The Sierra Madre Mountains, which happen to be the longest mountain range in the Philippines, is home to lush floral and faunal species as well as forest-based indigenous communities actively involved in preserving local biodiversity. With active reforestation efforts ongoing for decades, the locals are further encouraged to continue their long-standing practice of honey gathering as a form of cultural manifestation and as an important source of livelihood. To further inspire ongoing conservation efforts, we aim to show that the small molecule diversity in Sierra Madre forest honey reflects the local floral composition and is reflective of the positive impact of previous reforestation initiatives. In order to do this, liquid chromatography—mass spectrometry (LC–MS) based metabolomics was used to profile and compare metabolite diversity in honey produced by Apis cerana, Apis breviligula Maa. and Tetragonula biroi (Friese) honey from Palaui Island and Laiban in Northern and Southern Sierra Madre, respectively. Surprisingly, the Philippine National Tree and unfortunately endangered Pterocarpus indicus Willd (loc. Narra) proved to be important, especially in Palaui Island where honey from A. cerana is close to being monofloral. Aside from P. indicus and its small molecule marker hypaphorine, caffeine was detected in Palaui honey beautifully reflecting the way of life of native Agtas who manage a small coffee plantation. The abundance of caffeine, however, is higher in stingless honey samples from Tanay, Rizal where Coffea trees have been extensively included in restoration activities over the past few decades. Our results imply the possibility of using honey as an ecological monitoring tool while generating baseline chemical information that reflects the state of Philippine forests. Furthermore, the identification of unique chemical components in forest honey can be further used in programs that assist indigenous communities in safeguarding the ownership and origin of forest honey sources.

Mass Spectrometry Reviews, Volume 45, Issue 2, Page 149-151, March/April 2026.

Background: DDX53 (DEAD box helicase 53, known also as CAGE) is an intronless gene on the X chromosome, which expression shows strong testis specificity. It belongs to the group of cancer testis (CT) antigens, with most studies to date focusing on its role in cancer, but the precise biological function of DDX53 remains unclear. Previous reports identifying rare DDX53 variants in infertile men provided the rationale for investigating the role of DDX53 in the context of human spermatogenesis. By using the human seminoma cell line (TCam 2) as an in vitro male germline model, we aimed to investigate the function and molecular targets of DDX53. Methods: In our study, we used transcriptomic and proteomic approaches (RNA sequencing (RNAseq), enhanced crosslinking and immunoprecipitation (eCLIP), and Co-immunoprecipitation coupled with Mass Spectrometry (Co IP MS)) to investigate the role of DDX53 in the context of human spermatogenesis. By using modified TCam 2 cells to express either DDX53 FLAG or GFP FLAG, we identified regulated genes, RNA targets, and potential protein interactors of DDX53. In addition, we employed Western Blot, RTqPCR, immunostaining, and confocal microscopy to gain deeper insight into the DDX53 protein. Results: Our RNAseq and eCLIP data provide evidence that DDX53 regulates gene expression changes and directly interacts with a broad spectrum of RNA transcripts. Moreover, for the first time, we described RNAs and protein interactors of DDX53 in the context of spermatogenesis. Subcellular localization analysis by confocal microscopy indicated a predominantly cytoplasmic distribution of DDX53, with partial nuclear presence in TCam 2 cells. We also identified DDX53 positive structures that may correspond to germ granule like assemblies, although their precise nature remains to be determined. Additionally, we confirmed DDX53 presence in human testis using a specific, commercially available antiDDX53 antibody. Conclusions: This study's data indicate that DDX53 protein acts as a regulator of RNA metabolism in human cells. Collectively, we show that it participates in transcriptome regulation (including splicing) in male germ cells and exhibits transcriptome-wide RNA interactions, but its wider biological role remains to be clarified.

Glycosylation is critical for viral-host cell interactions in influenza A virus (IAV) infection, but we lack a comprehensive understanding of how IAV infection shapes the host glycoproteome and the implications of these changes. Here, we used a liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to perform proteomic, glycomic, and glycoproteomic characterisation of the dynamic subcellular responses to an in vitro time course infection of human A549 cells with two IAV strains (A/X-31, H3N2; and A/Puerto Rico/8/1934, H1N1). IAV infection resulted in only modest changes to the subcellular proteome, but robust and significant changes to the host secreted and organelle glycome and glycoproteome. Infection with either virus resulted in a widespread reduction in sialic acid across the N- and O-glyco(proteo)me; increased abundance of oligomannose, paucimannose, and phosphorylated glycans; and shorter hybrid/complex glycans. Reduced sialylation was consistent with desialylation of glycans by viral neuraminidase (NA), but with specific features of the glycan and protein controlling the extent of desialylation. Desialylation was greater when glycans were fucosylated; when the sialic acid was attached via an 2,3 linkage or positioned on the 3 arm; on larger, more complex glycans; and when present on proteins that are more accessible to IAV NA. Subtle but prolonged activation of the unfolded protein response in infection led to a doubling of oligomannose N-glycosylation. Glycans were shorter in infection, implicating IAV-induced disruption of Golgi glycoprotein flux as a mechanism that reduces host glycoprotein sialylation and promotes virion release, independent of NA activity. Our data provide important insights into the host glycoproteome during influenza virus infection, furthering our understanding of how influenza NA acts upon host glycans, and how cell stresses in infection perturb key mediators of protein stability and function, cell signalling and immunity.

