Mass-Spectrometry-Based Assay at Single-Base Resolution for Simultaneously Detecting m6A and m6Am in RNA.

The methylation modifications of adenosine, especially N6-methyladenosine (m6A) and N6, 2'-odimethyladenosine (m6Am), play vital roles in various biological, physiological, and pathological processes. However, current methods for detecting these modifications at single-base resolution have limitations. Mass spectrometry (MS), a highly accurate and sensitive technique, can be utilized to differentiate between m6A and m6Am by analyzing the molecular weight differences in their fragments during tandem MS analysis. In this study, we present an MS-based method that allows for the simultaneous determination of m6A and m6Am sites in targeted RNA fragments at single-nucleotide resolution. The approach involves the utilization of tandem MS in conjunction with targeted RNA enrichment and enzymatic digestion, eliminating the need for PCR amplification. By employing this strategy, we can accurately identify m6A and m6Am sites in targeted RNA fragments with high confidence. To evaluate the effectiveness of our method, we applied it to detect m6A and m6Am sites in cell and tissue samples. Furthermore, we verified the accuracy of our approach by performing CRISPR/Cas9-mediated knockout of the corresponding methyltransferases. Overall, our MS-based method offers a reliable and precise means for the simultaneous detection of m6A and m6Am modifications in targeted RNA fragments, providing valuable insights into the functional characterization of these modifications in various biological contexts.

On-Line Analysis of Cigarette Smoke Based on Microwave Plasma Torch Mass Spectrometry.

Cigarette smoke contains a large number of chemicals, including both flavor components and harmful substances. The mainstream smoke (MSS) generated by smoking is directly inhaled by individuals, making it crucial to establish an effective method for smoke detection and analysis. One promising technique for analyzing smoke is MPT-MS (Microwave plasma torch mass spectrometry). This approach offers several advantages in accurately detecting the composition of cigarette smoke. By combining MPT-MS with a smoke pumping device, we can achieve real-time online detection of smoke components. We successfully detected 22 flavor compounds present in the smoke. These compounds contribute to the distinct taste of cigarettes. Moreover, we identified 2 polycyclic aromatic hydrocarbons (PAHs) in the smoke. PAHs are known carcinogens and are of great concern in terms of their potential health risks. The successful detection and identification of flavor compounds and PAHs using our method confirm the online detection capability of MPT-MS. This approach provides an efficient and reliable means for analyzing the complex composition of cigarette smoke. By utilizing MPT-MS, we can gain valuable insights into the chemical composition of cigarette smoke and can inform the development of strategies and policies aimed at reducing the harmful effects of smoking and protecting public health.

Crystallization and Solvent Evaporation Ionization Mass Spectrometry (CSEI-MS) for Rapid Detection of Drugs in Complex Matrices.

Illegal addition of drugs is common but seriously threatens public health safety. Conventional mass spectrometry methods are difficult to realize direct analysis of drugs existing in some complex matrices such as seawater or soil due to the ion suppression effect and contamination to MS parts caused by nonvolatile salts. In this work, a novel crystallization and solvent evaporation ionization mass spectrometry (CSEI-MS) method was constructed and developed to achieve rapid desalting detection. CSEI only consists of a heated plate and a nebulizer and exhibits excellent desalting performance, enabling direct analysis of six drugs dissolved in eight kinds of salt solutions (up to 200 mmol/L) and three complex salty matrices. Under optimized conditions, CSEI-MS presents high sensitivity, accuracy, linearity, and intraday and interday precision. Finally, this method is applied to the quantitative analysis of drugs in seawater, hand cream, and soil. Furthermore, the highly sensitive detection of CSEI-MS is demonstrated to remain even if the detection processes are conducted within 5 s via common commercial tools.

Polysaccharides in fruits: Biological activities, structures, and structure-activity relationships and influencing factors-A review.

