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Electrochemical reactions are better understood by gaining insight into the molecular transformations at the electrodes. This paper introduces a straightforward experimental arrangement in which the voltammetry experiment in a standard electrochemical cell integrates with online electrospray‐ionization mass‐spectrometry. The procedure allows for monitoring of the ions produced at the working electrode. The ionic species sampling is facilitated by a silica capillary embedded in the working electrode and connected directly to the electrospray ionization source. This integration configures real‐time monitoring of the ions produced at the working electrode, enhancing our knowledge of the electrochemical process. The methodology is thoroughly described and exemplified by monitoring the reactive intermediates and products that arise during the electrochemical oxidation of carbazole. This design provides an opportunity to study intermediates in electrochemical reactions with advanced mass spectrometry methods such as ion mobility separation or ion spectroscopy. [ABSTRACT FROM AUTHOR]

Purpose: The management of blepharitis continues to challenge clinicians due to the poorly understood aetiology of the condition. We recently identified the family of intracellular plakin proteins as essential driving forces underlying anterior blepharitis. A large‐scale protein analysis was used to study if a topical dexamethasone/tobramycin solution could be used to reverse the expression of plakin proteins. Methods: Tear film samples from treatment naïve patients with anterior blepharitis (n = 15) were collected with Schirmer filtration paper. A subgroup of the patients (n = 10) received treatment with a dexamethasone/tobramycin 1 + 3 mg/mL ophthalmic suspension (Tobradex®) for 3 weeks and collection of tear film samples was repeated. The samples were analysed with label‐free quantification nano liquid chromatography–tandem mass spectrometry requiring quantification in at least 70% of the samples in each group. Proteins were considered differentially expressed if p < 0.05. Results: Following Tobradex® intervention, 27 proteins were upregulated while 61 proteins were downregulated. Regulated proteins after Tobradex® treatment were involved in intermediate filament cytoskeleton organization including downregulation of the plakin proteins envoplakin, epiplakin and periplakin. Plectin, a protein of the plakin family, remained unchanged after Tobradex® therapy. Tobradex® treatment resulted in the regulation of proteins involved in translation including a cluster of downregulated ribosomal proteins. Tobradex® intervention was associated with the regulation of proteins involved in fructose metabolism and glycolytic processes including fructose‐1.6‐bisphosphatase 1, fructose‐bisphosphate aldolases A and B, pyruvate kinase PKM and transketolase. Ig lambda chain V‐I region, prominin‐1, and protein Niban were upregulated after Tobradex® treatment. Conclusions: Tobradex treatment reversed the expression of plakin proteins in anterior blepharitis. Topical solutions which inhibit the expression of plakin proteins may have the potential to restore the ocular surface integrity in anterior blepharitis and should be explored further. [ABSTRACT FROM AUTHOR]

Interface phenomena refer to the phenomena caused by various physical and chemical processes occurring at phase interfaces. These phenomena can include adhesion, friction, lubrication, evaporation, condensation, adsorption, monolayer formation, and other phenomena and are applied in many fields, such as food, papermaking, rubber, material science, energy, and biomedicine. However, traditional detection equipment cannot meet the interface phenomena observation needs because the information detected by techniques such as electrochemistry, spectroscopy, chromatography, and mass spectrometry is limited, as are the sensitivity and minimum detection limit. Surface plasmon resonance (SPR) combined technology is a powerful tool for investigating interface phenomena. This paper reviews all combination technologies of SPR with various conventional detection systems, emphasizing the combination with electrochemistry, Raman spectroscopy, and mass spectrometry. These technologies can observe interface phenomena through SPR and provide redox, molecular structure, functional group change, and other information. Through this information, the reactions on the interface can be made clearer and more controllable, which plays an important role in practical detection. In the future, SPR combined technology will mainly develop toward signal enhancement, light source coupling mode, and sensor chip design, and SPR will be combined with various detection technologies to achieve real‐time in situ detection of interface phenomena. [ABSTRACT FROM AUTHOR]

Background: Salivary diagnostics and their utility as a nonaggressive approach for breast cancer diagnosis have been extensively studied in recent years. This meta‐analysis assesses the diagnostic value of salivary biomarkers in differentiating between patients with breast cancer and controls. Methods: We conducted a meta‐analysis and systematic review of studies related to salivary diagnostics published in PubMed, EMBASE, Scopus, Ovid, Science Direct, Web of Science (WOS), and Google Scholar. The articles were chosen utilizing inclusion and exclusion criteria, as well as assessing their quality. Specificity and sensitivity, along with negative and positive likelihood ratios (NLR and PLR) and diagnostic odds ratio (DOR), were calculated based on random‐ or fixed‐effects model. Area under the curve (AUC) and summary receiver‐operating characteristic (SROC) were plotted and evaluated, and Fagan's Nomogram was evaluated for clinical utility. Results: Our systematic review and meta‐analysis included 14 papers containing 121 study units with 8639 adult subjects (4149 breast cancer patients and 4490 controls without cancer). The pooled specificity and sensitivity were 0.727 (95% CI: 0.713–0.740) and 0.717 (95% CI: 0.703–0.730), respectively. The pooled NLR and PLR were 0.396 (95% CI: 0.364–0.432) and 2.597 (95% CI: 2.389–2.824), respectively. The pooled DOR was 7.837 (95% CI: 6.624–9.277), with the AUC equal to 0.801. The Fagan's nomogram showed post‐test probabilities of 28% and 72% for negative and positive outcomes, respectively. We also conducted subgroup analyses to determine specificity, sensitivity, DOR, PLR, and NLR based on the mean age of patients (≤52 or >52 years old), saliva type (stimulated and unstimulated saliva), biomarker measurement method (mass spectrometry [MS] and non‐MS measurement methods), sample size (≤55 or >55), biomarker type (proteomics, metabolomics, transcriptomics and proteomics, and reagent‐free biophotonic), and nations. Conclusion: Saliva, as a noninvasive biomarker, has the potential to accurately differentiate breast cancer patients from healthy controls. [ABSTRACT FROM AUTHOR]

Citron essential oil contains numerous health‐beneficial components, however, with relatively low level in plants. In this paper, the components and physicochemical properties of finger citron essential oil extract (FEOE) obtained by a novel continuous phase‐transition extraction (CPE) were investigated and compared with those achieved by supercritical fluid extraction (SFE). Results indicated that CPE‐derived FEOE significantly increased by 12% in yield compared to SFE‐derived FEOE. Gas chromatograph ‐ mass spectrometry (GC–MS) analysis showed that FEOE extracted by both methods contained acids, esters, olefins, and alcohols. However, aromatics and heterocycles were only found in CPE‐derived FEOE. Moreover, the relative contents of acids and esters in CPE‐derived FEOEdecreased in comparison with those in SFE‐derived FEOE. On the other hand, the relative contents of olefins, alcohols, aromatic, and heterocycle compounds increased, suggesting a rich and multi‐layered fragrance with plentiful characteristic aroma substances in CPE‐derived FEOE. In addition, FEOE extracted by CPE maintained strong antioxidant activity in a dose‐dependent manner. Together, our results demonstrated that CPE could be a promising technology for essential oil extraction. [ABSTRACT FROM AUTHOR]

Invited for this month's cover is the group of Jana Roithová at the Radboud University (The Netherlands). The cover picture shows a mini‐plant for automated monitoring of chemical reactions. Flow chemistry enables screening of chemical reactions under well‐defined conditions that can systematically vary. Mass spectrometry couples it with the detection of low abundant reaction intermediates. Therefore, this platform allows tracking reaction pathways, monitoring reaction kinetics of intermediates and is set for a discovery of novel chemical transformations in future. Read the full text of their Full Paper at 10.1002/cmtd.202100046. [ABSTRACT FROM AUTHOR]

High‐resolution mass spectrometry (HRMS) has become a vital tool for dissolved organic matter (DOM) characterization. The upward trend in HRMS analysis of DOM presents challenges in data comparison and interpretation among laboratories operating instruments with differing performance and user operating conditions. It is therefore essential that the community establishes metric ranges and compositional trends for data comparison with reference samples so that data can be robustly compared among research groups. To this end, four identically prepared DOM samples were each measured by 16 laboratories, using 17 commercially purchased instruments, using positive‐ion and negative‐ion mode electrospray ionization (ESI) HRMS analyses. The instruments identified ~1000 common ions in both negative‐ and positive‐ion modes over a wide range of m/z values and chemical space, as determined by van Krevelen diagrams. Calculated metrics of abundance‐weighted average indices (H/C, O/C, aromaticity, and m/z) of the commonly detected ions showed that hydrogen saturation and aromaticity were consistent for each reference sample across the instruments, while average mass and oxygenation were more affected by differences in instrument type and settings. In this paper we present 32 metric values for future benchmarking. The metric values were obtained for the four different parameters from four samples in two ionization modes and can be used in future work to evaluate the performance of HRMS instruments. [ABSTRACT FROM AUTHOR]

