A prostate cancer tissue specific spectral library for targeted proteomic analysis.

Prostate cancer is the most common cancer in males worldwide. Mass spectrometry-based targeted proteomics has demonstrated great potential in quantifying proteins from formalin-fixed paraffin-embedded (FFPE) and (fresh) frozen biopsy tissues. Here we provide a comprehensive tissue-specific spectral library for targeted proteomic analysis of prostate tissue samples. Benign and malignant FFPE prostate tissue samples were processed into peptide samples by pressure cycling technology (PCT)-assisted sample preparation, and fractionated with high-pH reversed phase liquid chromatography (RPLC). Based on data-dependent acquisition (DDA) MS analysis using a TripleTOF 6600, we built a library containing 108,533 precursors, 84,198 peptides and 9384 unique proteins (1% FDR). The applicability of the library was demonstrated in prostate specimens.

Comparative Evaluation of Proteome Discoverer and FragPipe for the TMT-Based Proteome Quantification.

Isobaric labeling-based proteomics is widely applied in deep proteome quantification. Among the platforms for isobaric labeled proteomic data analysis, the commercial software Proteome Discoverer (PD) is widely used, incorporating the search engine CHIMERYS, while FragPipe (FP) is relatively new, free for noncommercial purposes, and integrates the engine MSFragger. Here, we compared PD and FP over three public proteomic data sets labeled using 6plex, 10plex, and 16plex tandem mass tags. Our results showed the protein abundances generated by the two software are highly correlated. PD quantified more proteins (10.02%, 15.44%, 8.19%) than FP with comparable NA ratios (0.00% vs. 0.00%, 0.85% vs. 0.38%, and 11.74% vs. 10.52%) in the three data sets. Using the 16plex data set, PD and FP outputs showed high consistency in quantifying technical replicates, batch effects, and functional enrichment in differentially expressed proteins. However, FP saved 93.93%, 96.65%, and 96.41% of processing time compared to PD for analyzing the three data sets, respectively. In conclusion, while PD is a well-maintained commercial software integrating various additional functions and can quantify more proteins, FP is freely available and achieves similar output with a shorter computational time. Our results will guide users in choosing the most suitable quantification software for their needs.

Developing the Low-Temperature Oxidation Mechanism of Cyclopentane: An Experimental and Theoretical Study.

At present, the reactivity of cyclic alkanes is estimated by comparison with acyclic hydrocarbons. Due to the difference in the structure of cycloalkanes and acycloalkanes, the thermodynamic data obtained by analogy are not applicable. In this study, a molecular beam sampling vacuum ultraviolet photoionization time-of-flight mass spectrometer (MB-VUV-PI-TOFMS) was applied to study the low-temperature oxidation of cyclopentane (CPT) at a total pressure range from 1-3 atm and low-temperature range between 500 and 800 K. Low-temperature reaction products including cyclic olefins, cyclic ethers, and highly oxygenated intermediates (e. g., ketohydroperoxide KHP, keto-dihydroperoxide KDHP, olefinic hydroperoxides OHP and ketone structure products) were observed. Further investigation of the oxidation of CPT - electronic structure calculations - were carried out at the UCCSD(T)-F12a/aug-cc-pVDZ//B3LYP/6-31+ G(d,p) level to explore the reactivity of O2 molecules adding sequentially to cyclopentyl radicals. Experimental and theoretical observations showed that the dominant product channel in the reaction of CPT radicals with O2 is HO2 elimination yielding cyclopentene. The pathways of second and third O2 addition - the dissociation of hydroperoxide - were further confirmed. The results of this study will develop the low-temperature oxidation mechanism of CPT, which can be used for future research on accurately simulating the combustion process of CPT.

Developing the Low-Temperature Oxidation Mechanism of Cyclopentane: An Experimental and Theoretical Study.