Fruits are a rich source of polysaccharides, and an increasing number of studies have shown that polysaccharides from fruits have a wide range of biological functions. Here, we thoroughly review recent advances in the study of the bioactivities, structures, and structure-activity relationships of fruit polysaccharides, especially highlighting the structure-activity influencing factors such as extraction methods and chemical modifications. Different extraction methods cause differences in the primary structures of polysaccharides, which in turn lead to different polysaccharide biological activities. Differences in the degree of modification, molecular weight, substitution position, and chain conformation caused by chemical modification can all affect the biological activities of fruit polysaccharides. Furthermore, we summarize the applications of fruit polysaccharides in the fields of pharmacy and medicine, foods, cosmetics, and materials. The challenges and perspectives for fruit polysaccharide research are also discussed.

Prebiotic Formation of Peptides Through Bubbling and Arc Plasma.

The abiotic synthesis of peptides, widely regarded as one of the key chemical reactions on the prebiotic Earth, is thermodynamically constrained in solution. Herein, a simulation of the lightning phenomenon on the sea surface using bubble bursting and arc plasma under ambient conditions enables dipeptide formation of six amino acids with conversion ratios ranging from 2.6% to 25.5%. Additionally, we observed the formation of biologically active tripeptides and investigated the stereoselectivity of the dipeptide formation reaction. By utilizing a mixture of 20 amino acids in the reaction, 102 possible dipeptides were generated. These results establish experimental constructions to mimic achievable prebiotic conditions and provide a credible pathway for endogenous biopolymer synthesis on prebiotic Earth.

Ortho C-H Bond Activations in an Atmospheric Microwave Plasma Ion Source.

C-H bond ortho-substitution reaction has always been a significant and challenging topic in organic chemistry. We proposed a synthesis method based on microwave plasma torches. High-resolution mass spectrometry was used to monitor rapid reaction products. 2-Alkylbenzimidazole can be formed through the reaction of phenylnitrenium ion and nitriles on a millisecond scale. This reaction can achieve the one-step formation of benzimidazoles from benzene ring single-substituted compounds without the addition of external oxidants or catalysts. A similar C-H bond activation reaction can be accomplished with ketones. Meanwhile, the microwave plasma reactor was modified, and the resulting 2-methylbenzimidazole was successfully collected, indicating the device has good application potential in organic reactions such as C-H bond activation reaction.

Long term online desalting analysis of MS/LC-MS using thermal assisted recrystallization ionization.

Mass spectrometric analysis of non-volatile salts containing samples remains challenging due to salt-induced ion suppression and contamination. This challenge is even more pronounced for a liquid chromatography-mass spectrometry analysis, where the accumulation of salts in the transmission system poses an ongoing problem. In this study, a novel thermal assisted recrystallization ionization mass spectrometry (TARI-MS) device was developed to achieve efficient on-line desalting and prolonged analysis of saline samples. The core component of this device was a heated plate positioned between the electrospray unit and the MS inlet. The desalting mechanism was demonstrated as the spontaneous separation of target molecules from salts during the "crystallization" process. After optimization, the angle between the nebulizer and the heated plate was 45°; the distance between the front end of the heated plate and the MS inlet was 2 mm; the distance between the front edge of the heated plate and the center of the sample spray projected onto the heating plate was 3 mm; the distance between the emitter of nebulizer and the heated plate was 3 mm. TARI-MS realized direct analysis of eight drugs dissolved in eight commonly used non-volatile salts solutions (up to 0.5 mol/L). The high sensitivity, repeatability, linearity, accuracy, and intra- and inter-day precision of TARI-MS confirm its reliability as a robust tool for the analysis of saline samples. Furthermore, TARI-MS allowed continuous analysis of salty eluates of LC for up to nearly 1 h without maintenance and verified the feasibility of LC-MS analysis through detecting a five-drug mixture and a crude aripiprazole product. Finally, six impurities in the crude aripiprazole product were successfully detected by LC-TARI-MS. The established method holds promise for applications across academic and pharmaceutical domains.

Pulsed Direct Current Arc-Induced Nanoelectrospray Ionization Mass Spectrometry.

