Flower colour is known to be an automatic magic trait, undergoing divergent selection pressures exerted by distinct pollinators and involved in reproductive isolation. However, variation at this trait may also results from other eco-evolutionary factors whose interpretation requires throughout context-specific analyses. Here, we investigated the eco-evolutionary causes of pink- and yellow-flowered morphs in Pedicularis comosa where their parapatric ranges form a contact zone: in the East of the Pyrenees Mountains. First, we generated a near-chromosome-scale reference genome assembly for this species. We then used a Genotyping By Sequencing approach to infer patterns of genetic diversity and differentiation between populations and morphs at a total of 158 individuals from 11 localities. We found that neutral genetic structure is primarily consistent with geography rather than with colour. However, admixture analyses and clines suggest the existence of a cryptic hybrid zone between morphs. Outlier detection methods and examination of locus-by-locus cline features, then allowed to pinpoint candidate loci to explain colour variation. To gain insight into the functional aspects of these loci, we finally analysed floral transcriptomes and quantified pigments using Liquid Chromatography coupled with Mass Spectrometry (LC-MS) and confirmed the involvement of key genes in the anthocyanin metabolic pathway (e.g. DFR, FLS) and associated pigments (e.g. cyanidin and delphinidin). Our results show that implementing a highly integrative multi-omic approach can allow unraveling the genetic basis and the eco-evolutionary significance of adaptive traits with even very limited previous knowledge, on species with large and complex genomes.

Anal. Methods, 2026, Accepted Manuscript DOI: 10.1039/D5AY01923K, PaperBing Qian, Yonghua Hu, Qiong Wu, Hongxing Li, Chulian Su, Chengyuan Liu, Yang Pan, Bingjun Han A rapid in-situ analytical method combining ultrasonic nebulization extraction with atmospheric pressure photoionization mass spectrometry was developed for direct detection of endogenous compounds in complex tobacco matrices. The ultrasonic nebulization... The content of this RSS Feed (c) The Royal Society of Chemistry

We assess batch correction methods for MALDI mass spectrometry imaging experiments. ComBAT reduced batch-related technical variance, maintained biological variation, and improved the overall score by 19.4%.

T cell activation results in profound proteome remodeling that programs T cells into distinct cellular states. The mechanistic target of rapamycin (mTOR) biases T cell differentiation toward a cytotoxic fate at the expense of memory-precursor formation, making mTOR inhibition an attractive strategy to boost T cell memory during vaccination. Here, we used matched time-resolved mRNA sequencing and quantitative mass spectrometry to define how the human T cell proteome is remodeled during the first 24 hours of activation. We found that human T cells rapidly remodel their proteome in distinct, temporally ordered modules that drive translation and proliferation while promoting a cytotoxic T cell state. Notably, mTOR inhibition during the first 24 hours of T cell activation perturbed these protein modules. Strikingly, transient mTOR inhibition limited to the first 16 hours of T cell priming was sufficient to imprint a memory-like T cell state, while preserving the capacity to produce inflammatory cytokines and mediate target cell killing. Together, these findings indicate that mTOR activity dictates stable functional trajectories during early T cell activation, revealing a therapeutic window to refine vaccination responses.

This study evaluated the potential of the diffusive gradients in thin films (DGT) technique to assess radiogenic strontium (Sr) and lead (Pb) isotope signatures in bioavailable soil fractions as a proxy for plant uptake. Concentrations (cDGT) and isotope ratios of Sr (87Sr/86Sr) and Pb (207Pb/206Pb, 208Pb/206Pb, 206Pb/204Pb) assessed by DGT (TK100, Chelex), along with extractable (NH4NO3, NH4OAc, EDTA) and total Sr and Pb mass fractions and isotope ratios, were compared to those in Lactuca sativa L. (lettuce), Triticum aestivum L. (wheat), and Raphanus sativus L. (radish) grown on five geochemically distinct soils. Relative to conventional soil extraction, DGT significantly reduced matrix loads, facilitating isotope ratio measurements by multi-collector inductively coupled plasma mass spectrometry. DGT-labile Sr and Pb concentrations and isotope ratios reflected soil-specific geochemical signatures, allowing for clear differentiation among soils. Importantly, DGT-labile isotope ratios closely matched those in plant tissues across soils and species within analytical uncertainty, demonstrating that DGT captures the isotopically relevant bioavailable Sr and Pb pool without inducing significant mass-dependent isotopic fractionation. These findings establish DGT as a practical tool for bioavailable multi-isotope tracing with strong potential for applications in environmental forensics, food authentication, and archaeological provenance research. Graphical abstract