Invited for the cover of this issue are Zichao Tang and co-workers at Xiamen University, Yangtze University and the Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences. The image depicts molecular beam sampling vacuum ultraviolet photoionization time-of-flight mass spectrometer (MB-VUV-PI-TOFMS) as an advanced analytical tool for detecting highly oxygen intermediates in the low temperature oxidation of fuels. Read the full text of the article at 10.1002/chem.202103546.

Development of a miniature time-of-flight mass spectrometer coupled with an improved substrate-enhanced laser-induced acoustic desorption source (SE-LIAD/TOF-MS).

A novel, compact and sensitive SE-LIAD/TOF-MS has been described. It facilitates fast sample preparation, and a full mass spectrum is acquired efficiently and sensitively. More importantly, it features the detection of non-acidic and non-basic or non-polar species, which is not suitable for determination by ESI and MALDI techniques. In this technique, standard samples, carbazole and melamine, are prepared on a Ti foil with a quartz plate attached to the backside of the Ti foil to perform a laser-induced acoustic desorption experiment (SE-LIAD) coupled to TOF-MS for analysis. Enhanced signals are observed with about 5.6 to 13.8 times higher than that obtained in the standard LIAD method, dependent on different ionization techniques. Compared to the EI spectra, the PI spectra for both species show intact and sharp molecular peaks. The limits of detection (LOD) of melamine were evaluated experimentally in the range from ∼2-6 pg (EI/MS mode) to ∼0.3-0.5 ng (VUV-SPI/MS mode). Thus, the method in this study exhibits rapid qualitative and quantitative analysis with good sensitivity, being free of the complex matrix influences.

Aromaticity Criterion Is Not the Only Factor to Decide the Ring Stability of Boron Oxide Families: c-M2O2-/0 Clusters (M = B, Al, Ga, and In).

Generally, compared to conjugated chain molecules, aromaticity provides additional stability for the cyclic, planar, and conjugated molecules. Thus, the concept of aromaticity was undeniably utilized to explain the unique stability for extensive cyclic molecules (notably for benzene, recently reported boron rings, and all-metal multiply aromatic Al42- salts) to guide chemical syntheses. However, can aromaticity alone describe the stability for all of those cyclic and planar clusters or molecules? In this regard, we observed the four-membered prototypical rings: c-M2O2-/0 clusters (M = B, Al, Ga, and In) possessing unique rhombic (four-center, four-electron) π and σ o-bonds, which are considered to have 3-fold aromaticity. Moreover, we not only elucidated the key role of ring strain energy (RSE) to determine the stability of these rings but also unexpectedly revealed that the electrostatic interaction (ionicity) plays a fundamental role in the stability of Al2O2-/0 clusters through systematically experimental and theoretical investigations into the isolated M2O2-/0 clusters (M = B, Al, Ga, and In). Detailed geometries, molecular orbital, and chemical bonding nature were analyzed to unravel those influences. This work provides a clue in which RSE and the electrostatic effect should be carefully taken into account for the stability of diverse cyclic clusters or molecules compared to the expected stability factor from aromaticity.

Probing the geometric and electronic structures of the transition metal oxides RhOn-1/0 (n = 1-4) clusters.

The photoelectron spectroscopies of RhOn- (n = 1-2) were obtained via using the photoelectron velocity-map imaging (PE-VMI) approach. The experimental values of the adiabatic detachment energy (ADE) and vertical detachment energy (VDE) for RhO- were reported to be 1.58 ± 0.02 eV. The experimental AED and VDE values of RhO2- were reported to be 2.70 ± 0.02 eV and 2.79 ± 0.02 eV, respectively. The vibrational frequencies of RhO- and RhO2- measured from photoelectron spectra (PES) were 817(76) cm-1 and 932(55) cm-1, respectively. Based on the density functional theory (DFT), the RhOn-1/0 (n = 1-4) clusters were investigated. The optimized configurations of corresponding ground states and low-lying clusters were discovered. Meanwhile, the simulated photoelectron spectroscopy (PES) of RhOn- (n = 1-4) and the theoretical ADE and VDE values of RhOn- (n = 1-4) clusters were unveiled to assist future experimental studies of Rhodium oxide clusters. Moreover, the associated molecular orbitals (MOs), natural population analysis (NPA) and bond order analysis have been utilized to investigate the chemical bonding in these groups.

