Rapid Communications in Mass Spectrometry最新文献

{"title":"The Site of Protonation Affects the Dissociation of Protonated α- and β-Pinene Ions","authors":"Edgar White Buenger,&nbsp;Paul M. Mayer","doi":"10.1002/rcm.9978","DOIUrl":"10.1002/rcm.9978","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>In electrospray ionization and atmospheric pressure chemical ionization, the protonation site directly guides the ion's dissociation. But what if the site of protonation is ambiguous? In this study, we explored the unimolecular reactions of protonated α- and β-pinene ions with a combination of tandem mass spectrometry and theory. Each has multiple potential protonation sites that influence their chemistry.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Atmospheric pressure chemical ionization was employed to form the protonated pinene isomers. The unimolecular chemistry of these ions was explored with a Waters Ultima triple-quadrupole mass spectrometer using energy-resolved collision-induced dissociation with argon collision gas. Reaction mechanisms were calculated with CBS-QB3 single-point energy calculations on B3LYP/6-311+G(d,p) optimized structures.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The two main dissociation reactions in each ion lead to the loss of neutral propene and isobutene. Both ions were found to dissociate over the same minimum energy reaction pathway, the only difference being the site of initial protonation. α-Pinene preferentially protonates at the bridging carbon, while β-pinene can only significantly protonate at the exocyclic double bond. This leads to a lower appearance energy for loss of isobutene, and thus relatively greater m/z 81 fragment ion abundance for β-pinene.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The distinct sites of initial protonation result in the subtle differences observed in the CID of α- and β-pinene. The work highlights that it is not necessarily the “lowest energy” ion that will be formed in the ion source, and any distribution of initial structures must be accounted for when examining CID mass spectra.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11684416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142906391","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Combining the 15N Gas Flux Method and N2O Isotopocule Data for the Determination of Soil Microbial N2O Sources","authors":"Gianni Micucci,&nbsp;Dominika Lewicka-Szczebak,&nbsp;Fotis Sgouridis,&nbsp;Reinhard Well,&nbsp;Caroline Buchen-Tschiskale,&nbsp;Niall P. McNamara,&nbsp;Stefan Krause,&nbsp;Iseult Lynch,&nbsp;Felicity Roos,&nbsp;Sami Ullah","doi":"10.1002/rcm.9971","DOIUrl":"10.1002/rcm.9971","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>The analysis of natural abundance isotopes in biogenic N₂O molecules provides valuable insights into the nature of their precursors and their role in biogeochemical cycles. However, current methodologies (for example, the isotopocule map approach) face limitations, as they only enable the estimation of combined contributions from multiple processes at once rather than discriminating individual sources. This study aimed to overcome this challenge by developing a novel methodology for the partitioning of N₂O sources in soil, combining natural abundance isotopes and the use of a ¹⁵N tracer (¹⁵N Gas Flux method) in parallel incubations.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Laboratory incubations of an agricultural soil were conducted to optimize denitrification conditions through increased moisture and nitrate amendments, using nitrate that was either ¹⁵N-labeled or unlabeled. A new linear system combined with Monte Carlo simulation was developed to determine N₂O source contributions, and the subsequent results were compared with FRAME, a Bayesian statistical model for stable isotope analysis.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Our new methodology identified bacterial denitrification as the dominant process (87.6%), followed by fungal denitrification (9.4%), nitrification (1.5%), and nitrifier denitrification (1.6%). Comparisons with FRAME showed good agreement, although FRAME estimated slightly lower bacterial denitrification (80%) and higher nitrifier-denitrification (9%) contributions.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This approach provides an improved framework for accurately partitioning N₂O sources, enhancing understanding of nitrogen cycling in agroecosystems, and supporting broader environmental applications.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11671725/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142890763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid Analysis of Nucleic Acids by Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry With a Data Algorithm","authors":"Zhen Xu,&nbsp;Baolin Xiong,&nbsp;Wenbo Cheng,&nbsp;Bin Hu,&nbsp;Yuguo Tang","doi":"10.1002/rcm.9981","DOIUrl":"10.1002/rcm.9981","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is a powerful method for identifying viruses via nucleic acid detection. The data processing method is critical in recognizing nucleic acid obtained by MALDI-TOF-MS. Therefore, new development of data algorithm is needed for virus identification.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>In this work, we developed a new data processing algorithm of MALDI-TOF-MS to identify respiratory viruses and deafness gene mutation sites. The algorithm includes denoising, baseline correcting, peak identification, and extraction features for processing the MS spectrum.