In this special interview series, we profile members of The FEBS Journal editorial board to highlight their research and perspectives on the journal and more. Albert Heck is Professor of Chemistry and Pharmaceutical Sciences at Utrecht University, Scientific Director of the Netherlands Proteomics Center, and Head of the Biomolecular Mass Spectrometry and Proteomics group in Utrecht University since September 1998. He has served as Editorial Board Member of The FEBS Journal since 2020. [ABSTRACT FROM AUTHOR]

Protein copy numbers constrain systems-level properties of regulatory networks, but proportional proteomic data remain scarce compared to RNA-seq. We related mRNA to protein statistically using best-available data from quantitative proteomics and transcriptomics for 4366 genes in 369 cell lines. The approach starts with a protein's median copy number and hierarchically appends mRNA–protein and mRNA–mRNA dependencies to define an optimal gene-specific model linking mRNAs to protein. For dozens of cell lines and primary samples, these protein inferences from mRNA outmatch stringent null models, a count-based protein-abundance repository, empirical mRNA-to-protein ratios, and a proteogenomic DREAM challenge winner. The optimal mRNA-to-protein relationships capture biological processes along with hundreds of known protein-protein complexes, suggesting mechanistic relationships. We use the method to identify a viral-receptor abundance threshold for coxsackievirus B3 susceptibility from 1489 systems-biology infection models parameterized by protein inference. When applied to 796 RNA-seq profiles of breast cancer, inferred copy-number estimates collectively re-classify 26–29% of luminal tumors. By adopting a gene-centered perspective of mRNA–protein covariation across different biological contexts, we achieve accuracies comparable to the technical reproducibility of contemporary proteomics. Synopsis: A simple, data-driven method links transcript abundance from RNA-seq to per-cell protein abundance from mass spectrometry. Pinferna outperforms existing approaches, accurately parameterizes systems biology models, and reclassifies tumor subtypes. Pinferna uses three quantitative formalisms that capture measured RNA-protein relationships for 4366 human genes in 369 cancer cell lines. Pinferna consistently yields a more accurate inferred proteome than random sampling of existing proteomes. Using Pinferna-derived initial conditions, a systems-biology model correctly predicts a viral-receptor abundance threshold for infectability. Pinferna reclusters canonical subtypes of breast cancer and predicts new abundance dependencies for a cyclin-dependent kinase that are experimentally validated. A simple, data-driven method links transcript abundance from RNA-seq to per-cell protein abundance from mass spectrometry. Pinferna outperforms existing approaches, accurately parameterizes systems biology models, and reclassifies tumor subtypes. [ABSTRACT FROM AUTHOR]

Multifaceted interrogation of the proteome deepens the system‐wide understanding of biological systems; however, mapping the redox changes in the proteome has so far been significantly more challenging than expression and solubility/stability analyses. Here, the first high‐throughput redox proteomics approach integrated with expression analysis (REX) is devised and combined with the Proteome Integral Solubility Alteration (PISA) assay. The whole PISA‐REX experiment with up to four biological replicates can be multiplexed into a single tandem mass tag TMTpro set. For benchmarking this compact tool, HCT116 cells treated with auranofin are analyzed, showing great improvement compared with previous studies. PISA‐REX is then applied to study proteome remodeling upon stimulation of human monocytes by interferon α (IFN‐α). Applying this tool to study the proteome changes in plasmacytoid dendritic cells (pDCs) isolated from wild‐type versus Ncf1‐mutant mice treated with interferon α, shows that NCF1 deficiency enhances the STAT1 pathway and modulates the expression, solubility, and redox state of interferon‐induced proteins. Providing comprehensive multifaceted information on the proteome, the compact PISA‐REX has the potential to become an industry standard in proteomics and to open new windows into the biology of health and disease. [ABSTRACT FROM AUTHOR]

As a plant classified under the "medicine food homology" concept, garlic offers various health benefits and comes in many different varieties. In this study, the metabolite composition of different garlic varieties were analyzed using LC–MS/MS quadrupole‐Orbitrap mass spectrometry and ICP‐MS. A total of 30 chemical elements and 1256 metabolites were identified. Significant differences in chemical elements and metabolomics profiles were observed among the five garlic groups (VIP > 1.5). Compared to WG, PG contained 5 unique compounds, HG had 15 unique compounds, SCG had 18 unique compounds, and SBG had 26 unique compounds. Furthermore, the results showed that WG had smaller differences with PG and HG, but significant differences with SBG and SCG. KEGG analysis revealed metabolic pathways associated with the formation of differential metabolites. These findings uncover the differences and mechanisms in the composition of various garlic varieties, providing a theoretical foundation for distinguishing the nutritional components of different garlic types. [ABSTRACT FROM AUTHOR]

Glycoproteins, representing a significant proportion of posttranslational products, play pivotal roles in various biological processes, such as signal transduction and immune response. Abnormal glycosylation may lead to structural and functional changes of glycoprotein, which is closely related to the occurrence and development of various diseases. Consequently, exploring protein glycosylation can shed light on the mechanisms behind disease manifestation and pave the way for innovative diagnostic and therapeutic strategies. Nonetheless, the study of clinical glycoproteomics is fraught with challenges due to the low abundance and intricate structures of glycosylation. Recent advancements in mass spectrometry‐based clinical glycoproteomics have improved our ability to identify abnormal glycoproteins in clinical samples. In this review, we aim to provide a comprehensive overview of the foundational principles and recent advancements in clinical glycoproteomic methodologies and applications. Furthermore, we discussed the typical characteristics, underlying functions, and mechanisms of glycoproteins in various diseases, such as brain diseases, cardiovascular diseases, cancers, kidney diseases, and metabolic diseases. Additionally, we highlighted potential avenues for future development in clinical glycoproteomics. These insights provided in this review will enhance the comprehension of clinical glycoproteomic methods and diseases and promote the elucidation of pathogenesis and the discovery of novel diagnostic biomarkers and therapeutic targets. [ABSTRACT FROM AUTHOR]

Rationale: Quinolone antibiotics are extensively used clinically for human treatment and in agriculture. However, improper and excessive use can lead to the persistence of quinolone residues in animal tissues, potentially accumulating in the human body and posing health risks. Investigating the correlation between mass spectrometry cleavage patterns and molecular structural features enhances the analytical framework for detecting trace or unknown impurities in quinolones. Methods: To collect data, we employed triple quadrupole linear ion trap mass spectrometry in electrospray positive ion mode. Primary mass spectrometry scanning was utilized to confirm parent ions, while secondary mass spectrometry scanning enabled the observation of fragment ions. The cleavage characteristics and pathways of the compounds were inferred from accurate mass‐to‐charge ratios obtained from both primary and secondary mass spectrometry. Results: Under soft ionization conditions, the compounds generally exhibited characteristic fragment ions of [M+H−H2O]+, [M+H−CO]+, and [M+H−H2O−CO]+. Additionally, subtle variations were observed in each compound due to differences in modifying groups. For instance, upon deacidification, the piperazine ring structure underwent breakage and rearrangement, yielding fragment ion peaks devoid of neutral molecules such as C2H5N, C3H7N, or C4H8N. Notably, compounds featuring a cyclopropyl substituent group at the N‐1 position typically exhibited characteristic fragments resulting from the loss of the cyclopropyl radical (⋅C3H5). Moreover, substituents at the N‐1 and C‐8 positions, when linked to form a six‐membered carbocyclic ring, were prone to cleavage, releasing the neutral C3H6 molecule. Conclusion: Quinolone antibiotics share structural similarities in their parent nuclei, leading to partially similar cleavage pathways. Nevertheless, distinct cleavage patterns emerge due to variations in functional groups. According to the difference of mass spectrometry cleavage patterns, it can provide an identification basis for the measured detection of antibiotics. [ABSTRACT FROM AUTHOR]