Pulmonary and renal long COVID at two-year revisit.

This study investigated host responses to long COVID by following up with 89 of the original 144 cohorts for 1-year (N = 73) and 2-year visits (N = 57). Pulmonary long COVID, characterized by fibrous stripes, was observed in 8.7% and 17.8% of patients at the 1-year and 2-year revisits, respectively, while renal long COVID was present in 15.2% and 23.9% of patients, respectively. Pulmonary and renal long COVID at 1-year revisit was predicted using a machine learning model based on clinical and multi-omics data collected during the first month of the disease with an accuracy of 87.5%. Proteomics revealed that lung fibrous stripes were associated with consistent down-regulation of surfactant-associated protein B in the sera, while renal long COVID could be linked to the inhibition of urinary protein expression. This study provides a longitudinal view of the clinical and molecular landscape of COVID-19 and presents a predictive model for pulmonary and renal long COVID.

Bulk synthesis of monodisperse magnetic FeNi3 nanopowders by flow levitation method.

In this work, a novel bulk synthesis method for monodisperse FeNi3 nanoparticles was developed by flow levitation method (FL). The Fe and Ni vapours ascending from the high temperature levitated droplet was condensed by cryogenic Ar gas under atmospheric pressure. X-ray diffraction was used to identify and characterize the crystal phase of prepared powders exhibiting a FeNi3 phase. The morphology and size of nanopowders were observed by transmission electron microscopy (TEM). The chemical composition of the nanoparticles was determined with energy dispersive spectrometer (EDS). The results indicated that the FeNi3 permalloy powders are nearly spherical-shaped with diameter about 50-200 nm. Measurement of the magnetic property of nanopowders by a superconducting quantum interference device (SQUID, Quantum Design MPMS-7) showed a symmetric hysteresis loop of ferromagnetic behavior with coercivity of 220 Oe and saturation magnetization of 107.17 emu/g, at 293 K. At 5 K, the obtained saturation magnetization of the sample was 102.16 emu/g. The production rate of FeNi3 nanoparticles was estimated to be about 6 g/h. This method has great potential in mass production of FeNi3 nannoparticles.

[Study of density functional theory for surface-enhanced Raman spectra of furfural].

In the present paper, DFT method at the B3LYP/6-31+G* * (C, H, O)/LANL2DZ(Ag) level was used to optimize molecular configurations of furfural. Based on the optimized structure, the normal Raman spectrum (NRS) of FUR and the surface-enhanced Raman spectrum (SERS) of FUR adsorbed on Ag, Ag2 and Ag4 were all calculated, which were compared with the experimental values. The calculation results indicated that a good conformity was found between the computed and the experimental results. The results of furfural adsorbed on Ag4 were more approximate to the ever reported experimental date than those of furfural adsorbed on Ag and Ag2. At the end, detailed analysis of the Raman spectrum and more comprehensive assignments of the vibration mode for furfural were studied by the software of GaussView. The data of the SERS by comparing with the one of NRS show that furfural molecule and Ag atoms interact with each other. And we suppose that the molecular plane with the ring of adsorbed furfural molecule is vertically orientated to the silver surface. The work in this paper offers a theory evidence for detection and trace analysis of drinks containing furfural.

[Surface-enhanced raman spectra of thymine calculated by DFT and ab inition HF].