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Standard nucleic acid and respiratory virus samples were used to evaluate the performances of the newly developed algorithms. The errors of peak detection were found to be less than 200 ppm. Excellent sensitivity (91.67%–100%) and specificity (96.88–100%) were obtained by identifying 305 virus samples in this work, showing excellent performances. Additionally, accurate identification of the mutation sites of deafness genes was also obtained by the presented method.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Overall, our data showed that this method is accurate, sensitive, and specific for nucleic acid identification, showing the potential applications for qualitative analysis of respiratory viruses and deafness gene mutation screening.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142890765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A SIFT Study of Reactions of Positive and Negative Ions With Polyfluoroalkyl (PFAS) Molecules in Dry and Humid Nitrogen at 393 K","authors":"Stefan James Swift,&nbsp;Maroua Omezzine Gnioua,&nbsp;Kseniya Dryahina,&nbsp;Patrik Španěl","doi":"10.1002/rcm.9975","DOIUrl":"10.1002/rcm.9975","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Data are required for SIFT-MS analysis of perfluoroalkyl and polyfluoroalkyl substances (PFAS), which are persistent in the environment and cause adverse health effects. Specifically, the rate coefficients and product ion branching ratios of the reactions of H₃O⁺, NO⁺, O₂⁺•, O⁻•, OH⁻, O₂⁻•, NO₂⁻ and NO₃⁻ with PFAS vapours are needed.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The dual polarity SIFT-MS instrument (Voice200) was used to generate these eight reagent ions and inject them into the flow tube with N₂ carrier gas at a temperature of 393 K. Vapours of pentafluoropropionic acid, heptafluorobutyric acid, nonafluoro-1-hexanol, perfluoro-2-methyl-2-pentene, perfluorohexanoic acid, perfluoro(2-methyl-3-oxahexanoic) acid, tridecafluoro-1-octanol and nonafluorobutane-1-sulfonic acid were introduced in dry and humid air. Full-scan mass spectra were collected for all reagents at variable PFAS concentrations and analysed numerically.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>Rate coefficients were determined for 64 reactions, for which 55 positive and 71 negative product ions were identified. The branching ratios for the primary reaction channels were extracted from the data, and the secondary chemistry with H₂O molecules was qualitatively assessed. The thermochemical data were calculated for the H₃O⁺ reactions using density functional theory (DFT).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>An important observation is that secondary reactions with water molecules remove the positive product ions, making them unsuitable for practical SIFT-MS analysis of PFAS vapours. In contrast, most negative reaction product ions are not significantly affected by humidity and are thus preferred for the SIFT-MS analyses of PFAS substances in various gaseous matrices.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11671707/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142890762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a Matrix-Assisted Laser Desorption Ionization High Resolution Mass Spectrometry Method for the Quantification of Camalexin and Scopoletin in Arabidopsis thaliana","authors":"Leonardo Parasecolo,&nbsp;Ivan M. Monsalvo,&nbsp;Nikola Kovinich,&nbsp;Demian R. Ifa","doi":"10.1002/rcm.9973","DOIUrl":"10.1002/rcm.9973","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Understanding plant defense mechanisms against pathogens is essential for enhancing agricultural productivity and crop protection. This study focuses on the quantification of camalexin and scopoletin, two critical phytoalexins in <i>Arabidopsis thaliana</i>, using mass spectrometry techniques. Precise measurement of these compounds provides insights into plant resistance and supports agricultural research.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Camalexin and scopoletin were quantified using matrix-assisted laser desorption ionization high-resolution mass spectrometry (MALDI-HRMS). The matrix and solvent conditions were optimized to maximize sensitivity and accuracy. MS/MS experiments confirmed compound identification with high mass accuracy (mass error &lt; 5 ppm). The method was validated through comparative analysis of wild-type (WT) and mutant <i>Arabidopsis</i> lines, using internal standards and multiple replicates to ensure precision and reliability.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The method exhibited high linearity for scopoletin (<i>R</i>² = 0.9992) and camalexin (<i>R</i>² = 0.9987) across concentration ranges of 0.16–5 and 0.31–5 μM, respectively. Limits of detection (LOD) were 0.16 μM for camalexin and 0.04 μM for scopoletin, with limits of quantification (LOQ) at 0.2 μM and 0.08 μM, respectively. Samples analysis demonstrated reliable quantification in WT and mutant lines, with significant reductions in camalexin and scopoletin levels observed in the <i>atwrky33-2</i> and <i>atmyb15-1</i> mutants, respectively. Additionally, the method detected sub-physiological concentrations, confirming its sensitivity and robustness for low-level detection.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>This study presents a validated, precise, and accurate MALDI-HRMS method for the quantification of camalexin and scopoletin in <i>Arabidopsis thaliana</i>. The approach not only enhances understanding of plant defense mechanisms but also offers potential applications for biotechnological and agricultural research, especially for investigating genetic variations and stress-induced phytoalexin production.