Analytical ChemistryDOI: 10.1021/acs.analchem.5c06097

A Cu-Ni-W tri-component catalyst enables efficient nitrate-to-ammonia conversion under pulsed electrolysis. Combined experimental and theoretical studies attribute its performance to component synergism and regulated intermediates. Its facile adaptation for glycerol valorization to formic acid underscores a versatile system design concept, advancing electrochemical coupling strategies for a broad spectrum of industrially relevant reactions. ABSTRACT Electrochemical nitrate reduction represents a promising route for sustainable ammonia (NH3) production, yet its practical deployment is constrained by the limited efficiency of state-of-the-art electrocatalysts and immature system architectures. Here, we report a generalist copper–nickel–tungsten tri-component tandem electrocatalyst via a sequential microwave-hydrothermal deposition route. Under pulsed electrolysis conditions, the catalyst delivers a remarkable Faradaic efficiency of 97.1% and a record-high ammonia yield rate of 43.87 mg h−1 cm−2. Online differential electrochemical mass spectrometry (DEMS) identifies key intermediates and associated pathways, while density functional theory (DFT) calculations elucidate the cooperative roles of each component: the copper component facilitates nitrate adsorption and deoxygenation, the nickel component promotes water dissociation for steady *H supply, and the tungsten component serves as a dynamic *H reservoir. This synergy efficiently suppresses hydrogen evolution and enhances ammonia selectivity. Furthermore, coupling with glycerol valorization (to formic acid) as the anodic reaction demonstrates the potential for energy-efficient ammonia electrosynthesis. Collectively, this work offers both design strategies and mechanistic understanding for next-generation multi-component tandem electrocatalysts targeting advanced nitrogen-based chemical synthesis.

Environmental Science & Technology LettersDOI: 10.1021/acs.estlett.5c01047

Publication date: March 2026 Source: International Journal of Mass Spectrometry, Volume 521 Author(s):

Publication date: March 2026 Source: International Journal of Mass Spectrometry, Volume 521 Author(s):

Publication date: Available online 31 January 2026 Source: International Journal of Mass Spectrometry Author(s): Wenwu Yang, Can You, Xiaofei Qiu, Xirun Tong, Shansong Lu, Guiling Duan, Yingxiong Cai, Hanyu Deng, Hongmei Yang

Publication date: 1 June 2026 Source: Talanta, Volume 303 Author(s): Yihe Liu, Jianzheng Yang, Jianying Zhang, Yan Zhou, Yichuan Tang, Tao Zhou

Publication date: Available online 31 January 2026 Source: Journal of Chromatography B Author(s): Ting Zou, Xiangchang He, Zhiying Yuan, Weihe He, Jie Dai, Siyu Li, Guangming Xu

Publication date: 15 March 2026 Source: Journal of Proteomics, Volume 325 Author(s):

Publication date: Available online 31 January 2026 Source: Journal of Proteomics Author(s): Xiang Li, Zhiqiong Mao, Peichan Chao, Yajin Liao, Yalan Li

Capillary zone electrophoresis (CZE)-mass spectrometry (MS) has been proposed as a powerful analytical tool for bottom-up, top-down, and native proteomics (multi-level proteomics) decades ago to analyze complex biological samples at the levels of peptides (bottom-up), proteoforms (top-down), and complexoforms (native). However, its broad adoption has been impeded by the limited robustness and reproducibility. Here, we present multi-level proteomics data from nearly 170 CZE-MS runs (~170 hours of instrument time), demonstrating qualitatively (i.e., the number of identified peptides and proteoforms, the number of detected complexoforms, and their migration time) and quantitatively (i.e., peptide, proteoform, and complexoform intensity) reproducible measurement of complex samples with varying levels of complexity, i.e., Escherichia coli cells, HeLa cells, and human plasma. CZE-MS-based native proteomics enabled the detection of hundreds of complexoforms up to 800 kDa from the complex systems via consuming only nanograms of protein material. The results indicate that CZE-MS is sensitive and reproducible enough for broad adoption for multi-level proteomics-based biomedical research.

Stable carbon and nitrogen isotope ratios are widely used in the life sciences to investigate diet, trophic interactions, and metabolic fluxes, but conventional isotope ratio mass spectrometry requires milligram scale samples, limiting its applicability to small or rare biological specimens. Fourier Transform Isotopic Ratio Mass Spectrometry (FT IsoR MS) enables amino acid resolved isotope analysis in a proteomics compatible workflow and has previously been demonstrated at the microgram scale. Here, we assess the lower sample limit of FT IsoR MS by integrating it with single cell proteomics style sample preparation. Using human HeLa cells cultured in 13C-glucose enriched and control media, we show that reliable relative delta 13C measurements can be obtained from as few as 50 cells, corresponding to