In the present paper, B3LYP (Becke's three-parameter hybrid method with the Lee, Yang, and Parr gradient corrected correlation functional) and HF (Hartree-Fock) methods at 6-31+G* * (C, H, N, O)/LANL2DZ(Ag) level were used to optimize molecular configurations of thymine. Base on the optimized structure, the normal Raman spectrum (NRS) of thymine and the surface-enhanced Raman spectrum (SERS) of thymine adsorbed on Ag and Ag2 were calculated, which were compared with the experimental values. The calculation results indicated that the result of the DFT for NRS was more approximate to the ever reported experimental date than those of HF results. A better conformity of SERS was found between the HF computed and the experimental results. At the end, detailed analysis of the Raman spectrum and more comprehensive assignments of the vibration mode for thymine were studied by the software of GaussView.

[Theoretical study of the influence of different substituents on the electron-photon spectra of quinoline].

Different substituents result in different changes in electron-photon spectra, and to reveal the relationship between substituents and spectra, a theoretical investigation was elaborated via quantum chemical calculations. Density functional theory and single excitation configuration interaction were respectively employed in optimizing geometric and electronic structures of ground and excited states, and the absorption and emission spectra were studied by time-dependent density functional theory methods. The results show that all the different substituents bring on different geometric and electronic structures of ground and excited states, different energies of frontier molecular orbitals as well as different pi-conjugated systems, the spectra change with all the differences, and relationships are brought out in this paper, which gives theoretical reference for identifying different derivatives from electron-photon spectra.

Multiband-switchability and high-absorptivity of a metamaterial perfect absorber based on a plasmonic resonant structure in the near-infrared region.

Metamaterials are widely studied in bio-photonics because of their flexible and tunable resonance wavelengths in the near-infrared region and their particular relevance to biological tissues. In this paper, we propose for the first time a perfect absorber that is switchable between triple-band and dual-band absorption. The narrowband metamaterial perfect absorber has a conventional metal-dielectric-metal structure, which consists of an array of silver disks, a silica dielectric layer and a gold substrate. Its working performance is mainly determined by the height, radius and period of the top silver disks. By adjusting these parameters, the perfect absorber can be switched between triple-band and dual-band absorption with the peaks showing close to 100% absorbance. This makes it possible to use it as a multifunctional absorber in various applications, such as filters and sensors.

Identification of key pharmacodynamic markers of American ginseng against heart failure based on metabolomics and zebrafish model.

Background: American ginseng (Panax quinquefolium L., AG) is a traditional Chinese medicine with multiple cardiovascular protective properties. Many bioactive components have been discovered in AG over these years. However, the understanding of these key pharmacodynamic components of activity against heart failure is insufficient. Methods: A heart failure model was established using AB line wild-type zebrafish (Danio rerio) to evaluate the anti-heart failure activity of AG. Untargeted metabolomics analysis based on ultra-high performance liquid chromatography-quadrupole electrostatic field orbitrap-mass spectrometry technology (UHPLC-QE-Orbitrap-MS) was performed to screen differential components from AG samples. The potential active components were verified using the zebrafish model. Simultaneously, network pharmacology and molecular docking techniques were used to predict the possible mechanism. Finally, the key targets of six key pharmacodynamic components were verified in zebrafish using quantitative real-time-polymerase chain reaction (Q-PCR) techniques. Results: The heart failure model was successfully established in 48 h of post-fertilization (hpf) zebrafish larvae by treating with verapamil hydrochloride. The zebrafish assay showed that the anti-heart failure effects of AG varied with producing regions. The result of the herbal metabolomic analysis based on UHPLC-QE-Orbitrap-MS indicated that ginsenoside Rg3, ginsenoside Rg5, ginsenoside Rg6, malic acid, quinic acid, L-argininosuccinic acid, 3-methyl-3-butenyl-apinosyl (1→6) glucoside, pseudoginsenoside F11, and annonaine were differential components, which might be responsible for variation in efficacy. Further analysis using zebrafish models, network pharmacology, and Q-PCR techniques showed that ginsenoside Rg3, ginsenoside Rg5, ginsenoside Rg6, malic acid, quinic acid, and pseudoginsenoside F11 were the pharmacodynamic markers (P-markers) responsible for anti-heart failure. Conclusion: We have rapidly identified the P-markers against heart failure in AG using the zebrafish model and metabolomics technology. These P-markers may provide new reference standards for quality control and new drug development of AG.