The electrochemical applications of gold span the entire pH spectrum. Recently, gold dissolution in acidic and alkaline media has been studied, but less attention has been given to electrolytes at intermediate pH values. To address this gap, this work uses on‐line electrochemical dissolution inductively coupled plasma mass spectrometry (ICP‐MS) to examine gold dissolution across a pH range of 1 to 12.7 using phosphate buffer solutions. All experimental parameters, except pH, are kept constant, enabling a clear investigation of pH effects on anodic (gold oxidation) and cathodic (gold oxide reduction) dissolution processes. Results show that dissolution amounts are lowest at neutral pH values between 3 and 7, varying with the applied potential and exposure time. Anodic and cathodic dissolution dominate in acidic and alkaline electrolytes, respectively. Depending on the highest applied potentials and time exposure, the main dissolution mechanism shifts at pH=5, 7, and 9. The pH dependence of Au dissolution is proposed to be linked to the nature of gold oxides formed, the kinetics of oxide formation/reduction, gold ion redeposition, and the influence of the oxygen evolution reaction (OER) on dissolution. These results provide fundamental insights into gold dissolution under neutral pH conditions. [ABSTRACT FROM AUTHOR]

Crosslinking mass spectrometry is a powerful tool to study protein-protein interactions under native or near-native conditions in complex mixtures. Through novel search controls, we show how biassing results towards likely correct proteins can subtly undermine error estimation of crosslinks, with significant consequences. Without adjustments to address this issue, we have misidentified an average of 260 interspecies protein-protein interactions across 16 analyses in which we synthetically mixed data of different species, misleadingly suggesting profound biological connections that do not exist. We also demonstrate how data analysis procedures can be tested and refined to restore the integrity of the decoy-false positive relationship, a crucial element for reliably identifying protein-protein interactions. Synopsis: Accurate error estimation in crosslinking mass spectrometry (MS) is crucial for uncovering new biology. However, new data analysis methods may disrupt the decoy-false positive relationship that is at the basis of error estimation. This study offers tests and remedies to address this issue. Crosslinking MS error control easily breaks, obscuring true errors and inflating novel biology claims. Concatenated data and true positive estimation reveal data processing errors. Pairing targets and decoys throughout the analysis improves the robustness of error estimation. Accurate error estimation in crosslinking mass spectrometry (MS) is crucial for uncovering new biology. However, new data analysis methods may disrupt the decoy-false positive relationship that is at the basis of error estimation. This study offers tests and remedies to address this issue. [ABSTRACT FROM AUTHOR]

Fingerprints provide sufficient and reliable discriminative characteristics which have been considered one of the most robust evidence for individualization. The limitation of current minutiae‐based fingerprint technology seems to be solved with the development of level 3 features since they can offer additional information for problematic fingerprint recognition and even donor profiling. So far, tremendous efforts have been devoted to detecting and analysing the third‐level details. This review summarizes the advances in level 3 details with an emphasis on their reliability assessment, visualization methods based on physical interaction, residue‐response, mass spectrometry and electrochemical techniques, as well as the potentiality for individualization, donor profiling and even other application scenarios. In the end, we also give a personal perspective on the future direction and the remaining challenges in the third‐level‐detail‐related field. We believe that the new exciting progress is expected in the development of level 3 detail detection and analysis with continued interest and attention to this field. [ABSTRACT FROM AUTHOR]

We study the diffusive interaction between soda‐lime glass substrates and sputtered aluminum‐doped silica thin films at 650°C, the temperature of commercial soda‐lime glass shaping or tempering. A first rapid migration of alkali ions from substrate to thin film has been described in a companion paper (J Am Ceram Soc. 2018;101:1516). Using the same samples as (J Am Ceram Soc. 2018;101:1516), we focus here on later interactions, when the layer is consumed by the substrate resulting from diffusive interactions. Using Secondary Ion Mass Spectroscopy profilometry, we show that the interdiffusion rate increases with the aluminum doping content of the layer. We show that the alkali uptake of silica layers accelerates diffusive exchanges with the substrate, consistently with a decrease of viscosity of the layer. Diffusion profiles of silicon are well reproduced when solving the diffusion equation for a diffusivity having an exponential dependence with silicon concentration. The diffusivity of aluminum is shown to be 10 times slower than the diffusion of silicon. Specific exchanges of the two network formers with network modifiers are deduced from the composition‐space trajectories, providing evidence for multicomponent diffusive couplings between species. [ABSTRACT FROM AUTHOR]

Summary: Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi‐subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid‐encoded gene (clpP1) and multiple nuclear genes. TheclpP1gene is highly conserved across most green plants, but it is by far the fastest evolving plastid‐encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history ofclpP1molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns andRNA‐editing sites) within seed plants. AlthoughclpP1is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genusSilene, which has highly elevated and heterogeneous rates ofclpP1evolution. We confirmed thatclpP1is expressed as a stable protein and forms oligomeric complexes with the nuclear‐encoded Clp subunits, even in one of the most divergentSilenespecies. Additionally, there is a tight correlation between amino acid substitution rates inclpP1and the nuclear‐encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex. Significance statement: This paper examines the evolution of the clpP1 gene across green plants. We provide proteomic evidence that highly divergent clpP1 genes can still produce functional members of the plastid caseinolytic protease complex. [ABSTRACT FROM AUTHOR]

Proteins are major effectors and regulators of biological processes that can elicit multiple functions depending on their interaction with other proteins. The organization of proteins into macromolecular complexes and their quantitative distribution across these complexes is, therefore, of great biological and clinical significance. In this paper, we describe an integrated experimental and computational technique to quantify hundreds of protein complexes in a single operation. The method consists of size exclusion chromatography (SEC) to fractionate native protein complexes, SWATH/DIA mass spectrometry to precisely quantify the proteins in each SEC fraction, and the computational framework CCprofiler to detect and quantify protein complexes by error‐controlled, complex‐centric analysis using prior information from generic protein interaction maps. Our analysis of the HEK293 cell line proteome delineates 462 complexes composed of 2,127 protein subunits. The technique identifies novel sub‐complexes and assembly intermediates of central regulatory complexes while assessing the quantitative subunit distribution across them. We make the toolset CCprofiler freely accessible and provide a web platform, SECexplorer, for custom exploration of the HEK293 proteome modularity. Synopsis: The study presents an integrated framework for targeted, complex‐centric analysis based on size exclusion chromatography (SEC) and SWATH/DIA mass spectrometry. The workflow facilitates the parallel detection of hundreds of protein complexes and their variants at high selectivity and under error‐control. The presented workflow is based on the concept of complex‐centric proteome profiling and combines size exclusion chromatography (SEC) with SWATH/DIA mass spectrometry.The implementation of the complex‐centric data analysis is supported by the computational framework CCprofiler.Application of the SEC‐SWATH‐MS workflow to HEK293 cells led the detection and quantification of subunit distribution of 462 distinct protein complexes containing 2,127 proteins and identified novel complex variants such as assembly intermediates.The interactive platform, SECexplorer is presented to support custom complex‐centric exploration of SEC‐SWATH‐MS datasets. The study presents an integrated framework for targeted, complex‐centric analysis based on size exclusion chromatography (SEC) and SWATH/DIA mass spectrometry. The workflow facilitates the parallel detection of hundreds of protein complexes and their variants at high selectivity and under error‐control. [ABSTRACT FROM AUTHOR]

In this paper, we investigate dilepton production in heavy‐ion collisions from sNN=8 to 200 GeV with a focus on the competition between the thermal quark‐gluon plasma (QGP) radiation and the semi‐leptonic decays from correlated D‐meson pairs. As a "tool," we employ the parton–hadron string dynamics (PHSD) transport approach incorporating a fully microscopic treatment of the charm dynamics and their semi‐leptonic decays. We find that the dileptons from correlated D‐meson decays dominate the "thermal" radiation from the QGP in central Pb + Pb collisions at the intermediate masses (1.2 GeV < M < 3 GeV) for sNN>40GeV, while for sNN=5−20GeV, the contribution from D,D‾ decays to the intermediate mass dilepton spectra is subleading such that one should observe a rather clear signal from the QGP radiation, which is dominated by the annihilation channel qq‾→γ*. [ABSTRACT FROM AUTHOR]

