemination are essential components in mass spectrometry-based proteomics analysis. The visualization of fragment ions in mass spectrum provides strong evidence for peptide identification and modification localization. Here, we present an easy-to-use tool, named GP-Plotter, for ion annotation of tandem mass spectra and corresponding image output. Identification result files of common searching tools in the community and user-customized files are supported as input of GP-Plotter. Multiple display modes and parameter customization can be achieved in GP-Plotter to present annotated spectra of interest. Different image formats, especially vector graphic formats, are available for image generation which is favorable for data publication. Notably, GP-Plotter is also well-suited for the visualization and evaluation of glycopeptide spectrum assignments with comprehensive annotation of glycan fragment ions. With a user-friendly graphical interface, GP-Plotter is expected to be a universal visualization tool for the community. GP-Plotter has been implemented in the latest version of Glyco-Decipher (v1.0.4) and the standalone GP-Plotter software is also freely available at https://github.com/DICP-1809.

Joint antenna selection and resource allocation for mm‐wave directional D2D communications using distributed deep reinforcement learning

AbstractIn this paper, with the promising assumption of using adaptive directional microstrip antenna on user equipment, the problem of joint antenna selection, spectrum assignment, and transmit power allocation for mm‐wave device‐to‐device communications underlying cellular networks is tackled, with the goal of enhancing system throughput and energy efficiency. To address the complexity of this problem, a method based on multi‐agent distributed deep reinforcement learning in which an autonomous intelligent agent is deployed for each user equipment is proposed. The performance evaluation demonstrates its superiority over existing strategies, resulting in improved system performance, reduced outage probability, and enhanced energy efficiency.

On arbitrary matrix coefficient assignment for the characteristic matrix polynomial of block matrix linear control systems

For block matrix linear control systems, we study the property of arbitrary matrix coefficient assignability for the characteristic matrix polynomial. This property is a generalization of the property of eigenvalue spectrum assignability or arbitrary coefficient assignability for the characteristic polynomial from system with scalar $(s=1)$ block matrices to systems with block matrices of higher dimensions $(s>1)$. Compared to the scalar case $(s=1)$, new features appear in the block cases of higher dimensions $(s>1)$ that are absent in the scalar case. New properties of arbitrary (upper triangular, lower triangular, diagonal) matrix coefficient assignability for the characteristic matrix polynomial are introduced. In the scalar case, all the described properties are equivalent to each other, but in block matrix cases of higher dimensions this is not the case. Implications between these properties are established.

Mer-M(CO)3(PNP)0/+ pincer complexes (M = W(0) or Re(I); PNP = 4,5-bis(diphenylphosphino)acridine): synthesis, spectroscopy and anti-Kasha emission.

Two isoelectronic and isostructural W(0) and Re(I) complexes mer-W(CO)3(PNP) (1) and [mer-Re(CO)3(PNP)]Cl (2) (PNP = 4,5-bis(diphenylphosphino)acridine) were synthesized and characterized by X-ray diffraction, infrared, electronic absorption and emission spectroscopy, and cyclic voltammetry. Structures of these complexes show a metal center bonded to the pincer ligand and two axial CO and one equatorial CO ligands. DFT calculations showed that the LUMOs of both complexes are the lowest energy π* orbitals localized in the acridine part of the ligand. The HOMO of 1 is dominated by the dπ orbital of W(0) while the HOMO of 2 has a substantial contribution from the highest energy π orbital of the acridine ring. TD-DFT calculations were performed to assist assignment of the UV-vis absorption spectra. The UV-vis absorption spectrum of 1 shows a very low energy W → π* (acridine) metal-to-ligand-charge-transfer (MLCT) absorption band that ranges from visible (500 nm) to near-infrared (>900 nm) regions and an intense acridine π → π* absorption band at 410 nm. There is a blue-green window in the ∼450-500 nm range between the π → π* and W → π*(acridine) MLCT absorptions. The absorption spectrum of 2, dominated by intense π → π* absorptions, shows no distinct low energy MLCT band. Complex 1 is luminescent, displaying acridine-based ππ* fluorescence at 501 nm which is anti-Kasha as it is higher in energy than the lowest energy excited state.

