Per- and polyfluoroalkyl substances (PFAS) are synthetic fluorinated compounds used widely in industrial and consumer products. They are unusually stable due to carbon-fluorine bonds and resistant to degradation, making them persistent contaminants in water, soil, and biota. PFAS are associated with adverse health effects in humans including cancer and liver disease. The effects of PFAS on human-associated bacteria are largely unexplored, a significant gap in knowledge because these bacteria are exposed to PFAS in vivo at sites including the colon and bladder. One of the best studied PFAS compounds is perfluorooctanoic acid (PFOA), an eight-carbon perfluorinated carboxylic acid whose structure is analogous to a fatty acid. Here, we cultured Enterococcus faecalis, a Gram-positive bacterium, and Pseudomonas aeruginosa, a Gram-negative bacterium, in growth medium supplemented with PFOA and corresponding control conditions and performed lipidomic analyses using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to elucidate lipid remodeling in response to PFOA exposure. Strikingly, novel fluoroalkyl-containing membrane lipids are synthesized by both of these bacteria, with each species synthesizing unique fluoroalkyl-lipids. Moreover, a high-level daptomycin-resistant strain of E. faecalis produces strikingly high levels of fluoroalkyl-lipids, demonstrating that prior antibiotic exposure and concomitant effects on bacterial evolution can alter bacterial interactions with PFAS. Because bacterial lipids are important immunomodulators in vivo, we propose that PFAS-containing bacterial lipids may be novel mediators of host-microbe-pollutant interactions. Our results also establish a novel mechanism for the bioaccumulation of PFOA and, potentially, for bioremediation of PFOA in biological systems such as the human gastrointestinal tract.

Bacterial stress responses have been studied at the phenotypic, transcriptional, and translational levels, demonstrating the presence of an ''alarm'' phase immediately after stress exposure. However, the contributions of RNA modifications during stress adaptation remain largely unexplored. Here, we map the epitranscriptomic changes of Escherichia coli after exposure to oxidative and acid stress using direct RNA sequencing of mRNA, rRNA, and tRNA, combined with mass spectrometry, deletion mutant phenotyping, and single-nucleotide PCR. We identified widespread, dynamic RNA modifications that include central metabolism transcripts and increased levels of rRNA methylations (m4Cm and m5C) under both stresses, with potential consequences for translation. In uncharged tRNAs, stress-specific modifications via the Mnm and Q pathways accumulated at the wobble position; these modifications proved crucial for survival. Together, these findings reveal a multifaceted layer of post-transcriptional regulation, establishing the first comprehensive view of the bacterial epitranscriptome during the alarm phase of stress adaptation.

The Journal of Physical Chemistry ADOI: 10.1021/acs.jpca.5c04493

Esophageal-gastric cancers (EC) represent a significant global health concern, with esophageal cancer ranking seventh in terms of incidence and mortality worldwide. Gastric cancer is especially concerning, with an estimated one million new cases and 800,000 deaths annually. Late diagnoses often lead to poor outcomes, requiring critical interventions such as radical surgical resection with clear margins, in conjunction with chemotherapy, or radiotherapy to prevent recurrences and enhance survival. Thus, EC represents a significant clinical challenge, especially given the difficulty in achieving precise surgical margins in aggressive subtypes like poorly cohesive carcinoma (PCC). Moreover, pathological intraoperative margin assessment encounters significant issues, especially for PCCs, due to lacks of sensitivity for microscopic infiltration, potentially leading to recurrence and poorer patient outcomes. We address these critical limitations by integrating SpiderMass, an ambient mass spectrometry (MS) technology, with clinical metadata and microbiome profiling couple along with Machine learning. We demonstrate SpiderMass capability in real-time molecular margin delineation and identify distinct lipidomic and microbiome signatures correlating with tissue type and prognosis. Our integrative approach provides a more precise and biologically informative intraoperative diagnostic tool, significantly enhancing surgical decision-makin, to improve patient outcomes and extend survival.