The polysaccharide moiety of the lipopolysaccharide (polysaccharide I) from Escherichia coli F492 (08:K27-:H-) and the polysaccharide (polysaccharide II) from the rfa mutant F612 (derived from F492) were isolated by extraction with 450% aqueous phenol at 65 °C. Polysaccharide I was obtained in 1–2% yield (based on dry bacteria). It contained mannose (83.5%), glucose (5.7%), galactose (3.4%), heptose (4.6%) and 2-keto-3-deoxy-mannosulonic acid (0.8%). Polysaccharide II was obtained in 0.8–1% yield (based on dry bacteria). It contained 99.2% mannose. With the method of Yphantis it was found that the molecular weights of polysaccharides I and II were 12400 and 10400, respectively. The difference accounted for the core oligosaccharide which was present in polysaccharide I and absent in polysaccharide II. The specific optical rotation was 43 °C for polysaccharide I and 42 °C for polysaccharide II. Both polysaccharides were permethylated. Subsequent hydrolysis, reduction and acetylation, followed by gas-liquid chromatography and mass spectrometry indicated that in both polysaccharides two-thirds of the mannose units were substituted at C-2 and one-third at C-3. These results were confirmed by periodate oxidation. From polysaccharide II nine oligosaccharides were obtained after partial acid hydrolysis by chromatography on Biogel P2, paper chromatography and paper electrophoresis of the borate complexes. The oligosaccharides were reduced with sodium borodeuterate (which labelled the reducing mannose units) and methylated. After hydrolysis, reduction and acetylation the products were analyzed by gas chromatography and mass spectrometry. It is concluded that the poIysaccharides I and II contain about 20 repeating units of α-mannosyl-1,2-α-mannosyl-1,2-α-mannose which are joined through &alph;-1,3 linkages. [ABSTRACT FROM AUTHOR]

Boron carbide is a prominent material for high-brilliance synchrotron optics as it remains stable up to very high temperatures. The present study shows a significant change taking place at 550 °C in the buried interface region formed between the Cr adhesive layer and the native oxide layer present on the silicon substrate. An in situ annealing study is carried out at the Indus-1 Reflectivity beamline from room temperature to 550°C (100°C steps). The studied sample is a mirror-like boron carbide thin film of 400 A ° thickness deposited with an adhesive layer of 20 A ° Cr on a silicon substrate. The corresponding changes in the film structure are recorded using angle-dependent soft X-ray reflectivity measurements carried out in the region of the boron K-edge after each annealing temperature. Analyses performed using the Parratt recursive formalism reveal that the top boron carbide layer remains intact but interface reactions take place in the buried Cr-SiO2 region. After 300°C the Cr layer diffuses towards the substrate. At higher temperatures of 500°C and 550 °C the Cr reacts with the native oxide layer and tends to form a low-density compound of chromium oxysilicide (CrSiOx). Depth profiling of Si and Cr distributions obtained from secondary ion mass spectroscopy measurements corroborate the layer model obtained from the soft X-ray reflectivity analyses. Details of the interface reaction taking place near the substrate region of boron carbide/Cr sample are discussed. [ABSTRACT FROM AUTHOR]

Previous simulations have suggested that O+ outflow plays a role in driving the sawtooth oscillations. This study investigates the role of O+ by identifying the differences in ionospheric outflow between sawtooth and non‐sawtooth storms using 11 years of FAST/Time of flight Energy Angle Mass Spectrograph (TEAMS) ion composition data from 1996 through 2007 during storms driven by coronal mass ejections. We find that the storm's initial phase shows larger O+ outflow during non‐sawtooth storms, and the main and recovery phases revealed differences in the location of ionospheric outflow. On the pre‐midnight sector, a larger O+ outflow was observed during the main phase of sawtooth storms, while non‐sawtooth storms exhibited stronger O+ outflow during the recovery phase. On the dayside, the peak outflow shifts significantly toward dawn during sawtooth storms. This strong dawnside sector outflow during sawtooth storms warrants consideration. Plain Language Summary: A sawtooth event is a convection mode in Earth's magnetosphere, which transports solar wind plasma and energy into the inner magnetosphere and ionosphere. Despite three decades since their discovery, the mechanism behind sawtooth oscillations remains uncertain. One theory suggests that O+ outflow induces sawtooth oscillations through an internal feedback mechanism. In line with this theory, some simulations have generated sawtooth oscillations under steady geomagnetic conditions. Furthermore, previous observations indicate that some, but not all, geomagnetic storms exhibit sawtooth oscillations. This study utilizes data from the FAST/TEAMS instrument (1996–2007) and compares O+ outflow variations during geomagnetic storms with and without sawtooth oscillations. Findings indicate that during the storms' initial phase, sawtooth storms produce less O+ outflow than non‐sawtooth storms. Additionally, non‐sawtooth storms exhibit higher O+ outflow in the dayside during the main phase and in the pre‐midnight sector during the recovery phase, challenging the key role of O+ outflow in driving the feedback mechanism. However, observing large O+ outflow in the dawnside sector of sawtooth events suggests more investigation is needed. Key Points: The intensity and location of O+ outflow during storms are different in storms with and without sawtooth oscillationsThe peak dayside outflow is significantly shifted toward dawn during storms with sawtooth observationsThe nightside picture is mixed; the pre‐midnight O+ outflow is higher in the main phase but lower in the recovery phase of sawtooth storms [ABSTRACT FROM AUTHOR]

Objectives: Disruption of the oxidative stress defense system is involved in developing various diseases. Sulfur compounds such as glutathione (GSH) and cysteine (CysSH) are representative antioxidants in the body. Recently, supersulfides, including reactive persulfide and polysulfide species, have gained attention as potent antioxidants regulating oxidative stress and redox signaling. However, their involvement in the pathogenesis of chronic rhinosinusitis (CRS) remains unclear. Methods: To clarify the changes in sulfur compounds within the sinus mucosa of each CRS subtype, we measured sulfur compound levels in the sinus mucosa of control individuals (n = 9), patients with eosinophilic CRS (ECRS) (n = 13), and those with non‐ECRS (nECRS) (n = 11) who underwent sinus surgery using mass spectrometry. Results: GSH and CysSH levels were significantly reduced, and the glutathione disulfide (GSSG)/GSH ratio, an oxidative stress indicator, was increased in patients with ECRS. Despite the absence of notable variations in supersulfides, patients with ECRS and nECRS exhibited a significant reduction in glutathione trisulfide (GSSSG), which serves as the precursor for supersulfides. Conclusions: This study is the first quantitative assessment of supersulfides in normal and inflamed sinus mucosa, suggesting that sulfur compounds contribute to the pathogenesis of CRS. Level of Evidence: N/A. [ABSTRACT FROM AUTHOR]

Mass spectrometry has revolutionized cell signaling research by vastly simplifying the analysis of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to perturbations is crucial for further illuminating the functionality of the phosphoproteome. Here we describe µPhos ('microPhos'), an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture and small tissue amounts in <8 h total processing time. By greatly minimizing transfer steps and liquid volumes, we demonstrate increased sensitivity, >90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify ~17,000 Class I phosphosites in a human cancer cell line using 20 µg starting material, and confidently localize ~6200 phosphosites from 1 µg. This depth covers key signaling pathways, rendering sample-limited applications and perturbation experiments with hundreds of samples viable. We employ µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain we reveal distinct spatial kinase activities in subregions of the hippocampal formation. Synopsis: The study introduces µPhos, an accessible, plate-based workflow for low-input mass spectrometry-based phosphoproteomics. µPhos greatly facilitates high-dimensional experimental designs, as demonstrated by a 96-well drug response screen and analysis of small anatomical regions in the mouse brain. Systematic optimization results in sensitive and selective enrichment of phosphopeptides in <100 µL, allowing direct processing of 96-well plates within one working day. µPhos combined with dia-PASEF reproducibly quantifies 6000 to 17,000 confidently localized phosphosites from 1 to 20 µg protein starting material. Sub-region resolved analysis of the mouse brain phosphoproteome infers spatially distinct kinase activity. Time-course analysis of chronic myeloid leukemia cells treated with tyrosine kinase inhibitors reveals drug-specific responses. The study introduces µPhos, an accessible, plate-based workflow for low-input mass spectrometry-based phosphoproteomics. µPhos greatly facilitates high-dimensional experimental designs, as demonstrated by a 96-well drug response screen and analysis of small anatomical regions in the mouse brain. [ABSTRACT FROM AUTHOR]