Spectroscopic characterization of black N- and P-doped zeolite templated carbons

The incorporation of heteroatoms (X) into the zeolite-templated carbon (ZTC) structure is a widely used technique to tailor its properties for specific applications such as gas adsorption, methane and hydrogen storage, and catalysis. However, the literature lacks sufficient data on Fourier-transform infrared spectroscopy (FTIR) analysis of ZTCs due to the challenge in obtaining high-quality FTIR spectra required for accurate assignment of the C–X bands, primarily caused by the black mass effect. In this work we prepared nitrogen (N) and phosphorus (P) doped ZTC samples using FAU type zeolite as a template and furfuryl alcohol as a carbon precursor. The Raman results confirmed the presence of medium-sized aromatic structures and also showed that doping these structures with N and P leads to some defects, although the overall conformation remains structurally intact. The FTIR spectra of the ZTC materials were obtained by controlling the preparation procedure and humidity, enabling clear analysis of the black samples. A Density Functional Theory (DFT) model based on the dimeric buckybowl structure was developed and complemented by experimental results obtained from X-ray photoelectron spectroscopy (XPS), nuclear magnetic resonance (NMR), and FTIR. The proposed DFT model was then used for deconvolution and precise band assignment of the experimental FTIR spectra. The FTIR deconvolution study also supported the incorporation of N and P into the ZTC as well as the presence of primarily two types of nitrogen species, amide (primary and secondary) and pyridine-like, while P was mainly incorporated as triphenylphosphine oxide and phosphonic acid.

Assignment and modeling of 13CH4 spectrum at 298 K in the lower part of the Tetradecad in the 4970–5300 cm−1 range

The absorption spectrum of the 13CH4 methane isotopologue was recorded on a Bruker IFS-125HR Fourier transform spectrometer at 298 K in the 4970–6200 cm−1 range. In this paper we report the results of assignment and modelling of the line positions and intensities of 13CH4 in the range of weaker absorption between 4970 and 5300 cm−1, corresponding to the lower part of Tetradecad, dominated by the 4ν4 band system near 5180 cm−1. The empirical list in this spectral range contains 1642 lines. Using an effective Hamiltonian initially derived from the analyses of cold Fourier transform (4970–5853 cm−1) and laser direct absorption (5853–6200 cm−1) spectra of the 13CH4, we assigned 1600 lines belonging to four bands of the Tetradecad up to Jmax=16. The 1548 line positions were fitted with an rms deviation of 1.7 × 10−3 cm−1. Measured line intensities were modeled for 674 transitions using the effective dipole transition moments to an rms deviation of about 7 %. The new data were used for the simultaneous global fit of the 13CH4 Hamiltonian parameters for the {Ground state / Dyad / Pentad / Octad / Tetradecad} system and the dipole moment parameters for the {Ground state - Tetradecad} system.

Machine-learning-based impairment-aware dynamic RMSCA in multi-core elastic optical networks

This paper presents a routing, modulation, spectrum, and core assignment (RMSCA) algorithm for space-division-multiplexing-based elastic optical networks (SDM-EONs) comprising multi-core links. A network state-dependent route and core selection method is proposed using a deep neural network (DNN) classifier. The DNN is trained using a metaheuristic optimization algorithm to predict lightpath suitability, considering the quality of transmission and resource availability. Physical layer impairments, including inter-core crosstalk, amplified spontaneous emission, and Kerr fiber nonlinearities, are considered, and a random forest (RF)-based link noise estimator is proposed. A feature importance selection analysis is provided for all the features considered for the DNN classifier and the RF link noise estimator. The proposed machine-learning-enabled RMSCA approach is evaluated on three network topologies, USNET, NSFNET, and COST-239 with 7-core and 12-core fiber links. It is shown to be superior in terms of blocking probability, bandwidth blocking probability, and acceptable computational speed compared to the standard and published benchmarks at different traffic loads.

Physical layer-aware circuit reallocation to eons using make-before-break and push-pull techniques

This paper proposes a new circuit reallocation algorithm with make-before-break and push-pull techniques that considers the effects of physical layers in transparent elastic optical networks called Just One Circuit Reallocation (JOC). The JOC algorithm reallocates just one already established circuit to avoid blocking new circuit requests due to impairments in the physical layer. The results of the JOC algorithm were compared to three other algorithms: Circuit Reallocation Strategy - Physical Layer (CRS-PL), Circuit Reallocation for Block Reduction related to the QoT of the circuits (R-RQoT), and Make-Before- Break based defragmentation algorithm (MBBr). The reallocation algorithms are evaluated under the Bandwidth Blocking Probability (BBP), Circuit Blocking Probability (CBP), and the Number of reallocated circuits (N), external fragmentation, and percerntual of circuit by modulation for USA and EON topologies. Moreover, we also evaluated the performance of reallocation algorithms using complete sharing, K-shortest path computation, modified Dijkstra paths computation, and K-shortest path with reduction of QoTO to routing and spectrum assignment. Simulation results show that the proposed algorithm performs better than the CRS-PL, R-RQoT and MBBr algorithms regarding BBP, PBC, and N. Regarding BBP our algorithm presented minimum reductions of approximately 65.36% e 55.6% for the USA and EON topology, respectively.