Bulk proteomics has been demonstrated to differentiate subpopulations within pleiotropic bacterial colonies, yet advanced analyses by mass spectrometry imaging (MSI) hold even greater promise for high-throughput phenotyping and differentiation through spatial insights while reshaping biological discovery through visualization of biomolecular mechanisms directly from samples. High mass resolving power and high spatial resolution analyses are now routine for modern instruments and confidently enable proteoform-informed imaging directly from samples with little preparation. Pairing those analyses with experimental libraries can provide high confidence in annotations of post-translational modifications (PTMs) and truncations, revealing their localization within the sample, and unlocks a direct window into unknown biology at the microscale. However, this profiling is not commonplace for many microbial species, considering the theoretical proteome of Bacillus subtilis was only partially mapped until recently. With little still known about the form and function of many of these proteins - let alone uncharacterized bacterial proteoforms, where PTMs and truncations on the same protein may possess unique physiological roles - there is a wealth of work to still be completed. With the joint application of top-down proteomics (TDP) and MSI, we outline preliminary results from microscale spatial proteomics on B. subtilis to probe a dynamic proteome. B. subtilis forms dense biofilms with rigid extracellular matrix to protect the colonies, and we use these samples to fundamentally demonstrate the feasibility of subpopulation differentiation through detection of proteins and proteoforms throughout the microbiome.

Purpose: Peroxisomes are ubiquitous organelles that compartmentalize metabolic reactions including lipid catabolism and cellular detoxification. Biallelic loss-of-function variants in genes responsible for peroxisome assembly and function cause peroxisome biogenesis disorders (PBDs). Approximately three-quarters of PBDs are due to pathogenic variants in PEX1 or PEX6 and result in multisystem disease, including retinal degeneration and blindness. Despite retinal pigment epithelial (RPE) dysfunction and retinal degeneration occurring frequently in PBDs, precisely how impaired peroxisome activity disrupts retinal function remains to be fully explored. To address this, we differentiated PEX1 knockout (PEX1-/-), PEX6 knockout (PEX6-/-), and wildtype human induced pluripotent stem cells (iPSCs) into RPE to study the consequences of peroxisome dysfunction in this disease-relevant cell type. Methods: CRISPR/Cas9-mediated genome editing was used to generate PEX1-/- and PEX6-/- in human iPSCs. The knockouts and isogenic wildtype iPSCs were differentiated into RPE (iRPE) and characterized by morphology, pigmentation, transepithelial electrical resistance (TEER), and expression of proteins associated with differentiated RPE using immunofluorescence microscopy and flow cytometry. Immunoblot analysis of whole iRPE lysates was used to evaluate the proteolytic processing of peroxisome enzymes, a measure of the integrity of peroxisome matrix protein import. Immunofluorescence detection of peroxisome membrane proteins was used to determine the abundance of peroxisomes across iRPE lines. Targeted lipidomics by gas and liquid chromatography with mass spectrometry were used to quantitatively compare the profiles of wildtype, PEX1-/-, and PEX6-/- iRPE. Accumulation of intracellular neutral lipid, and more specifically lipid droplets, in iRPE was measured using flow cytometry and perilipin-2 immunoblotting, respectively. Phagocytosis of photoreceptor outer segments (POS) by iRPE was evaluated using rhodopsin immunoblotting. Results: PEX1-/-, PEX6-/-, and wildtype iRPE all had comparable hexagonal morphology and integrity of tight junctions, developed pigment, and similarly expressed proteins characteristic of RPE. Immunoblot analysis demonstrated aberrant processing of ACOX1, MFP2, and ACAA1 in PEX1-/- and PEX6-/- iRPE, suggesting impaired peroxisome matrix protein import. Targeted lipid profiling, including total fatty acid (FA) lipid profile analysis, revealed that in comparison to wildtype, PEX1-/- and PEX6-/- iRPE had significantly reduced docosahexaenoic acid (C22:6{omega}3) (p

Single-cell proteomic (scProteomic) measurements of peripheral blood mononuclear cells (PBMCs) are of considerable value in human health, given their involvement in the maintenance of healthy and diseased states. However, the high heterogeneity and relatively small size of immune cell types demand maximal throughput and sensitivity in proteomic measurements that have yet to be fully realized. Here, we describe an approach that addresses sensitivity and throughput through the implementation of Real-Time spectral Library Searching (RTLS), TMTpro 32-plex labelling, an updated nested-nanodroplet processing in One pot for Trace Samples (N2), and a dual-column liquid chromatography system. By prioritizing tandem mass spectrometry (MS2) features with high similarity to library spectra, RTLS enables greater identification depth and feature reproducibility than a standard shotgun MS2 approach in low-input and single-cell samples. The platform permitted 660 single PBMCs to be measured per day, with an average of 750 protein identifications per cell and 1,648 proteins in total, achieving the necessary throughput and depth to characterize immune cell populations. Application of this scProteomic method and a new cell typing informatics approach to 2,130 PBMCs enabled the identification of both major and low-frequency cell types (~1-2%), as well as associated proteomic markers.

Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00373

Per- and polyfluoroalkyl substances (PFAS) continue to increase in concentration and prevalence in the environment due to the creation of emerging PFAS and the lack of breakdown of legacy compounds. PFAS are known to both bioaccumulate and biomagnify; therefore, species higher on the food chain, such as marine mammals, are highly exposed to these chemicals. Although studies suggest that considerable maternal transfer of persistent organic pollutants occurs via lactation, data are still lacking on the temporal trends associated with PFAS exposure. In this study, we first optimized the extraction for PFAS from 5 and 1 mL of goat’s milk using a QuEChERS extraction method to account for precious breast milk samples that are often only available in small volumes. We then utilized a set of dolphin breastmilk samples from an individual mother across a 2-year lactation period to evaluate longitudinal trends in PFAS concentrations and profiles. Thirty PFAS were detected using a multidimensional platform combining liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS), and of these, 20 PFAS were detected continuously across the nursing window of 103–706 days. Quantitative analysis using LC-IMS-MS specifically showed concentrations of perfluorooctanesulfonic acid (PFOS) alone surpass weekly intake recommendations, allometrically scaled to dolphins, from the European Food Safety Authority and Food Standards Australia New Zealand by more than 25-fold. PFOS, however, decreased slightly over time, possibly due to transfer from feedings. Suspect screening and non-targeted analysis also identified 12 compounds including 2 long-chained perfluorosulfonic acids not traditionally evaluated in targeted analyses, as well as the PFOS precursors, perfluoroethylcyclohexane sulfonate (PFECHS) and 2-(N-ethylperfluorooctanesulfonamido) ethyl phosphate (SAmPAP). This study therefore suggests that breastmilk is a major contributor to early-life PFAS exposure for mammals, particularly to long-chained PFAS. Graphical Abstract

Chemical identification of adhesive remains on prehistoric stone tools is of great interest for archaeologists, as the residues contain interesting information on tool use and the exploitation of natural resources by hominins. Adhesives were used to form a wrapping around the stone tool to protect the hand from the sharp edges and improve grip, or to secure a handle out of organic material to the stone tool. This invention, of adding a handle to a stone tool, marks a fundamental change in prehistoric technology. Adhesives can be manufactured from readily available exudates, like pine resin, but could also be man-made, in the case of birch tar that is obtained by dry distillation of birch bark. The glueing properties of the adhesives could be enhanced with the addition of an additive (e.g. charcoal, ochre, beeswax). Given that adhesive manufacture is considered to indicate planning abilities and complex thought, its identification in archaeological assemblages is important for understanding the evolution of human cognition. However, given long-term burial, organic residues on stone tools are generally significantly degraded, which raises numerous chemical challenges and interpretative difficulties that need to be tackled through close collaboration between archaeologists and chemists. Without this interaction between two vastly different research fields, studies can suffer from an overinterpretation of analytical data or a lack of understanding of the archaeological context. This review discusses the main pitfalls encountered in the chemical analysis of prehistoric adhesives and offers analytical recommendations to avoid them. Applying the analytical practices as proposed here will increase the reliability and credibility of the analytical results and allow a strong chemical foundation for the archaeological interpretations. The main focus is on the use of gas chromatography-mass spectrometry for the chemical identification of prehistoric adhesives; however, other commonly used analytical techniques are also briefly discussed. Graphical abstract

Lactose intolerance is common, so accurate detection of lactose in supplements and pharmaceuticals is critical. We validated an ultra-high performance liquid chromatography–tandem mass spectrometry (U-HPLC–MS/MS) method with high sensitivity and specificity for trace lactose in products labeled “lactose-free.” The workflow mitigates matrix effects through solid-phase extraction and filtration and explicitly accounts for α/β mutarotation to ensure correct identification and quantification. Validation per ISO and ICH Q2 confirmed robustness and performance superior to enzymatic/colorimetric assays for quality control and regulatory compliance. The method achieved excellent linearity (R2 > 0.995) over 0.05–10 ppm, recoveries of 95–105%, precision with RSD < 2%, LOQ 0.05 ppm, and matrix effect < 15%. These results enable reliable verification of “lactose-free” claims across diverse matrices, reducing false positives, enhancing reproducibility, and improving labeling transparency.

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):