This study explores the innovative field of pulsed direct current arc-induced nanoelectrospray ionization mass spectrometry (DCAI-nano-ESI-MS), which utilizes a low-temperature direct current (DC) arc to induce ESI during MS analyses. By employing a 15 kV output voltage, the DCAI-nano-ESI source effectively identifies various biological molecules, including angiotensin II, bradykinin, cytochrome C, and soybean lecithin, showcasing impressive analyte signals and facilitating multicharge MS in positive- and negative-ion modes. Notably, results show that the oxidation of fatty acids using a DC arc produces [M + O - H]- ions, which aid in identifying the location of C═C bonds in unsaturated fatty acids and distinguishing between isomers based on diagnostic ions observed during collision-induced dissociation tandem MS. This study presents an approach for identifying the sn-1 and sn-2 positions in phosphatidylcholine using phosphatidylcholine and nitrate adduct ions, accurately determining phosphatidylcholine molecular configurations via the Paternò-Büchi reaction. With all the advantages above, DCAI-nano-ESI holds significant promise for future analytical and bioanalytical applications.

Nonderivatized Method for the Detection of Perfluoroalkane Sulfonyl Fluorides by Liquid Chromatography-Microwave Plasma Torch Ionization Mass Spectrometry.

Per- and polyfluoroalkyl substances (PFAS) have caused widespread environmental concern in recent years. Among them, the levels of perfluoroalkane sulfonyl fluorides (PFASFs) in the environment have rarely been reported due to the lack of sensitive analytical methods. Herein, a novel liquid chromatography-microwave plasma torch ionization-mass spectrometry (LC-MPTI-MS) technique was designed for the direct analysis of PFASFs in the environment. The collaborative action of reactive oxygen species (such as hydroxyl radicals) and the elevated temperature within the ambient MPTI environment results in the replacement of the fluorine atom in sulfonyl fluoride by oxygen, leading to the detection of perfluoroalkanesulfonic acid (PFSA) ions by MS. Concurrently, LC was employed to separate other PFSAs that are present in the environment. Three PFASFs exhibited good linearity within the range of 1-500 µg/L with R2 > 0.994. The limit of detections (LODs) and the limit of quantifications (LOQs) were measured at 39.32-87.87 and 131.07-292.90 ng/L, respectively. The method was utilized for the direct detection of spiked perfluorooctane sulfonyl fluoride (PFOSF) in wastewater with recoveries of 77.16 to 124.81%. Our approach circumvents the laborious process of chemical derivatization and is anticipated to serve as a robust tool for determining the levels and behaviors of PFASFs in the environment.

Gas-Phase Alcoholysis of Benzylic Halides in the Atmospheric Pressure Ionization Source.

The present study investigates the gas-phase alcoholysis reaction of benzylic halides under atmospheric pressure chemical ionization (APCI) conditions. The APCI corona discharge is used to initiate the novel reaction, which is monitored by ion trap mass spectrometry (IT-MS). The model compound α,α,α-trifluorotoluene is applied to observe the cascade methoxylation reaction during the +APCI-MS analysis, resulting in the formation of [PhC(OCH3)2]+. Based on the results of isotopic labeling and substrate expansion experiments, an addition-elimination mechanism is proposed: initially, the reaction was initiated by the dissociation of fluorine from PhCF3 under APCI condition, leading to the formation of [PhCF2]+; subsequently, two methanol molecules nucleophilicly attack [PhCF2]+ stepwisely, accompanied by the elimination of HF, yielding the product ion [PhC(OCH3)2]+. The proposed mechanism was further corroborated by theoretical calculations. The results of substrate scope expansion experiments suggest that this in-source reaction has the potential to differentiate the positional isomers of alcohols and phenols.

Whole­exome sequencing reveals Lewis lung carcinoma is a hypermutated Kras/Nras-mutant cancer with extensive regional mutation clusters in its genome.

Lewis lung carcinoma (LLC), as a widely used preclinical cancer model, has still not been genetically and genomically characterized. Here, we performed a whole-exome sequencing analysis on the LLC cell line to elucidate its molecular characteristics and etiologies. Our data showed that LLC originated from a male mouse belonging to C57BL/6L (a transitional strain between C57BL/6J and C57BL/6N) and contains substantial somatic SNV and InDel mutations (> 20,000). Extensive regional mutation clusters are present in its genome, which were caused mainly by the mutational processes underlying the SBS1, SBS5, SBS15, SBS17a, and SBS21 signatures during frequent structural rearrangements. Thirty three deleterious mutations are present in 30 cancer genes including Kras, Nras, Trp53, Dcc, and Cacna1d. Cdkn2a and Cdkn2b are biallelically deleted from the genome. Five pathways (RTK/RAS, p53, cell cycle, TGFB, and Hippo) are oncogenically deregulated or affected. The major mutational processes in LLC include chromosomal instability, exposure to metabolic mutagens, spontaneous 5-methylcytosine deamination, defective DNA mismatch repair, and reactive oxygen species. Our data also suggest that LLC is a lung cancer similar to human lung adenocarcinoma. This study lays a molecular basis for the more targeted application of LLC in preclinical research.