Analytical ChemistryDOI: 10.1021/acs.analchem.5c02694

Analytical ChemistryDOI: 10.1021/acs.analchem.5c04341

J. Anal. At. Spectrom., 2025, Advance Article DOI: 10.1039/D5JA00320B, PaperShaohua Dong, Youwei Chen, Jian-Feng Gao, Xianwu Bi, Ruizhong Hu Online matrix correction for boron isotopes: Fe–Mn-driven IMF in tourmaline corrected via NanoSIMS co-measurement of δ11B, Fe/B and Mn/B, enabling efficient high-precision δ11B analysis without EPMA. To cite this article before page numbers are assigned, use the DOI form of citation above. The content of this RSS Feed (c) The Royal Society of Chemistry

Ices are sources of organic matter in various astrophysical environments, but the impact of their composition on the formation of volatile organic compounds (VOCs) remains underexplored. Here, the authors use gas chromatography coupled to high-resolution mass spectrometry (GC-Orbitrap-MS) to show that ice photo-processing and thermal evolution are directly correlated to VOC formation during the warming of different H2O:CH3OH:NH3 ices and highlight the role of NH3 in driving the formation of nitrogen refractory compounds.

Giant viruses challenge traditional boundaries of virology with their large particle sizes, complex genomes, and unique replication strategies. Yet, despite its 750 nm diameter and incorporation of dozens of proteins, mimivirus' virion retains an icosahedral symmetry, a trait often associated with smaller viruses. The functional roles and interactions of most proteins composing such complex icosahedral particles remain elusive. Here, we dissect the spatial and functional organization of mimivirus morphogenesis by integrating bioinformatics, genetics and interactomics. We performed protein clustering using a structure-informed approach integrating AlphaFold models with sequence information to classify and functionally annotate the ORFan-rich mimivirus proteome. To map the protein-protein interaction network during morphogenesis, we employed endogenous tagging and co-immunoprecipitation coupled to mass spectrometry. This strategy revealed distinct interaction modules associated with the virion membrane, nucleoid and viral factory compartments. Comparative analyses with other icosahedral and non-icosahedral giant viruses uncovered conserved assembly nodes and virion shape-specific adaptations. Our findings shed light on the global organization of mimivirus virion biogenesis and highlight the evolutionary plasticity of viral morphogenetic networks within the Nucleocytoviricota.

Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00152

Analytical ChemistryDOI: 10.1021/acs.analchem.4c06368

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous toxic pollutants that pose significant risks to human health. However, because of their intrinsic non-polar properties, only moderate detection sensitivity can be achieved in the mass spectrometric detection of PAHs. In this work, we presented a novel electrochemically assisted derivatization nano-electrospray ionization mass spectrometry (ECAD-nESI-MS) method to permit the rapid and ultrasensitive analysis of PAHs in complicated samples. In ECAD-nESI-MS, the in situ electrochemical derivatization of PAHs with pyridine and the electrospray ionization are simultaneously activated by applying a high voltage onto the Pt electrode. Notably, the derivatization takes advantage of the inherent electrochemical aspect of electrospray ionization, that is, the electrooxidation of substrates in the positive-ion mode, thus requiring no extra electrochemical cell and potentiostat. Through the electrochemical derivatization of PAHs into the corresponding pyridinium ions, the ECAD-nESI-MS method achieved remarkably improved detection sensitivity, where the limit of detection (LOD) is 3~10 times lower than the state-of-the-art atmospheric pressure chemical ionization mass spectrometry (APCI-MS) and gas chromatography mass spectrometry (GC-MS). With advantages in low detection limit, wide linear range, fast analysis speed (