A recent genome mining study identified class II lanthipeptides encoded in Nostoc punctiforme PCC73102 that contain acyl groups conjugated to Lys side chains. The structure and bioactivity of these peptides, named nostolysamides, were not determined. In this study, we heterologously produced the nostolysamides by co-expression of the NpuA precursor peptide with an N-terminal SUMO tag with the class II lanthipeptide synthetase NpuM in Escherichia coli. We structurally characterized the NpuA-derived product and established the position of the thioether crosslinks. All four lanthionine and methyllanthionine residues were shown to have the DL configuration by Marfey's analysis. Tandem mass spectrometry as well as mutagenesis studies indicate an N-terminal non-overlapping methyllanthionine ring and three overlapping rings at the C-terminus for which the most likely ring pattern is proposed. After removal of the leader peptide, the resulting lanthipeptide exhibits antifungal activity against Candida species as well as antimicrobial activity against gram positive bacteria by disrupting cell membranes. The antibacterial activity is shown not to involve lipid II, consistent with the observed antifungal activity because fungi do not contain this bacterial cell wall precursor. The biosynthetic gene cluster also encodes an acetyltransferase NpuN that transfers long chain acyl groups to the side chain of a Lys residue in position 1 of the precursor peptide. In vitro studies of NpuN shows relatively broad substrate specificity with NpuN conjugating various acyl groups from acyl-CoA substrates to Lys1 in the nostolysamides. The acylation did not appreciably change the antifungal and antimicrobial activity of nostolysamide showing that it is not required for these activities.

Base excision repair (BER) is the primary pathway that removes oxidatively-induced DNA base damage from the nuclear and mitochondrial genomes, with 8-oxoguanine DNA glycosylase (OGG1) initiating repair at the two most frequently-formed base lesions: 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxoGua) and 2,6-diamino-4-oxo-5-formamidopyrimidine (FapyGua). Humans expressing a catalytically-compromised variant of OGG1 (S326C) are at increased risk for type 2 diabetes, Alzheimers disease, and Parkinsons disease. To potentially enhance the overall catalytic efficiency of this variant, a prior medicinal chemistry screen discovered seven chemically distinct agonists of OGG1 that stimulated activity in vitro and attenuated a paraquat (PQ) challenge in cultured cells. Herein, we developed structure-activity relationships around one specific core structure, F01. Using fluorescence-based DNA cleavage assays, we assessed the abilities of these compounds to stimulate the overall rate of OGG1 catalysis. Multiple compounds were identified that increased OGG1 activity on DNAs containing a site-specific 8-oxoGua by 2-fold or greater, with 9 compounds showing EC50 concentrations lower than F01 and were specific for OGG1. Selected agonists were shown to enhance OGG1-catalyzed release of 8-oxoGua and FapyGua from {gamma}-irradiated high-molecular-weight DNA using gas chromatography tandem mass spectrometry analyses. Since these assays did not reveal which step in the overall reaction was stimulated, we used a separation of function OGG1 mutant that possessed glycosylase, but not abasic-site (AP) lyase activity to demonstrate that the glycosylase step was not enhanced. In contrast, all agonists stimulated the AP lyase activity to levels equal to or greater than the magnitude of stimulation observed for overall chemistry, implicating agonist-mediated turnover as a potential contributor to the overall rate stimulation. The biological activities of selected agonists were evaluated in OGG1-deficient Kasumi-1 cells under conditions of paraquat (PQ)-induced oxidative stress, with several compounds mitigating PQ challenge.

Protein function is governed by more than abundance alone. Here, the authors introduce a supercharging-enhanced nDIA-MS workflow to map drug-induced solubility changes across the proteome, enabling high-throughput analysis of protein state transitions.

The growing demand for rare earth elements (REEs) underscores the need for sustainable recovery methods and a reliable supply. Here the authors establish a platform using a yeast to produce bio-oxalic acid for REE recovery, achieving 99% REE recovery from low-grade ore.

Amyloid-beta (Aβ) oligomers are key contributors to the pathology and progression of Alzheimer’s disease (AD), making their characterization essential for understanding aggregation processes and developing potential therapeutic strategies. This study provides a systematic framework for analyzing Aβ(1–42) oligomers in vitro using cyclic ion mobility-mass spectrometry (cIMS). Compared to previous generations of traveling wave ion mobility (TWIM) devices, the cIMS platform offers superior resolution through its scalable ion mobility path length. However, the multistage character of the cIMS platform requires thorough investigation of parameters affecting oligomer transmission and activation to ensure reliable analysis of labile and dynamic systems such as Aβ oligomers. Our findings highlight the critical influence of cone voltage (CV) on in-source ion activation, subsequent structural changes, and oligomer detection. By balancing CV, we achieved detection of a broad range of oligomeric species while limiting their activation and maximizing signal intensity. Moreover, we present the first comprehensive set of optimized ion optics and ion mobility parameters that enable effective transmission and separation of oligomer Aβ(1–42) ions. Using the optimized method, we successfully detected a spectrum of Aβ(1–42) oligomers ranging from dimers to dodecamers. Additionally, the method was applied in collision-induced unfolding experiments, revealing size-dependent conformational transitions proving its applicability. This optimized cIMS methodology establishes a foundation for future studies on Aβ(1–42) aggregation mechanisms, AD pathogenesis, and therapeutic applications. Furthermore, our results offer valuable insights into cIMS instrument tuning, with potential applications in the analysis of other complex biological systems. Graphical Abstract