Arc-Induced Electrospray Ionization Mass Spectrometry.

Arc-induced electrospray ionization mass spectrometry (AESI-MS) was developed during which alternating current electrospray is simply achieved through the arc plasma. The AESI source exploits the arc's temperature and charge properties to generate aerosols consisting of charged microdroplets. The electrospray region, in which organic molecules are contained within microdroplets, partially overlaps with the arc plasma region. Guided by the electric field, these molecules undergo ionization, yielding ionic target analytes. AESI represents a soft ionization method that combines the mechanisms of atmospheric pressure chemical ionization and electrospray ionization, facilitating the ionization of analytes with wide ranging polarities. The precisely targeted spraying area enhances ion entry into the mass analyzer, thereby enabling excellent ionization efficiency. The AESI source exhibits several notable advantages over the electrospray ionization source, including an elevated but comparable level of active species concentrations and types, simplified mass spectra for direct amino acid analysis, high salt tolerance, versatile analysis of compounds with varying polarities, and reliable quantitative analysis of amino acids in complex matrices. Overall, AESI broadens the methodologies employed to generate microdroplets, providing a technological and scientific framework for creating distinctive electrospray ionization techniques.

α-Cyano-3-aminocinnamic acid: A novel reactive matrix for qualitative and quantitative analysis of plant N-glycans by MALDI-MS.

N-glycans have a diversity of crucial biological roles in organisms. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become an indispensable analytical instrument for biomolecules. However, due to the inherent low abundance, high structural heterogeneity, and poor ionization efficiency of N-glycans, as well as the extremely inhomogeneous co-crystal property using traditional matrices, the qualitation and quantitation of N-glycans by MALDI-MS remains challenging. In the present study, α-cyano-3-aminocinnamic acid (3-CACA) was reasonably designed and synthesized as a novel reactive matrix for N-glycan analysis. Combining with traditional matrix α-cyano-4-hydroxycinnamic acid (CHCA) as an acidic catalyst, a combinational matrix 3-CACA/CHCA was obtained with homogeneous co-crystallization and high derivatization efficiency, achieving the sensitive qualitation with the limits of detection low to femtomole and reproducible quantitation with good linearity (R2 > 0.998). As a result, the established method was successfully applied to the on-target derivatization and high-throughput quantification of N-glycans in eight varieties of the peach complex system, indicating that N-glycan has the potential to become a new biomarker for food allergy, and elucidating the prospective correlation between N-glycan epitopes and allergic reactions.

Separation, identification, and structural characterization of sucrose ester isomers from tobacco.

Sucrose esters (SEs) are crucial tobacco smoke flavor precursors and play a significant role in tobacco's functionality. Due to their structural complexity, the separation and analysis of SEs in tobacco remain a major challenge, and massive structures of SEs have not yet been fully identified. In this study, the fractions enriched in SEs were obtained from oriental and flue-cured tobacco through a series of pretreatments, and two types of SEs (Types I and II) were distinguished by liquid chromatography-tandem mass spectrometry (LC-MSn ) analysis, with Type II SEs newly characterized in tobacco. Five groups of main SEs were further purified using preparative high-performance LC (HPLC) coupled to an evaporative light scattering detector, and their structures were characterized by nuclear magnetic resonance spectrometry techniques including 1 H, 13 C, correlation spectroscopy, heteronuclear single quantum correlation, and heteronuclear multiple bond correlation. By combining LC-MSn and nuclear magnetic resonance spectrometry, the structures of eight SE isomers were finally proposed, of which four were newly identified. These findings further enhance the understanding of the structural diversity of SEs in tobacco, serving as a valuable reference for future research on the elucidation, synthesis, and metabolism of SEs.