Journal of the American Society for Mass SpectrometryDOI: 10.1021/jasms.5c00208

ABSTRACT Rationale Shexiang Baoxin Pill (SBP) has been shown to assist in lowering blood glucose levels in patients with type 2 diabetes mellitus (T2DM) in clinical studies. However, the antidiabetic metabolism of SBP has not yet been fully elucidated. Methods Male db/db mice were used as an animal model of T2DM. Mice were given metformin (Met), SBP, and a combination of Met and SBP in low dosage (Met-SBP) and high dosage (Met-HSBP) via gavage for a duration of 8 weeks, respectively. Metabolomics analysis of serum samples was performed on ultra-high-performance liquid chromatography coupled with Orbitrap Exploris 120 mass spectrometry. Results The animal experiment showed that SBP effectively assists in lowering fasting blood glucose levels and significantly attenuating insulin resistance in db/db mice. A total of 30 metabolites with significant changes were identified, mainly involving lipids, amino acids, and acylcarnitines. Among these regulated metabolites, 9 metabolites were affected by Met, 10 by SBP, 27 by Met-SBP, and 9 by Met-HSBP. The results revealed that SBP specifically regulated the dysfunction of medium-chain acylcarnitines in the fatty acid oxidation (FAO) pathway. Additionally, the combined use of SBP and Met may play a synergistic role in treating T2DM. Conclusions SBP has a positive effect in regulating fasting glucose and insulin sensitivity in T2DM db/db mice, possibly through the FAO metabolic pathway. SBP in combination with Met may play a positive role in the inflammatory response. The results of this study may offer a theoretical foundation for the clinical application of SBP on T2DM and provide new insights for the research of traditional Chinese medicine in treating diseases.

Analytical ChemistryDOI: 10.1021/acs.analchem.5c04489

Publication date: December 2025 Source: International Journal of Mass Spectrometry, Volume 518 Author(s):

Publication date: December 2025 Source: International Journal of Mass Spectrometry, Volume 518 Author(s):

Publication date: December 2025 Source: International Journal of Mass Spectrometry, Volume 518 Author(s):

Publication date: Available online 11 October 2025 Source: Journal of Chromatography A Author(s): Rizky Ilhamsyah, Daniel R. Struk, Christopher A. Heist, Alexander T. Adams, Lou Ann Brown, Jean-Marie D. Dimandja, Peter J. Hesketh

The full complement of chromatin-associated proteins -- collectively referred to as the chromatome -- enables genome functioning in eukaryotes by participating in a wide range of physico-chemical processes. These include mediating diverse specific and non-specific intermolecular interactions, catalyzing in situ synthesis and modification of macromolecules, facilitating ATP-dependent chromatin remodeling, etc. Despite considerable progress in epigenomics and the structural characterization of many nuclear proteins and their complexes, our understanding of chromatin organization at the proteome scale remains incomplete. This gap hinders the development of a holistic view of genome regulation. In this study, we present a state-of-the-art characterization of the human chromatome based on an integrative meta-analysis of diverse data sources describing the composition, abundance, and sub-nuclear localization of chromatin proteins. This effort is complemented by original analyses of their physico-chemical properties, domain architectures, and interaction patterns. To support and streamline these analyses, we developed a reference dataset of chromatin proteins, integrated with an empirical, function-based classification ontology and an associated interactive web resource - SimChrom - accessible at https://simchrom.intbio.org/. The reference dataset was carefully curated by reconciling data among protein databases, localization, and mass spectrometry-based experimental studies. Sequence-based and AI-assisted structural analyses revealed previously unannotated domains within chromatin proteins that warrant experimental validation, as well as the widespread use of multivalent interaction strategies that underpin chromatin organization. Together, our findings establish a robust framework for future studies aimed at elucidating genome function through detailed analysis of protein-protein and protein-nucleic acid interactions within chromatin.

Publication date: Available online 11 October 2025 Source: Journal of Mass Spectrometry and Advances in the Clinical Lab Author(s): Maria M. Derkach, Anatoly A. Sorokin, Andrey A. Kuzin, Eugene N. Nikolaev, Igor A. Popov, Stanislav I. Pekov