[Study of density functional theory for surface-enhanced Raman spectra of p-aminothiophenol].

In the present paper, DFT method at the B3LYP/6-31++G** (C, H, N, S)/LANL2DZ(Ag) level was used to optimize molecular configurations of p-aminothiophenol. Based on the optimized structure, the normal Raman scattering (NRS) spectrum of PATP and the surface-enhanced Raman scattering(SERS) spectrum of PATP adsorbed on Ag and Ag2 were both calculated, and were compared with the results of other literatures values. The calculation results indicated that a good conformity was found between the computed and experimental results. The results of PATP adsorbed on Ag2 were more approximate to the ever reported experimental data than those of PATP adsorbed on Ag. At the end, detailed analysis of the Raman spectrum and more comprehensive assignments of the vibration mode for p-aminothiophenol were studied by the software of GaussView. In comparison with SERS spectrum and NRS spectrum of PATP molecule, the authors observed the stretching vibration bands in the SERS spectrum at about 213 cm(-1), which is due to Ag-S stretching vibration mode. The work in this paper has greatly directive value in understanding and explaining some experiment phenomenon, and helps to study the mechanism of surface-enhanced Raman scattering of PATP.

An Integrated Strategy for Rapid Discovery and Identification of Quality Markers in Gardenia Fructus Using an Omics Discrimination-Grey Correlation-Biological Verification Method.

Background: Gardenia Fructus (GF), a traditional Chinese medicine of Gardenia Ellis in Rubiaceae family, has the potential to clear heat and purge fire and has been widely used to treat multiple infection-related diseases. However, the quality markers (Q-Markers) of GF have not been revealed comprehensively. Methods: In this experiment, the transgenic zebrafish lines, Tg (l-fabp:EGFP) and Tg (lyz:EGFP), were used to evaluate two main kinds of traditional efficacies of GF, hepatoprotective and anti-inflammatory effects. All the GF samples from different production areas were tested their anti-liver injury and anti-inflammantory activities. High-performance liquid chromatography-quadrupole time-of-flight mass spectrometry method (HPLC-Q-TOF/MS) was employed for herbal metabonomic analysis of GF samples. Gray correlation analysis (GCA) was utilized to screen out the components closely associated with the activities. Finally, the zebrafish model was applied to verify the bioactivity of the crucial components to determine the Q-Markers of GF. Results: The zebrafish models were established by inducing with hydrogen peroxide or copper sulfate and applied to quickly evaluate the hepatoprotective effect and inflammation of GF samples. 27 potentially active components for liver protection and 21 potentially active components with anti-inflammatory properties were identified by herbal metabolomic analysis based on HPLC-Q-TOF/MS. The GCA result showed that five of the 27 components were highly correlated with liver protection, 15 of the 21 components were highly correlated with anti-inflammatory activity. Among them, geniposide and crocin-1 were confirmed their bioactivities on zebrafish experiment to be responsible for the protective effects of GF against liver injury, and genipin-1-ß-D-gentiobioside, quinic acid, gardenoside, d-glucuronic acid, l-malic acid, mannitol, rutin, and chlorogenic acid were confirmed to be responsible for the anti-inflammatory effects. Finally, according to the screening principles of Q-Markers, genipin-1-ß-D-gentiobioside, geniposide, and gardenoside were preliminarily identified to be the Q-Markers of GF. Conclusion: This study established an effective research strategy of "Omics Discrimination-Grey Correlation-Biological Verification," which enabled the rapid identification of key pharmacological components of GF. These markers have provided a scientific basis for constructing a modern quality evaluation system for GF.

Deciphering the Superatomic Behavior of Group V Metal Monoxides.