PtrNet-RSA: A Pointer Network-Based QoT-Aware Routing and Spectrum Assignment Scheme in Elastic Optical Networks

PtrNet-RSA: A Pointer Network-Based QoT-Aware Routing and Spectrum Assignment Scheme in Elastic Optical Networks

Rotational spectra of ten new fluoroethylene/CO2 clusters, (C2H3F)x(CO2)y: Application of data-centered methods to the assignment of spectra in complex mixtures

Chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy has been used to measure the spectra of ten previously unobserved fluoroethylene (FE)/CO2 clusters, (FE)x(CO2)y, with x from 1 to 4 and y from 0 to 4. Multiple spectra were recorded with varying concentrations of CO2 in the sample, and at least 400,000 free induction decays averaged per data set. This allowed implementation of data-centered approaches, using intensity variation, to identify subsets of transitions belonging to the same cluster species or those of similar composition, simplifying the assignment process for the complex mixture of clusters present. All spectra were fitted to Watson A-reduction Hamiltonians, including quartic distortion constants, with very few species requiring higher order distortion constants for satisfactory fits to be obtained. Computational data at MP2/6-311++G(2d,2p) and ωB97X-D/6-31+G(d,p) levels suggested FE:CO2 ratios and likely structural arrangements of each cluster based on comparisons with experimental rotational constants.

Dynamic routing, spatial channel, and spectrum assignment in spatial channel networks based on a granularity switching threshold

Dynamic routing, spatial channel, and spectrum assignment in spatial channel networks based on a granularity switching threshold

On non-superperfection of edge intersection graphs of paths

The routing and spectrum assignment problem in modern flexgrid elastic optical networks asks for assigning to given demands a route in an optical network and a channel within an optical frequency spectrum so that the channels of two demands are disjoint whenever their routes share a link in the optical network. This problem can be modeled in two phases: firstly, a selection of paths in the network and, secondly, an interval coloring problem in the edge intersection graph of these paths. The interval chromatic number equals the smallest size of a spectrum such that a proper interval coloring is possible, the weighted clique number is a natural lower bound. Graphs where both parameters coincide for all possible non-negative integral weights are called superperfect. Therefore, the occurrence of non-superperfect edge intersection graphs of routing paths can provoke the need of larger spectral resources. In this work, we examine the question which minimal non-superperfect graphs can occur in the edge intersection graphs of routing paths in different underlying networks: when the network is a path, a tree, a cycle, or a sparse planar graph with small maximum degree. We show that for any possible network (even if it is restricted to a path) the resulting edge intersection graphs are not necessarily superperfect. We close with a discussion of possible consequences and of some lines of future research.

Symmetry-free routing and spectrum assignment: a universal algorithm based on first-fit

First-fit (FF) is a well-known and widely deployed algorithm for spectrum assignment (SA), but until our recent study [J. Opt. Commun. Netw. 14, 165 (2022)JOCNBB1943-062010.1364/JOCN.445492], investigations of the algorithm had been experimental in nature and no formal properties of the algorithm with respect to SA were known. In this work, we make two contributions. First, we show that FF is a universal algorithm for the SA problem in the sense that, for any variant, 1) it can be used to construct solutions equivalent to, or better than, any solution obtained by any other algorithm, and 2) it can construct an optimal solution. This universality property applies to both the min-max and min-frag objectives and to variants of the SA problem with or without guard band constraints. Consequently, the spectrum symmetry-free model of our recent study [J. Opt. Commun. Netw. 14, 165 (2022)JOCNBB1943-062010.1364/JOCN.445492] extends to all known SA variants, which therefore reduce to permutation problems. Second, we extend the spectrum symmetry-free model to the routing and spectrum assignment (RSA) problem in general topologies. This model allows for the design of more efficient algorithms as it eliminates from consideration an exponential number of equivalent symmetric solutions. By sidestepping symmetry, the RSA solution space is naturally and optimally decomposed into a routing space and a connection permutation space. Building upon this property, we introduce a two-parameter, symmetry-free universal algorithm that can be used to tackle any RSA variant in a uniform manner. The algorithm is amenable to multi-threaded execution to speed up the search process, and the value of the parameters can be adjusted to strike a balance between running time and solution quality. Our evaluation provides insight into the relative benefits of path diversity (which determines the size of the routing space) and connection diversity (which determines the size of the permutation space).