A one-pot enzymatic platform enables the biosynthesis and site-specific incorporation of chalcogen-containing tyrosine analogues (O, S, Se) into proteins in E. coli. Engineered tyrosine phenol lyase (TPL) variants and orthogonal synthetases are combined to expand the genetic code with redox-active residues, paving the way for designer proteins with tunable electronic and catalytic properties. ABSTRACT Expanding the genetic code with unnatural amino acids (UAAs) offers powerful opportunities to engineer proteins with novel redox and catalytic functions, but is often limited by the need for multistep UAA synthesis and inefficient cellular uptake. Here, we report an integrated biosynthetic–genetic incorporation strategy for chalcogen-containing proteins from the respective phenols. Structure-guided engineering of tyrosine phenol lyase (TPL) enabled the enzymatic production of 3-methoxy-, 3-methylthio-, and 3-methylseleno-L-tyrosine (MeSeY) directly in living cells. Using evolved orthogonal aminoacyl-tRNA synthetases, these analogues were site-specifically incorporated into green fluorescent protein (GFP), as confirmed by fluorescence assays, spectroscopy, and mass spectrometry. We further established a one-pot in vivo system that unifies analogue biosynthesis with translation, reducing precursor requirements and cellular toxicity. This work introduces selenium as a genetically encoded handle for protein engineering and establishes a scalable strategy that couples biocatalysis with genetic code expansion to access redox-active designer proteins. Importantly, installation of MeSeY at the GFP chromophore residue Tyr66 provides redox-responsive fluorescence. In a circularly permuted GFP (cpGFP) scaffold, improved chromophore accessibility enables reversible redox switching under H2O2/thiol cycling.

Stressful events are a leading factor in development of depression. The medial prefrontal cortex (mPFC) is strongly associated with depression etiology and exposure to uncontrollable stressors results in synaptic dysfunction and loss. Learned helplessness is a behavioral paradigm that measures effects of repeated exposure to uncontrollable, inescapable stress on later responses to escapable stress. We therefore performed a proteomic analysis of mPFC synaptosomes in a mouse learned helplessness model to identify molecular changes that could contribute to functional consequences of inescapable stress. Male and female mice were evaluated at baseline and following exposure to escapable or inescapable stress followed by an active avoidance test. Label-free mass spectrometry followed by pathway and protein-protein interaction network analyses identified alterations in signaling pathways involved in energy metabolism, neurotransmitter signaling, and protein shuttling. Furthermore, phosphoproteomics revealed alterations related to synaptic function, neurotransmitter signaling and protein internalization, as well as changes in activity of kinases previously identified as mediators of antidepressant efficacy (GSK3B) and receptor internalization (ADRBK1). We more deeply examined alterations in the Acetylcholine Receptor Signaling Pathway, and identified muscarinic receptor proteins (Chrm1, Chrm2, Chrm4) and key proteins involved in their translocation to and from the membrane. These results identify substantial changes in the mPFC proteome following exposure to inescapable stressors. In addition, mPFC muscarinic cholinergic signaling is well placed to mediate responses to an inescapable stressor. This proteomic study will be useful in guiding studies of human mPFC relevant to depression. Data are available via ProteomeXchange with identifier PXD073765.

The RNA exosome is an essential and ubiquitous RNase with exonucleolytic activity, involved in ribosome biogenesis and RNA quality control in eukaryotes. It is present both in nucleus and cytoplasm, and interacts with specific cofactors in each cell compartment, which are essential for recruitment and activity control of the exosome. Posttranslational modifications are known to regulate enzyme activity and protein interaction, although their precise roles are individually specific. In this study, we investigated the phosphorylation status of proteins associated with the nuclear (Rrp6) and core (Rrp46) subunits of the RNA exosome in Saccharomyces cerevisiae. Using co-immunoprecipitation followed by phosphopeptide enrichment and high-resolution mass spectrometry, we identified 121 phosphorylation sites on proteins functionally related to rRNA processing. Differential phosphorylation patterns between Rrp6 and Rrp46 co-immunoprecipitations are consistent with distinct exosome assemblies and suggest potential regulatory roles for phosphorylation. The results shown here highlight the role of phosphorylation in the recruitment and control of the exosome in RNA processing and degradation, offering new insights into the posttranscriptional control of gene expression.