The valence orbitals of Group V metal monoxides exhibit atomic-like properties which mimic that of coinage metal element atoms. The electronic structures of MO-1/0 (M = V, Nb, and Ta) have been determined by negative ion photoelectron velocity map imaging. Electron affinities and vibrational frequencies for the ground state and excited states of MO (M = V, Nb, and Ta) molecules have been identified as well as photoelectron angular distributions. On the basis of the equivalent-electron principle, MO- (M = V, Nb, and Ta) molecules bear valence electron configurations similar to those of coinage metal elemental atoms, despite having more complicated electronic states for molecules, and concomitant mimicry of magnetic superatom. Generally, other than low-spin states of coinage metal atoms, Group V metal monoxides demonstrate a high-spin state except for TaO, possessing the potential applications to inexpensive superatoms in industrial catalysis.

Theoretical investigation of the low lying electronic states of MgGa.

In this work, we investigate the low-lying electronic states correlated to the first and the second dissociation channels of MgGa molecule, neglecting and including the spin-orbit coupling effect. High-level ab initio calculations have been performed by using the icMRCI + Q method. Potential energy curves, spectroscopic constants, electron configurations and dipole moments are derived and discussed. Molecular structures of several magnesium-group 13 diatomics have been probed and analyzed. Information associated with transition dipole moments, Franck-Condon factors, vibrational branching ratios and radiative lifetimes between the Ω states are also well characterized. It is anticipated this work will provide some inspiration for further studies on MgGa.

Probing the geometric and electronic structures of the lanthanide oxide HoOn-1/0 (n = 1-3) clusters.

The complex 4f and 5d orbits of lanthanide oxide clusters increases the complexity and difficulty in both theoretical and experimental research. Combining the photoelectron imaging spectroscopy and ab initio calculations, the structural and electronic properties of HoO- were studied. The adiabatic detachment energy (ADE) and vertical detachment energy (VDE) of HoO- have been measured to be 1.31(3) eV and 1.42(2) eV, respectively. To determine the vibrational structure and observed spectral bands in the photoelectron spectrum, Franck-Condon simulation of the ground-state transition for HoO- has been performed. The fundamental frequency of ground-state HoO is estimated to be 893 ± 73 cm-1. Density functional method (DFT) was used to study the neutral and anionic clusters of HoOn-1/0 (n = 1-3), and the most stable cluster structures were obtained. Based on the DFT calculations, the theoretical ADEs and VDEs of anionic HoOn- (n = 1-3) clusters were obtained and the photoelectron spectra (PES) of HoOn- (n = 1-3) clusters were simulated, which might stimulate further experimental investigations on the Ho oxide clusters. In addition, the corresponding molecular orbitals (MOs) were also discussed to reveal the interaction between Ho and O atoms. This study can help us to understand the chemical bonding in Ho-containing molecules and will provide some light in their surface chemistry and photochemistry investigation.

The photoelectron-imaging spectroscopic study and chemical bonding analysis of VO2 -, NbO2 - and TaO2.

The transition-metal di-oxides, namely VO2 -, NbO2 - and TaO2 - have been studied using photoelectron velocity map imaging (PE-VMI) in combination with theoretical calculations. The adiabatic electron affinities of VO2 -, NbO2 - and TaO2 - are confirmed to be 2.029(8), 1.901(10) and 2.415(8) eV, respectively. By combining Franck-Condon (FC) simulation with theoretical calculations, the vibrational feature related to Nb-O and Ta-O stretching modes for the ground state has been unveiled. The photoelectron angular distribution (PAD) for VO2 -, NbO2 - and TaO2 - is correlated to the photo-detachment of the highest occupied molecular orbitals (HOMOs), which primarily gets involved in s- and d-orbitals of the V, Nb and Ta atoms. A variety of theoretical calculations have been used to analyze the chemical bonding features of VO2 -1/0, NbO2 -1/0 and TaO2 -1/0, which show that the strong M-O (M = V, Nb and Ta) bond is mainly characterized as ionicity.