A comprehensive statistical study is conducted on O+ and H+ outflows obtained from the TEAMS/FAST data during the 23rd solar cycle (1996–2007). The study investigates interhemispheric asymmetry in ionospheric outflows during local summer, winter, and equinox seasons. Data are classified into two distinct periods: the pre‐storm and geomagnetic storm phases. Numerous statistical asymmetries are identified. The findings indicate that the dayside cusp consistently demonstrates more outflow rates of O+ and H+ in the northern hemisphere than southern hemisphere during geomagnetic storms in all seasons as well as during the pre‐storm period in the summer season with the exception of H+ during summer storms. Conversely, the nightside O+ and H+ outflow rates are higher in the southern hemisphere during pre‐storm and storm periods in the summer season. Additionally, the dawnside and duskside outflow rates of O+ and H+ are predominantly stronger in the southern hemisphere. Plain Language Summary: The Earth's hemispheres receive different solar extreme ultraviolet radiation levels in different local seasons. In addition, there is a displacement between Earth's magnetic and geographic poles. Both mentioned factors cause interhemispheric asymmetries in ionospheric parameters. For the first time, this study investigates asymmetry in O+ and H+ ionospheric outflows between the northern and southern hemispheres by focusing on similar local seasons with comparable solar radiation levels. Data from the FAST/Time‐of‐flight Energy Angle Mass Spectrograph (TEAMS) instrument (1996–2007) are used for storms and pre‐storms. Hemispherical ionospheric outflows are categorized into summer, winter, and equinox and are spatially averaged in the polar regions. Findings reveal asymmetric ion outflows between hemispheres. The dayside cusp outflows are higher in the northern hemisphere than in the southern hemisphere during geomagnetic storms in all seasons except for H+ in summer. Conversely, nightside O+ and H+ outflows are more in the southern hemisphere than in the northern hemisphere during pre‐storm and storm periods in summer. Additionally, in dawnside and duskside, O+ and H+ outflows are predominantly stronger in the southern hemisphere than in the northern hemisphere. Key Points: 11‐year statistics find the northern and southern hemispheres exhibit asymmetric ion outflow even during similar local seasonsDuring storms, the cusp dayside exhibits higher O+ and H+ outflow rates in the northern hemisphere compared to the southern hemisphereThe dawnside and duskside O+ and H+ outflow rates are stronger in the southern hemisphere than in the northern hemisphere [ABSTRACT FROM AUTHOR]

Atomically precise nanoclusters hold promise for supramolecular assembly and (opto)electronic‐ as well as magnetic materials. Herein, this work reports that treating palladium(0) precursors with a triphosphirane affords strongly colored Pd8(PDip)6 that is fully characterized by mass spectrometry, heteronuclear and Cross‐Polarization Magic‐Angle Spinning (CP‐MAS) NMR‐, infrared (IR), UV–vis, and X‐ray photoelectron (XP) spectroscopies, single‐crystal X‐Ray diffraction (sc‐XRD), mass spectrometry, and cyclovoltammetry (CV). This coordinatively unsaturated 104‐electron Pd(0) cluster features a cubic Pd8‐core, µ4‐capping phosphinidene ligands, and is air‐stable. Quantum chemical calculations provide insight to the cluster's electronic structure and suggest 5s/4d orbital mixing as well as minor Pd─P covalency. Trapping experiments reveal that cluster growth proceeds via insertion of Pd(0) into the triphosphirane. The unsaturated cluster senses ethylene and binds isocyanides, which triggers the rearrangement to a tetrahedral structure with a reduced frontier orbital energy gap. These experiments demonstrate facile cluster manipulation and highlight non‐destructive cluster rearrangement as is required for supramolecular assembly. [ABSTRACT FROM AUTHOR]

The physical interactome of a protein can be altered upon perturbation, modulating cell physiology and contributing to disease. Identifying interactome differences of normal and disease states of proteins could help understand disease mechanisms, but current methods do not pinpoint structure-specific PPIs and interaction interfaces proteome-wide. We used limited proteolysis–mass spectrometry (LiP–MS) to screen for structure-specific PPIs by probing for protease susceptibility changes of proteins in cellular extracts upon treatment with specific structural states of a protein. We first demonstrated that LiP–MS detects well-characterized PPIs, including antibody–target protein interactions and interactions with membrane proteins, and that it pinpoints interfaces, including epitopes. We then applied the approach to study conformation-specific interactors of the Parkinson's disease hallmark protein alpha-synuclein (aSyn). We identified known interactors of aSyn monomer and amyloid fibrils and provide a resource of novel putative conformation-specific aSyn interactors for validation in further studies. We also used our approach on GDP- and GTP-bound forms of two Rab GTPases, showing detection of differential candidate interactors of conformationally similar proteins. This approach is applicable to screen for structure-specific interactomes of any protein, including posttranslationally modified and unmodified, or metabolite-bound and unbound protein states. Synopsis: A structural proteomics approach for identifying candidate interactors of any protein within a complex lysate is presented. It is applied to identify conformation-specific interactors of Rab GTPases and of the monomeric and fibrillar forms of the disease-associated protein alpha-synuclein. A method is presented for identifying candidate interactors of any bait protein within a complex lysate. It is applicable to the identification of conformation-specific interactors and pinpoints interaction sites. A resource of candidate interactors of monomeric and fibrillar forms of alpha-synuclein is presented. Candidate interactors of GTP- and GDP-bound forms of Rab GTPases are identified. A structural proteomics approach for identifying candidate interactors of any protein within a complex lysate is presented. It is applied to identify conformation-specific interactors of Rab GTPases and of the monomeric and fibrillar forms of the disease-associated protein alpha-synuclein. [ABSTRACT FROM AUTHOR]

From the lipopolysaccharide of the gram-negative bacterium Rhodopseudomonas capsulata (Athiorhodaceae) a lipophilic sugar was isolated by chromatographic procedures and characterized by mass spectrometry as belonging to the group of 3-O-methyl-6-deoxy-hexoses. Demethylation showed that the parental sugar had the same properties in borate electrophoresis as rhamnose. Comparison with an authentic sample of 3-O-methyl-rhamnose in gas liquid chromatography, paper chromatography and borate electrophoresis showed that the sugar under examination is 3-O-methylrhamnose (acofriose). Investigation of its optical rotation indicates that the sugar has the L-configuration. L-Acofriose (3-O-methyl-L-rhamnose) has not hitherto been found in lipopolysaccharides of gram-negative bacteria. [ABSTRACT FROM AUTHOR]

The mechanism of formation of the formyl group of chlorophyll b has long been obscure but, in this paper, the origin of tile 7-formyl-group oxygen of chlorophyll b in higher plants was determined by greening etiolaled maize leaves, excised from dark-grown plants, by illumination under while light in the presence of either H2 18O or 18O2 and examining the newly synthesized chlorophylls by mass spectroscopy. To minimize the possible loss of 18O label from the 7-formyl substituent by reversible formation of chlolophyll b-7¹-gem-diol (hydrate) with unlabelled water in the cell, the formyl group was reduced to a hydroxymethyl group during extraction with methanol containing NaBH4: chlorophyll a remained unchanged during this rapid reductive extraction process, Mass spectra of chlorophyll a and 17-hydroxymethyll-chlorophyll b extracted from leaves greened in the presence of either H, 18O or 18O. revealed that so was incorporated only from molecular oxygen but into both chlorophylls: the mass spectra were consistent with molecular oxygen providing an oxygen atom not only for incorporation into the 7-formyl group of chlorophyll b but also for the well-documented incorporation into the 13¹-oxo group of both chlorophylls a and b [see Walker. C. J., Mansfield, K. E., Smith, K. M. & Casteffranco. P. A. (1989) Biochem. J. 257, 599–602]. The incorporation of isotope led to as much as 77% enrichment of the 13¹-oxo group of chlorophyll a: assuming identical incorporation into the 13¹ oxygen of chlorophyll b, then enrichment of the 7-formyl oxygen was as much as 93%. Isotope dilution by re-incorporation of photosyn-thetically produced oxygen from unlabelled water was negligible as shown by a greening experiment in the presence of 3-(3.4-dichlorophenyl)-l.1-dimethylurea. The high enrichment using 18O, and the absence of labelling by unequivocally demonstrates that molecular oxygen is the sole precursor of the 7-formyl oxygen of chlorophyll b in higher plants and strongly suggests a single pathway for the formation of the chlorophyll b formyl group involving the participation of an oxygenase-type enzyme. [ABSTRACT FROM AUTHOR]

Phenylketonuria (PKU) is the most common inherited metabolic disease in humans. Clinical screening of newborn heel blood samples for PKU is costly and time‐consuming because it requires multiple procedures, like isotope labeling and derivatization, and PKU subtype identification requires an additional urine sample. Delayed diagnosis of PKU, or subtype identification can result in mental disability. Here, plasmonic silver nanoshells are used for laser desorption/ionization mass spectrometry (MS) detection of PKU with label‐free assay by recognizing metabolic profile in dried blood spot (DBS) samples. A total of 1100 subjects are recruited and each DBS sample can be processed in seconds. This platform achieves PKU screening with a sensitivity of 0.985 and specificity of 0.995, which is comparable to existing clinical liquid chromatography MS (LC‐MS) methods. This method can process 360 samples per hour, compared with the LC‐MS method which processes only 30 samples per hour. Moreover, this assay enables precise identification of PKU subtypes without the need for a urine sample. It is demonstrated that this platform enables high‐performance and fast, low‐cost PKU screening and subtype identification. This approach might be suitable for the detection of other clinically relevant biomarkers in blood or other clinical samples. [ABSTRACT FROM AUTHOR]