Background: Reactive oxygen species are increased across most pulmonary hypertension (PH) etiologies, resulting in increased reactive lipid dicarbonyls, which form protein adducts and impair mitochondrial function. We hypothesized that reducing reactive lipids would reduce right ventricular systolic pressure (RVSP) and improve cardiac function by eliminating protein-lipid damage feedback loops. Methods: We used 2-hydroxybenzylamine (2-HOBA) to scavenge reactive lipids in three complimentary mouse models of PH: AKR-high fat diet (HFD, metabolic stress), LNAME-HFD (cardiometabolic syndrome), and pulmonary artery banding (PAB, load stress). Cardiac function was measured by echocardiography and catheterization. RV energy metabolism was determined by oxygraphy. Mass spectrometry analyzed lipids and ceramides; O-link and RNA-Seq evaluated proteomic and gene expression in lungs, RV, and LV. Results: Reducing reactive lipids with 2-HOBA resulted in a ~10% reduction in RVSP, reduced diastolic dysfunction, reduced plasma lipids and ceramides, and normalized RV fatty acid oxidation that was severely impaired in the AKR-HFD and PAB models. Proteomic and RNA changes in the lungs, RV, and LV suggested reduced oxidative damage and inflammatory signaling and altered developmental and actin organization signaling; these changes are plausibly associated with the improved adaptation. Some changes were sex specific, including a 4x higher cardiac fatty acid content in males than females. Conclusions: Reactive lipid scavenging improves cardiac metabolic and diastolic function and pulmonary vascular resistance through restoration of mitochondrial function and reduced oxidative protein damage. The magnitude of hemodynamic improvement combined with substantial diastolic function improvement suggests clinical potential, particularly for PH patients with metabolic comorbidities.

Since the first high-resolution structures of recombinantly assembled nucleosomes, efforts have shifted towards understanding chromatin structure in a native context. Most of these efforts have focused on native-like, yet still recombinantly assembled, nucleosomes that contain native DNA sequences. To date, no high-resolution structures of native human nucleosomes have been reported. Here we report the high-resolution cryo-EM structure of native human nucleosomes isolated from HEK293 cells. The HEK293-NCP structure reveals that native human nucleosomes store 145 bp of DNA. Despite the DNA sequence diversity of native nucleosomes, we observe conserved nucleotides that support the idea of a nucleosome positioning code. In addition to these striking features of nucleosomal DNA, we note alternate conformations of several DNA contacting histone residues that hint at dynamics in the HEK293-NCP. To complement the HEK293-NCP structure, we provide a mass spectrometry analysis of histone modifications and variants present in the sample, which demonstrates that a typical HEK293-NCP is composed of canonical histones with N-terminal tails that are methylated at K9, K27 and/or K36 of histone H3. Altogether these findings have implications for biological processes such as chromatin remodelling and transcription and improve our understanding of nucleosome and chromatin structure in a native context.

Publication date: Available online 10 October 2025 Source: Journal of Chromatography A Author(s): Attilio Naccarato, Rosangela Elliani, Antonio Tagarelli

This study investigated the effectiveness of natural deep eutectic solvents (NADES) as a green alternative to traditional organic solvents for the extraction of anthocyanins from three Amazonian matrices: açaí, mangosteen pericarp, and purple yam. High-intensity ultrasound-assisted extraction (HIUS) was evaluated by varying key processing parameters such as molar ratio, solid-to-liquid ratio (S/L), added water, extraction time, and ultrasound power. Results showed that both molar ratio and added water had a significant impact on extraction efficiency. The addition of water to NADES was crucial in reducing viscosity and enhancing anthocyanin solubility, thereby improving mass transfer. However, excessive water led to decreased extraction yields, likely due to the disruption of hydrogen bonds within the NADES system. The extraction time and ultrasound power proved to be critical factors, as prolonged extraction periods and high power resulted in the degradation of anthocyanins. This study concluded that NADES yielded promising results for anthocyanin extraction. The optimal anthocyanin extraction conditions for açaí (132.20 mg/100 g) were a 1:2 molar ratio, 1:120 S/L, 30% added water, 5 min extraction, and 600 W power. For mangosteen pericarp, the optimal anthocyanin extraction conditions (58.81 mg/100 g) were a 1:2 molar ratio, 1:120 S/L, 30% added water, 5 min, and 1200 W power. For purple yam, the optimal anthocyanin extraction conditions (25.95 mg/100 g) were a 1:3 molar ratio, 1:120 S/L, 20% added water, 5 min, and 1200 W power. Additionally, the NADES-extracted anthocyanins demonstrated good stability across a range of pH values. Liquid chromatography coupled with electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) analysis revealed variability in phenolic profiles, while açaí and mangosteen pericarp showed diverse bioactive compounds, including isorhamnetin and epicatechin. Purple yam exhibited no detectable phenolics. Compared to conventional solvents, NADES extraction exhibited a lower environmental impact, as assessed by Ecoscale and Analytical GREEnness Metric (AGREE) tools. Graphical Abstract