Radical-Induced Dissociation for Oligonucleotide Sequencing by TiO2/ZnAl-Layered Double Oxide-Assisted Laser Desorption/Ionization Mass Spectrometry.

De novo sequencing of oligonucleotides remains challenging, especially for oligonucleotides with post-transcriptional or synthetic modifications. Mass spectrometry (MS) sequencing can reliably detect and locate all of the modification sites in oligonucleotides via m/z variance. However, current MS-based sequencing methods exhibit complex spectra and low ion abundance and usually require coupled instrumentation. Herein, we demonstrate a method of oligonucleotide sequencing using TiO2/ZnAl-layered double oxide (LDO)-assisted laser desorption/ionization (LDI)-MS based on radical-induced dissociation (RID). ·CH2OH radicals can be produced on the surface of a TiO2/ZnAl-LDO matrix via ultraviolet light, inducing an attack on the active site of the oligonucleotide phosphate skeleton to create typical "a-, a-B-, c·-, d-, w-, and y"-type fragments. Compared with the spectra obtained via collision-based methods, such as collision-induced dissociation and higher-energy collisional dissociation, the LDI-MS spectra based on RID exhibit single-charged signals, fewer types of fragments, and a lower proportion of unknown noise peaks. We demonstrate full sequence coverage for a 6-mer 2'-O-methyl-modified oligonucleotide and a 21-mer small interfering RNA and show that RID can sequence oligonucleotides with modifications. Importantly, the mechanism responsible for the RID of the oligonucleotide phosphate skeleton was investigated through offline experiments, demonstrating consistent results with density functional theory calculations.

Ultrasensitive and Green Bubbling Extraction Strategies: An Extensible Solvent-Free Re-Enrichment Approach for Ultratrace Pollutants in Aqueous Samples.

Ultratrace organic pollutants in the environment pose severe threats to human health; hence, their accurate detection is essential. In this study, we develop a secondary solvent-free enrichment strategy based on bubbling extraction (BE). Especially, we used BE solid-phase microextraction and BE carbon nanotube paper absorption to capture aerosols from a liquid water surface, desorb analytes, and analyze the analytes using mass spectrometry. The application of a solvent-free enrichment strategy helps overcome technical challenges in implementing BE technology, including reproducibility, quantification, and sensitivity. This approach objectively demonstrates the enrichment efficiency of BE, resulting in improved mass spectrometry response and quantification. It effectively tackles the difficulties in detecting and quantifying ultratrace environmental pollutants in mass spectrometric analysis. The present study successfully conducted a quantitative analysis of 16 polycyclic aromatic hydrocarbons and 7 antibiotics in 48 environmental water samples. This strategy proved effective in detecting the presence and distribution of polar and nonpolar environmental pollutants in rivers and lakes. Moreover, this strategy has several advantages, such as ultrahigh sensitivity at the femtograms per liter level, good greenness, multiplexed quantitation, low sample consumption, and ease of operation. Overall, the utilization of the ultrasensitive and environmentally friendly BE approach presents a reliable and adaptable method for the identification of ultratrace environmental pollutants in water specimens, thereby enabling early monitoring of pollutant levels.

A novel turn-on fluorescent probe for detection of pH in extremely acidic environment and its application.

A water-soluble turn-on fluorescent probe PNAP for pH has been designed and synthesized. PNAP was consist of pyrene as fluorophore and morpholine as receptor. Owing to the photoinduced electron transfer (PET) effect, the fluorescence of PNAP was quenched, while PNAP exhibited a remarkable "turn-on" fluorescence with the increase of acidity. Notably for its pKa of 2.15, PNAP was one of the pH fluorescent probes used in extremely acidic environments. Furthermore, PNAP also displayed good repeatability, strong anti-ion interference ability, high sensitivity and selectivity toward pH. In addition, PNAP has been successfully applied to the test strips and monitor the pH of environment water samples and realistic samples, showing its good promising prospect.

Discovery of 35 novel classes of per- and polyfluoroalkyl substances in representative commercial fluorinated products in China.