Analysis was conducted to compare levodopa/carbidopa pharmacokinetics and drug‐related material in plasma of healthy participants after receiving a continuous infusion of Levodopa/Carbidopa Intestinal Gel (LCIG) to a continuous subcutaneous infusion of foslevodopa/foscarbidopa. Study samples were from a randomized, open‐label, 2‐period crossover study in 20 healthy participants. Participants received either 24‐h foslevodopa/foscarbidopa SC infusion to the abdomen or LCIG delivered for 24 h to the jejunum through a nasogastric tube with jejunal extension. Serial blood samples were collected for PK. Comparability of the LD PK parameters between the two treatment regimens was determined. Selected plasma samples were pooled per treatment group and per time point for metabolite profiling. LC–MSn was performed using high‐resolution mass spectrometry to identify drug‐related material across the dosing regimens and time points. The LD PK parameter central values and 90% confidence intervals following the foslevodopa/foscarbidopa subcutaneous infusion were between 0.8 and 1.25 relative to the LCIG infusion. With LCIG administration, LD, CD, 3‐OMD, DHPA, DOPAC, and vanillacetic acid were identified in plasma at early and late time points (0.75 and 24 h); the metabolic profile after administration of foslevodopa/foscarbidopa demonstrated the same drug‐related compounds with the exception of the administered foslevodopa. 3‐OMD and vanillacetic acid levels increased over time in both treatment regimens. Relative quantification of LC–MS peak areas showed no major differences in the metabolite profiles. These results indicate that neither the addition of monophosphate prodrug moieties nor SC administration affects the circulating metabolite profile of foslevodopa/foscarbidopa compared to LCIG. [ABSTRACT FROM AUTHOR]

For years, proteasomal degradation was predominantly attributed to the ubiquitin-26S proteasome pathway. However, it is now evident that the core 20S proteasome can independently target proteins for degradation. With approximately half of the cellular proteasomes comprising free 20S complexes, this degradation mechanism is not rare. Identifying 20S-specific substrates is challenging due to the dual-targeting of some proteins to either 20S or 26S proteasomes and the non-specificity of proteasome inhibitors. Consequently, knowledge of 20S proteasome substrates relies on limited hypothesis-driven studies. To comprehensively explore 20S proteasome substrates, we employed advanced mass spectrometry, along with biochemical and cellular analyses. This systematic approach revealed hundreds of 20S proteasome substrates, including proteins undergoing specific N- or C-terminal cleavage, possibly for regulation. Notably, these substrates were enriched in RNA- and DNA-binding proteins with intrinsically disordered regions, often found in the nucleus and stress granules. Under cellular stress, we observed reduced proteolytic activity in oxidized proteasomes, with oxidized protein substrates exhibiting higher structural disorder compared to unmodified proteins. Overall, our study illuminates the nature of 20S substrates, offering crucial insights into 20S proteasome biology. Synopsis: A systematic investigation of the repertoire of protein substrates degraded by the 20S proteasome under basal and oxidized conditions reveals hundreds of substrates and differential functionality of naïve and oxidized 20S proteasome complexes. 20S proteasome substrates are primarily RNA- and DNA-binding proteins with intrinsically disordered regions. The 20S proteasome not only fully degrades substrates but also cleaves proteins at their N- and C-termini, indicating regulatory actions. Oxidized proteasomes show lower proteolytic activity in comparison to naïve proteasomes. Oxidized protein substrates display higher structural disorder than naïve substrates. A systematic investigation of the repertoire of protein substrates degraded by the 20S proteasome under basal and oxidized conditions reveals hundreds of substrates and differential functionality of naïve and oxidized 20S proteasome complexes. [ABSTRACT FROM AUTHOR]

Endometrial cancer (EC) stands as the most prevalent gynecological tumor in women worldwide. Notably, differentiation diagnosis of abnormity detected by ultrasound findings (e.g., thickened endometrium or mass in the uterine cavity) is essential and remains challenging in clinical practice. Herein, we identified a metabolic biomarker panel for differentiation diagnosis of EC using machine learning of high-performance serum metabolic fingerprints (SMFs) and validated the biological function. We first recorded the high-performance SMFs of 191 EC and 204 Non-EC subjects via particle-enhanced laser desorption/ionization mass spectrometry (PELDI-MS). Then, we achieved an area-under-the-curve (AUC) of 0.957–0.968 for EC diagnosis through machine learning of high-performance SMFs, outperforming the clinical biomarker of cancer antigen 125 (CA-125, AUC of 0.610–0.684, p < 0.05). Finally, we identified a metabolic biomarker panel of glutamine, glucose, and cholesterol linoleate with an AUC of 0.901–0.902 and validated the biological function in vitro. Therefore, our work would facilitate the development of novel diagnostic biomarkers for EC in clinics. Synopsis: Endometrial cancer (EC) diagnostic suffers from a lack of non-invasive, specific and sensitive tools. Machine learning of high-performance serum metabolic fingerprints (SMFs) was used to identify a metabolic biomarker panel for differentiation diagnosis of EC vs. Non-EC. An SMFs database of 191 EC and 204 Non-EC subjects was built via particle-enhanced laser desorption/ionization mass spectrometry (PELDI-MS). A metabolic biomarker panel for differentiation diagnosis of EC was identified, with an AUC of 0.901–0.902 and an accuracy of 82.8–83.1%. The metabolite biomarker functions on EC cell behavior were evaluated in vitro (including proliferation, colony formation, migration, and apoptosis). Endometrial cancer (EC) diagnostic suffers from a lack of non-invasive, specific and sensitive tools. Machine learning of high-performance serum metabolic fingerprints (SMFs) was used to identify a metabolic biomarker panel for differentiation diagnosis of EC vs. Non-EC. [ABSTRACT FROM AUTHOR]

Cells modify their internal organization during continuous state transitions, supporting functions from cell division to differentiation. However, tools to measure dynamic physiological states of individual transitioning cells are lacking. We combined live-cell imaging and machine learning to monitor ERK1/2-inhibited primary murine skeletal muscle precursor cells, that transition rapidly and robustly from proliferating myoblasts to post-mitotic myocytes and then fuse, forming multinucleated myotubes. Our models, trained using motility or actin intensity features from single-cell tracking data, effectively tracked real-time continuous differentiation, revealing that differentiation occurs 7.5–14.5 h post induction, followed by fusion ~3 h later. Co-inhibition of ERK1/2 and p38 led to differentiation without fusion. Our model inferred co-inhibition leads to terminal differentiation, indicating that p38 is specifically required for transitioning from terminal differentiation to fusion. Our model also predicted that co-inhibition leads to changes in actin dynamics. Mass spectrometry supported these in silico predictions and suggested novel fusion and maturation regulators downstream of differentiation. Collectively, this approach can be adapted to various biological processes to uncover novel links between dynamic single-cell states and their functional outcomes. Synopsis: The prediction certainty of machine learning classification models can be used as a continuous measurement to quantitatively monitor single cell state transitions, as demonstrated for myoblast differentiation during muscle fiber formation. Live imaged single myoblast continuous differentiation states are computationally derived from motility and actin dynamics. The model distinguishes between cells that differentiated but failed to fuse to predict molecules specifically involved in fusion, as well as changes in actin dynamics. Mass spectrometry supports these in silico predictions and suggests novel fusion and maturation regulators downstream of differentiation. p38 is essential for the transition from terminal differentiation to fusion. The prediction certainty of machine learning classification models can be used as a continuous measurement to quantitatively monitor single cell state transitions, as demonstrated for myoblast differentiation during muscle fiber formation. [ABSTRACT FROM AUTHOR]

Extracellular matrix (ECM) plays central roles in cell architecture, innate defense and cell wall integrity (CWI) signaling. During transition to multicellularity, modular domain structures of ECM proteins and proteoforms have evolved due to continuous adaptation across taxonomic clades under different ecological niche. Although this incredible diversity has to some extent been investigated at protein level, extracellular phosphorylation events and molecular evolution of ECM proteoform families remains unexplored. We developed matrisome proteoform atlas in a grain legume, chickpea and performed meta‐analyses of 74 plant matrisomes. MS/MS analysis identified 1,424 proteins and 315 phosphoproteins involved in diverse functions. Cross‐species ECM protein network identified proteoforms associated with CWI maintenance system. Phylogenetic characterization of eighteen matrix protein families highlighted the role of taxon‐specific paralogs and orthologs. Novel information was acquired on gene expansion and loss, co‐divergence, sub functionalization and neofunctionalization during evolution. Modular networks of matrix protein families and hub proteins showed higher diversity across taxonomic clades than among organs. Furthermore, protein families differ in nonsynonymous to synonymous substitution rates. Our study pointed towards the matrix proteoform functionality, sequence divergence variation, interactions between wall remodelers and molecular evolution using a phylogenetic framework. This is the first report on comprehensive matrisome proteoform network illustrating presence of CWI signaling proteins in land plants. [ABSTRACT FROM AUTHOR]