Enhanced Declustering Enables Native Top-Down Analysis of Membrane Protein Complexes using Ion-Mobility Time-Aligned Fragmentation.

Native mass spectrometry (MS) is proving to be a disruptive technique for studying the interactions of proteins, necessary for understanding the functional roles of these biomolecules. Recent research is expanding the application of native MS towards membrane proteins directly from isolated membrane preparations or from purified detergent micelles. The former results in complex spectra comprising several heterogeneous protein complexes; the latter enables therapeutic protein targets to be screened against multiplexed preparations of compound libraries. In both cases, the resulting spectra are increasingly complex to assign/interpret, and the key to these new directions of native MS research is the ability to perform native top-down analysis, which allows unambiguous peak assignment. To achieve this, detergent removal is necessary prior to MS analyzers, which allow selection of specific m/z values, representing the parent ion for downstream activation. Here, we describe a novel, enhanced declustering (ED) device installed into the first pumping region of a cyclic IMS-enabled mass spectrometry platform. The device enables declustering of ions prior to the quadrupole by imparting collisional activation through an oscillating electric field applied between two parallel plates. The positioning of the device enables liberation of membrane protein ions from detergent micelles. Quadrupole selection can now be utilized to isolate protein-ligand complexes, and downstream collision cells enable the dissociation and identification of binding partners. We demonstrate that ion mobility (IM) significantly aids in the assignment of top-down spectra, aligning fragments to their corresponding parent ions by means of IM drift time. Using this approach, we were able to confidently assign and identify a novel hit compound against PfMATE, obtained from multiplexed ligand libraries.

Multi-objective optimization of asymmetric bit rate partitioning for multipath protection in elastic optical networks

In survivable elastic optical networks, multi-path protection combined with traffic squeezing has gained attention. Link-disjoint multipath routing (LD-MPR) and bandwidth squeezing protection (BSP) when applied to the routing, modulation level and spectrum assignment problem are efficient strategies to address the excessive bandwidth demanded by protected services, spectral fragmentation and link-load balancing. LD-MPR enables the division of service transmission bit rate into independent flows, whereas BSP tolerates traffic reduction under link failure. An open issue in the literature is how to efficiently divide demanded traffic among the link-disjoint routes under dynamic-traffic and BSP, while complying the service level agreement (SLA). We propose in this paper a multi-objective-optimization genetic algorithm that defines how service transmission bit rate should be partitioned among the candidate link-disjoint routes. A customized partitioning definition is made for each source–destination node pair in the network, aiming the simultaneous minimization of network blocking probability and average squeezing transmission bit rate experienced by the services during single-link failure. We also propose, a fixed-alternate routing using groups of disjoint paths (FARgdp). Complex dynamic-traffic network scenarios that simultaneously consider BSP, LD-MPR and FARgdp are addressed.

PowerNovo: de novo peptide sequencing via tandem mass spectrometry using an ensemble of transformer and BERT models

The primary objective of analyzing the data obtained in a mass spectrometry-based proteomic experiment is peptide and protein identification, or correct assignment of the tandem mass spectrum to one amino acid sequence. Comparison of empirical fragment spectra with the theoretical predicted one or matching with the collected spectra library are commonly accepted strategies of proteins identification and defining of their amino acid sequences. Although these approaches are widely used and are appreciably efficient for the well-characterized model organisms or measured proteins, they cannot detect novel peptide sequences that have not been previously annotated or are rare. This study presents PowerNovo tool for de novo sequencing of proteins using tandem mass spectra acquired in a variety of types of mass analyzers and different fragmentation techniques. PowerNovo involves an ensemble of models for peptide sequencing: model for detecting regularities in tandem mass spectra, precursors, and fragment ions and a natural language processing model, which has a function of peptide sequence quality assessment and helps with reconstruction of noisy sequences. The results of testing showed that the performance of PowerNovo is comparable and even better than widely utilized PointNovo, DeepNovo, Casanovo, and Novor packages. Also, PowerNovo provides complete cycle of processing (pipeline) of mass spectrometry data and, along with predicting the peptide sequence, involves the peptide assembly and protein inference blocks.

MS-PyCloud: A Cloud Computing-Based Pipeline for Proteomic and Glycoproteomic Data Analyses.