Per- and polyfluoroalkyl substances (PFAS) have received increasing scientific and regulatory attention due to their global distribution and health hazards. However, little is known about the PFAS composition of fluorinated products commercially available in China. In this study, a sensitive and robust analytical method was proposed for the comprehensive characterization of PFAS in aqueous film-forming foam and fluorocarbon surfactants in the domestic market based on liquid chromatography-high resolution mass spectrometry in full scan acquisition mode followed by parallel reaction monitoring mode. Consequently, a total of 102 PFAS from 59 classes were elucidated, of which 35 classes are reported for the first time, including 27 classes of anionic, seven classes of zwitterionic, and one class of cationic PFAS. The anionic-type products are mainly C6 fluorotelomerization-based (FT-based) PFAS. Perfluorooctanoic acid and perfluorooctane sulfonate are negligible, while some known electrochemical fluorination-based long-chain precursors in zwitterionic products are worthy of concern because of their high abundance and potential degradation. New precursors detected in zwitterionic products are FT-based PFAS, for example, 6:2 FTSAPr-AHOE and 6:2 FTSAPr-diMeAmPrC. The structural elucidation of PFAS in commercial products facilitates a better assessment of human exposure and environmental release.

A PdPt nanoparticle-decorated thiol-functionalized MOF with high peroxidase-like activity for colorimetric sensing of D-glucose and chlorophenol isomers.

The peroxidase (POD)-like catalytic activity of various nanozymes was extensively applied in many significant fields. In this study, a thiol-functionalized MOF-loaded PdPt nanocomposite (UiO-66-(SH)2@PdPt) was fabricated, which possesses superior and selective POD-like activity with strong affinity towards H2O2 and 3,3',5,5'-tetramethylbenzidine under mild conditions. The POD-like property of UiO-66-(SH)2@PdPt was used to sensitively detect the concentration of D-glucose under near-neutral (pH = 6.5) conditions. The detection limit of D-glucose was as low as 2.7 µM, and the linear range of D-glucose was 5-700 µM. In addition, UiO-66-(SH)2@PdPt could accelerate the oxidative coupling chromogenic reaction of chlorophenol (CP) and 4-aminoantipyrine (4-AAP) in the presence of H2O2. Based on this phenomenon, a simple and visualized sensing array for the identification of chlorophenol contaminant isomers was further constructed to finally achieve the effective differentiation of three monochlorophenol isomers and six dichlorophenol isomers. Furthermore, a colorimetric detection method for 2-chlorophenol and 2,4-dichlorophenol was established. This work provides an effective means to improve the catalytic activity and selectivity of nanozymes by introducing an ideal carrier, which will be of significant value for the design of efficient nanozymes.

Determination of Perfluorooctane Sulfonyl Fluoride and Perfluorohexane Sulfonyl Fluoride in Soil by Chemical Derivatization and Liquid Chromatography-Tandem Mass Spectrometry.

Perfluorooctane sulfonyl fluoride (PFOSF) and perfluorohexane sulfonyl fluoride (PFHxSF) were listed as persistent organic pollutants by the Stockholm Convention in 2009 and 2022, respectively. To date, their concentrations in environmental samples have not been reported due to the lack of sensitive methods. Herein, a novel chemical derivatization was developed for quantitative analysis of trace PFOSF and PFHxSF in soil by derivatizing them to the corresponding perfluoroalkane sulfinic acids. The method showed good linearity in the range from 25 to 500 ng L-1 with correlation coefficients (R2) better than 0.99. The detection limit of PFOSF in soil was 0.066 ng g-1 with recoveries in the range of 96-111%. Meanwhile, the detection limit of PFHxSF was 0.072 ng g-1 with recoveries in the range of 72-89%. Simultaneously, perfluorooctane sulfonic acid (PFOS) and perfluorohexane sulfonic acid (PFHxS) were also detected accurately without being affected by the derivative reaction. By applying this method in an abandoned fluorochemical manufacturing facility, PFOSF and PFHxSF were successfully detected at concentrations ranging from 2.7 to 357 ng g-1 and 0.23 to 26 ng g-1 dry weight, respectively. It is very interesting that 2 years after factory relocation, there still exists high concentrations of PFOSF and PFHxSF, which is of concern.