4-Deoxy-D-arabino-hexose has been identified as a constituent of the four Citrobacter sero-types 4, 23, 27 and 36a. Its structure was evaluated by the aid of mass spectrometry and gas liquid chromatography in comparison with known deoxyhexoses. [ABSTRACT FROM AUTHOR]

An increasingly sophisticated array of approaches are now available for the study of the activities of reactive oxygen species and oxidative modifications in skeletal muscle, but the most up-to-date techniques are not readily available to many researchers in this field due to their requirement for sophisticated mass spectrometry, imaging or other high cost technologies. Most papers published therefore rely on a number of established approaches although the choice of approach is also clearly dependent upon the experimental model and access to skeletal muscle that is available to the investigator, how much detail is required and the overall question to be addressed. Numerous reports have described the problems associated with some of the popular approaches that are widely followed, including measurement of thiobarbituric acid substances and the sole use of fluorescence-based probes such as dichlorodihydrofluorescein. This brief review reports the areas in which methods are improving to allow valid assessments to made in this area and indicates some of the more recent developments that provide alternative ways to assess the activity of individual species and endpoints in the various experimental models that may be examined. [ABSTRACT FROM AUTHOR]

Metabolomics is recognized as a crucial scientific domain, promising to advance our understanding of cell biology, physiology and medicine. Tandem mass spectrometry (MS/MS) has strong potential to elucidate the metabolites in complex biological samples and to become a standard tool complementing established techniques. However, despite its potential for answering many key questions, a major challenge in the use of tandem mass spectrometry for characterizing metabolites lies in a lack of computational tools for accurate annotation and structure identification allowing us to turn complex data into molecular knowledge. Chemo‐informatics and related machine‐learning in silico fragmentation tools have already been established and used for different classes of metabolites. For the classes of metabolites where existing chemo‐informatics approaches produce insufficiently accurate predictions a supervised machine learning based strategy can be used to predict possible molecular structures from "unassigned" experimental tandem MS data. Here, we propose a new innovative in silico approach employing quantum mechanical (QM) methods in order to predict ion formation and subsequent fragmentation patterns of arbitrary small molecules and validate putative annotations of tandem mass spectrometry (MS) data. The focus is on the evaluation of a new conceptual density functional theory (CDFT) nuclear reactivity descriptor of the nuclear Fukui function type, that characterizes the forces that the atomic nuclei experience due to proton attachment and captures the onset of the change in the nuclear positions induced by it. A series of test compounds for which high quality experimental data exist and that were investigated before in a more approximate theoretical framework have been examined. The output of these calculations provides a list of the most probable molecular structures predicted to match the experimental tandem MS spectrum ("de novo metabolite identification"). [ABSTRACT FROM AUTHOR]

T‐2 toxin causes renal dysfunction with proteinuria and glomerular podocyte damage. This work explores the role of metabolic disorder/reprogramming‐mediated epigenetic modification in the progression of T‐2 toxin‐stimulated podocyte injury. A metabolomics experiment is performed to assess metabolic responses to T‐2 toxin infection in human podocytes. Roles of protein O‐linked‐N‐acetylglucosaminylation (O‐GlcNAcylation) in regulating T‐2 toxin‐stimulated podocyte injury in mouse and podocyte models are assessed. O‐GlcNAc target proteins are recognized by mass spectrometry and co‐immunoprecipitation experiments. Moreover, histone acetylation and autophagy levels are measured. T‐2 toxin infection upregulates glucose transporter type 1 (GLUT1) expression and enhances hexosamine biosynthetic pathway in glomerular podocytes, resulting in a significant increase in β‐arrestin‐1 O‐GlcNAcylation. Decreasing β‐arrestin‐1 or O‐GlcNAc transferase (OGT) effectively prevents T‐2 toxin‐induced renal dysfunction and podocyte injury. Mechanistically, O‐GlcNAcylation of β‐arrestin‐1 stabilizes β‐arrestin‐1 to activate the mammalian target of rapamycin (mTOR) pathway as well as to inhibit autophagy during podocyte injury by promoting H4K16 acetylation. To sum up, OGT‐mediated β‐arrestin‐1 O‐GlcNAcylation is a vital regulator in the development of T‐2 toxin‐stimulated podocyte injury via activating the mTOR pathway to suppress autophagy. Targeting β‐arrestin‐1 or OGT can be a potential therapy for T‐2 toxin infection‐associated glomerular injury, especially podocyte injury. [ABSTRACT FROM AUTHOR]

The deposition of highly phosphorylated and aggregated tau is a characteristic of tauopathies, including Alzheimer's disease. It has long been known that different isoforms of tau are aggregated in different cell types and brain regions in each tauopathy. Recent advances in analytical techniques revealed the details of the biochemical and structural biological differences of tau specific to each tauopathy. In this review, we explain recent advances in the analysis of post‐translational modifications of tau, particularly phosphorylation, brought about by the development of mass‐spectrometry and Phos‐tag technology. We then discuss the structure of tau filaments in each tauopathy revealed by the advent of cryo‐EM. Finally, we describe the progress in biofluid and imaging biomarkers for tauopathy. This review summarizes current efforts to elucidate the characteristics of pathological tau and the landscape of the use of tau as a biomarker to diagnose and determine the pathological stage of tauopathy. [ABSTRACT FROM AUTHOR]

Here, the authors report that co‐crystallization of fluorophores with matrix‐assisted laser desorption/ionization (MALDI) imaging matrices significantly enhances fluorophore brightness up to 79‐fold, enabling the amplification of innate tissue autofluorescence. This discovery facilitates FluoMALDI, the imaging of the same biological sample by both fluorescence microscopy and MALDI imaging. The approach combines the high spatial resolution and specific labeling capabilities of fluorescence microscopy with the inherently multiplexed, versatile imaging capabilities of MALDI imaging. This new paradigm simplifies registration by avoiding physical changes between fluorescence and MALDI imaging, allowing to image the exact same cells in tissues with both modalities. Matrix‐fluorophore co‐crystallization also facilitates applications with insufficient fluorescence brightness. The authors demonstrate feasibility of FluoMALDI imaging with endogenous and exogenous fluorophores and autofluorescence‐based FluoMALDI of brain and kidney tissue sections. FluoMALDI will advance structural‐functional microscopic imaging in cell biology, biomedicine, and pathology. [ABSTRACT FROM AUTHOR]

Dementia is a leading cause of death worldwide, with increasing prevalence as global life expectancy increases. The most common neurodegenerative disorders are Alzheimer's disease (AD), dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD). With this study, we took an in‐depth look at the proteome of the (non‐purified) cerebrospinal fluid (CSF) and the CSF‐derived extracellular vesicles (EVs) of AD, PD, PD‐MCI (Parkinson's disease with mild cognitive impairment), PDD and DLB patients analysed by label‐free mass spectrometry. This has led to the discovery of differentially expressed proteins that may be helpful for differential diagnosis. We observed a greater number of differentially expressed proteins in CSF‐derived EV samples (N = 276) compared to non‐purified CSF (N = 169), with minimal overlap between both datasets. This finding suggests that CSF‐derived EV samples may be more suitable for the discovery phase of a biomarker study, due to the removal of more abundant proteins, resulting in a narrower dynamic range. As disease‐specific markers, we selected a total of 39 biomarker candidates identified in non‐purified CSF, and 37 biomarker candidates across the different diseases under investigation in the CSF‐derived EV data. After further exploration and validation of these proteins, they can be used to further differentiate between the included dementias and may offer new avenues for research into more disease‐specific pharmacological therapeutics. [ABSTRACT FROM AUTHOR]

In this paper, we propose a superjunction trench gate MOSFET (SJ TGMOSFET) fabricated through a simple p-pillar forming process using deep trench and boron silicate glass doping process technology to reduce the process complexity. Throughout the various boron doping experiments, as well as the process simulations, we optimize the process conditions related with the p-pillar depth, lateral boron doping concentration, and diffusion temperature. Compared with a conventional TGMOSFET, the potential of the SJ TGMOSFET is more uniformly distributed and widely spread in the bulk region of the n-drift layer due to the trenched p-pillar. The measured breakdown voltage of the SJ TGMOSFET is at least 28% more than that of a conventional device. [ABSTRACT FROM AUTHOR]