Rapid development and wide adoption of mass spectrometry-based glycoproteomic technologies have empowered scientists to study proteins and protein glycosylation in complex samples on a large scale. This progress has also created unprecedented challenges for individual laboratories to store, manage, and analyze proteomic and glycoproteomic data, both in the cost for proprietary software and high-performance computing and in the long processing time that discourages on-the-fly changes of data processing settings required in explorative and discovery analysis. We developed an open-source, cloud computing-based pipeline, MS-PyCloud, with graphical user interface (GUI), for proteomic and glycoproteomic data analysis. The major components of this pipeline include data file integrity validation, MS/MS database search for spectral assignments to peptide sequences, false discovery rate estimation, protein inference, quantitation of global protein levels, and specific glycan-modified glycopeptides as well as other modification-specific peptides such as phosphorylation, acetylation, and ubiquitination. To ensure the transparency and reproducibility of data analysis, MS-PyCloud includes open-source software tools with comprehensive testing and versioning for spectrum assignments. Leveraging public cloud computing infrastructure via Amazon Web Services (AWS), MS-PyCloud scales seamlessly based on analysis demand to achieve fast and efficient performance. Application of the pipeline to the analysis of large-scale LC-MS/MS data sets demonstrated the effectiveness and high performance of MS-PyCloud. The software can be downloaded at https://github.com/huizhanglab-jhu/ms-pycloud.

Coupled internal rotations and 14N quadrupole hyperfine structure of 2,4-dimethylpyrrole investigated by microwave spectroscopy and quantum chemistry.

The microwave spectrum of 2,4-dimethylpyrrole was investigated using a Fourier-transform microwave spectrometer in a supersonic expansion. Torsional splittings arising from two inequivalent methyl internal rotors in combination with hyperfine splittings due to the nuclear quadrupole coupling of the 14N nucleus were observed. The experiments were accompanied by quantum chemical calculations. A total of 1561 rotational lines were assigned and fitted in global fits using the programs XIAM and BELGI-Cs-2Tops-hyperfine, both achieved the measurement accuracy of 4kHz. Local separate fits were also performed to verify the correctness of the assignment. Accurate experimental molecular and internal rotation parameters could be deduced and compared to the calculated ones. The barrier to internal rotation of the 2-methyl rotor was determined to be 277.830(26) cm-1, essentially the same as the value of about 280cm-1 found for 2-methylpyrrole but lower than the value of 317cm-1 found for 2,5-dimethylpyrrole. The torsional barrier value of the 4-methyl rotor is 262.210(27) cm-1, slightly higher than the value of 246cm-1 found for 3-methylpyrrole. Benchmarking the rotational constants for 2,4- and 2,5-dimethylpyrrole revealed that the MP2/6-31G(d,p) level could be helpful to guide the assignment of microwave spectra of pyrrole derivatives.

Enhancing the Efficiency of Resilient Multipath-Routed Elastic Optical Networks: A Novel Approach for Coexisting Protected and Unprotected Services with Idle Slot Reuse.

In this paper, we investigate a scenario in which protected and unprotected services coexist in an elastic optical network under dynamic traffic. In the investigated scenario, unprotected services can reuse the reserved idle bandwidth to provide protection to the protected services. Under this scenario, we propose a new heuristic algorithm that enables such reuse as well as define and introduce a new assignment problem in elastic optical networks, named a Transmission Spectrum Assignment (T-SA) problem. In this paper, we consider a scenario in which services may be routed using the multipath routing approach. Additionally, protection using bandwidth squeezing is also considered. We assess our proposal through simulations on three different network topologies and compare our proposal against the classical protection approach, in which bandwidth reuse is not allowed. For the simulated range of network loads, the maximum (minimum) blocking probability reduction obtained by our proposal is approximately 48% (10%) in the European topology, 46% (7%) in the NSFNET topology, and 32% (6%) in the German topology.

Investigation of infra-red spectra of three chiral liquid crystalline compounds with different fluorosubstitution of benzene ring

The IR spectra of three liquid crystalline compounds, differing only by the number of fluorine atoms in the molecular core, are investigated. The DFT+D3/BLYP-def2SVP calculations for isolated molecules are applied for the band assignments of the experimental IR spectra collected in the crystal phase. Additional DFT calculations, including the B3LYP exchange-correlation functional and def2TZVPP basis set, are also performed for the compound without the fluorine atoms in the molecular core. The scaling factors between the experimental and calculated peak positions, obtained at different levels of theory, are compared. For all compounds, the absorption bands assigned to the C=O stretching vibrations are analyzed as a function of temperature in the isotropic liquid, smectic phases, and crystal phase. The formation of hydrogen bonding involving the C=O groups during crystallization is inferred. The differences in the crystallization temperature of three compounds and the presence of the hexatic smectic phase for only one compound are discussed.