Please cite this paper as: Getie-Kebtie et al. (2012) Label-free mass spectrometry-based quantification of hemagglutinin and neuraminidase in influenza virus preparations and vaccines. Influenza and Other Respiratory Viruses 7(4), 521-530. Background Influenza vaccination is the primary method for preventing influenza and its severe complications. An accurate rapid method to determine hemagglutinin (HA) concentration would facilitate reference antigen preparation and consequently expedite availability of seasonal as well as pandemic vaccines. Objective The goal of this study was to develop a label-free mass spectrometry (MS) based method that enables simultaneous identification and quantification of HA, neuraminidase (NA), and other viral proteins and protein contaminations in influenza vaccine or virus preparations. Methods The method presented is based on LC/MSE analysis of vaccine or virus preparations tryptic digests spiked with a known amount of protein standard from which a universal response factor is generated and applied to calculate the concentration of proteins identified in the mixture. Results We show that, with the use of an appropriate internal standard, the label-free MS-based protein quantification method is applicable for simultaneous identification and absolute quantification of HA and identification and relative quantification of other influenza proteins as well as protein impurities in influenza vaccines and virus preparations. We show that different subtype recombinant HA is preferred internal standard that provides the most accurate results in absolute quantification of HAs and other influenza proteins. We applied this method to measure the absolute quantity of HA as well as relative quantities of other viral proteins and impurities in preparations of whole virus and monovalent vaccine, providing data to demonstrate strain-dependent differences in the amount of NA. Conclusion The label-free MS method presented here is ideally suited for timely preparation of reference material needed for potency testing of seasonal and pandemic vaccines. [ABSTRACT FROM AUTHOR]

GMP synthetase is a glutamine amidotransferase that incorporates ammonia derived from glutamine into the nucleotide xanthosine 5′-monophosphate (XMP) to form guanosine 5′-monophosphate (GMP). Functional coordination of domains in glutamine amidotransferases leads to upregulation of glutamine hydrolysis in the presence of acceptor substrates and is a common feature in this class of enzymes. We have shown earlier that binding of substrates to the acceptor domain of Plasmodium falciparum GMP synthetase (PfGMPS) leads to enhancement in both glutaminase activity and rate of glutaminase inactivation, by the irreversible inhibitors acivicin and diazo-oxonorleucine [Bhat JY et al. (2008) Biochem J 409, 263-273], a process that must be driven by conformational alterations. In this paper, through the combined use of biochemical assays, optical spectroscopy and mass spectrometry, we demonstrate that PfGMPS undergoes conformational transitions upon binding of substrates to the acceptor domain. Limited proteolysis and hydrogen-deuterium exchange in conjunction with mass spectrometry unveil region-specific conformational changes in the ATP + XMP bound state of PfGMPS. Decreased accessibility of R294 and K428 residues to trypsin in the ATP pyrophosphatase domain and reduced deuterium incorporation in the 143-155 region, pertaining to the glutaminase domain, suggest that in PfGMPS ligand-induced conformational changes are not only local but also transmitted over a long range across the domains. Overall, these results provide a detailed understanding of the substrate-induced changes in PfGMPS that could be essential for the overall catalytic process. [ABSTRACT FROM AUTHOR]

new analytical procedure for the determination of alcohol ethoxylates (AE) in environmental samples such as influents, effluents and sludge from waste water treatment plants (WWTPs) was developed. Although some work had been previously published on the detection of AE in water samples, this is the first paper that deals with AE in sludge. Alcohol ethoxylates were removed from water samples by sorption on polymeric discs followed by extraction with methanol. The methanol extracts were cleaned up with two alumina solid-phase extractions (SPE) at different conditions of solvent polarity, one before and the other after derivatization with naphthoyl chloride. A final polishing step was carried out on a Florisil SPE column. Liquid chromatography/mass spectrometry with electrospray ionization was used to quantify AE as naphthoyl derivatives. The detection limits for AE ethoxymers range from 0.07 to 0.005 μg/L in water samples. The method was applied to an Italian WWTP in order to follow the fate of AE during treatment, AE concentrations of 839 μg/L, 0.46 μg/L and 10.6 mg/kg were respectively found in the inlet, outlet and sludge samples. AE removals of each ethoxymer in the plant were in the range 99.6-100% and no difference was observed between high or low-mole ethoxymers and between AE with odd or even carbon chain lengths. An overall 99.7% removal was also determined on the mass balance of AE in the inlet, the outlet, and sludge of the plant. [ABSTRACT FROM AUTHOR]

The present paper introduces a highly sensitive and selective method for simultaneous quantification of 12 cytokinins (free form and their conjugates). The method includes a protocol of extraction with methanol/water/formic acid (15/4/1, v/v/v) to the micro-scale samples, pre-purification with solid phase extraction (SPE) cartridges of the extracts, separation with a high performance liquid chromatography (HPLC) and detection by an electrospray ionization ion trap mass spectrometry (ESI-Ion trap-MS) system in a consecutive ion monitoring (CRM) mode at the three stage fragmentation of mass spectrometry (MS3). The lowest detection level of the cytokinins of the method reaches 0.1-2.0 pg with a very wide range of linear regression from 1-512 pg, at the coefficient factors of 0.98-0.99. The feasibility of this method has been proven in the application of the method to the analysis of the trace-amount contents of cytokinins in the micro-scale samples of various types of plant materials, such as aerial parts of rice and poplar leaves etc. 12 endogenous cytokinins had been identified and quantified in the plant tissues, with an acceptable relatively higher recovery rate from 40% to 70%. [ABSTRACT FROM AUTHOR]

WHAT IS ALREADY KNOWN ABOUT THE SUBJECT • Ciclosporin's nephrotoxicity initially targets the proximal tubule and is, at least in part, driven by increased formation of oxygen radicals. • 1H-nuclear magnetic resonance spectroscopy (NMR)- and mass spectrometry (MS)-based biochemical profiling (metabolomics) allows for the sensitive detection of metabolite pattern changes in urine. • In systematic studies in rats we showed that ciclosporin caused urine metabolite pattern changes typical for proximal tubule damage and that these pattern changes seemed to be more sensitive than established clinical kidney function markers such as serum creatinine concentrations. WHAT THIS PAPER ADDS • This study showed that urine metabolite pattern changes as assessed by 1H-NMR and HPLC-MS are sensitive enough to detect the effect of ciclosporin as early as 4 h after a single oral dose. • In our previous rat studies, changes in urine metabolite pattern in response to ciclosporin translated into healthy humans, indicating the involvement of the same toxicodynamic mechanisms. • The results provide proof of concept for further development of this combination molecular marker strategy into diagnostic tools for the detection and monitoring of drug nephrotoxicity. AIMS The immunosuppressant ciclosporin is an efficient prophylaxis against transplant organ rejection but its clinical use is limited by its nephrotoxicity. Our previous systematic studies in the rat indicated urine metabolite pattern changes to be sensitive indicators of the negative effects of ciclosporin on the kidney. To translate these results, we conducted an open label, placebo-controlled, crossover study assessing the time-dependent toxicodynamic effects of a single oral ciclosporin dose (5 mg kg−1) on the kidney in 13 healthy individuals. METHODS In plasma and urine samples, ciclosporin and 15- F2t-isoprostane concentrations were assessed using HPLC-MS and metabolite profiles using 1H-NMR spectroscopy. RESULTS The maximum ciclosporin concentrations were 1489 ± 425 ng ml−1 (blood) and 2629 ± 1308 ng ml−1 (urine). The increase in urinary 15- F2t-isoprostane observed 4 h after administration of ciclosporin indicated an increase in oxidative stress. 15- F2t-isoprostane concentrations were on average 2.9-fold higher after ciclosporin than after placebo (59.8 ± 31.2 vs. 20.9 ± 19.9 pg mg−1 creatinine, P < 0.02). While there were no conclusive changes in plasma 15- F2t-isoprostane concentrations or metabolite patterns, non-targeted metabolome analysis using principal components analysis and partial least square fit analysis revealed significant changes in urine metabolites typically associated with negative effects on proximal tubule cells. The major metabolites that differed between the 4 h urine samples after ciclosporin and placebo were citrate, hippurate, lactate, TMAO, creatinine and phenylalanine. CONCLUSION Changes in urine metabolite patterns as a molecular marker are sufficiently sensitive for the detection of the negative effects of ciclosporin on the kidney after a single oral dose. [ABSTRACT FROM AUTHOR]