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 6","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/rcm.9973","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142851689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Establishment of a Mass Spectrometric Fingerprint of the Most Common Phytocannabinoids in Electrospray Ionization in Positive Ion Mode","authors":"Radwa Mahmoud,&nbsp;Amir Khajavinia,&nbsp;Sedigheh Barzegar,&nbsp;Randy W. Purves,&nbsp;Robert B. Laprairie,&nbsp;Anas El-Aneed","doi":"10.1002/rcm.9952","DOIUrl":"10.1002/rcm.9952","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Analysis of the phytocannabinoids holds significant importance because of their various pharmacological properties and potential therapeutic applications. Tandem mass spectrometry (MS/MS) coupled with electrospray ionization in positive ion mode is employed in this study to describe the collision-induced dissociation (CID) behavior of a series of common phytocannabinoids with the aim of establishing a generalized MS/MS fingerprint.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Materials and Methods</h3>\u0000 \u0000 <p>Eight phytocannabinoids, namely, ∆⁹-tetrahydrocannabinol (THC), cannabidiol (CBD), cannabichromene (CBC), cannabigerol (CBG), tetrahydrocannabivarin (THCV), 11-hydroxy-Δ⁹-tetrahydrocannabinol (11-OH-THC), 6-hydroxy-cannabidiol (6-OH-CBD), and 7-hydroxy-cannabidiol (7-OH-CBD), were studied. A Quadrupole-Orbitrap mass spectrometer equipped with a heated electrospray ionization (HESI-Q Orbitrap) is used to provide accurate mass measurement data for single-stage and MS/MS analysis. In addition, a triple quadrupole-linear ion trap mass spectrometer was used to perform MS/MS and second-generation MS/MS (MS³) analyses.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>An abundant, singly charged [M + H]⁺ species during single-stage MS analysis was observed for all phytocannabinoids, with mass accuracies less than 5 ppm. Because of their structural similarities, all compounds showed some common fragmentation behavior in their MS/MS analysis. By comparing the fragmentation patterns and identifying diagnostic ions, a universal MS/MS fragmentation pattern was established. The structures of the various product ions proposed in the fragmentation pathway were confirmed with exact mass measurements and MS³ experiments.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>The evaluated compounds contain varying functional groups, resulting in unique product ions, specific to each structure. The MS/MS fingerprints will be utilized in the future for the identification of new structures as well as the development of targeted quantification methods.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 4","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142823475","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Colicin Immunity Proteins of Pathogenic Bacteria Detected by Antibiotic-Induced SOS Response, Plasmid Sequencing, MALDI-TOF-TOF Mass Spectrometry, and Top-Down Proteomic Analysis","authors":"Clifton K.  Fagerquist,&nbsp;Yanlin  Shi,&nbsp;Jihyun  Park","doi":"10.1002/rcm.9964","DOIUrl":"10.1002/rcm.9964","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale:</h3>\u0000 \u0000 <p>Plasmids can play a major role in the survival of pathogenic bacteria. Plasmids are acquired through horizontal gene transfer resulting in their spread across various strains, species and genera of bacteria. Colicins are bacterial protein toxins expressed by plasmid genes and released against co-located bacterial competitors.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods:</h3>\u0000 \u0000 <p>Three Shiga toxin-producing <i>E. coli</i> (STEC), whose genomes were sequenced previously, were analyzed using a combination of antibiotic induction, MALDI-TOF-TOF mass spectrometry, top-down proteomic analysis, and small plasmid sequencing. Protein biomarkers were identified using in-house software that matches protein mass and fragment ions of backbone cleavage by the <i>aspartic acid effect</i>. Predicted in silico protein structures assisted in the interpretation of protein ion fragmentation.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results:</h3>\u0000 \u0000 <p>In addition to proteomic identification of phage-encoded Shiga toxin, we were able to identify plasmid-encoded immunity proteins for colicin D and E3. The genes for these plasmid-encoded proteins were not found in the previous genomic sequencing. However, resequencing of these strains for small plasmids revealed the genes to be present on 7–8 kb sized plasmids. Upstream of the colicin/immunity genes was an inverted repeat of the SOS/LexA box that represses gene expression until antibiotic challenge.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions:</h3>\u0000 \u0000 <p>Our top-down proteomic method demonstrates that it is possible to screen putative pathogenic bacteria (whose genomes have been sequenced in full, in part or not at all) for the presence of phage- and plasmid-encoded toxin and colicin genes under SOS control. Small plasmid sequencing confirmed the presence of colicin/immunity genes (and their regulatory control) suggested from induction and top-down proteomic analysis.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816786","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative multi-omics reveals the mechanism of ulcerative colitis treated with Ma-Mu-Ran antidiarrheal capsules","authors":"Hailing Huang,&nbsp;Bailu Duan,&nbsp;Zhuang Huang,&nbsp;Shanshan Wang,&nbsp;Yuxin Wen,&nbsp;Qi Jiang,&nbsp;Pengyu Chen,&nbsp;Ping Huang,&nbsp;Jiajing Liu,&nbsp;Sili Zheng,&nbsp;Yan Ye,&nbsp;Dongning Zhang,&nbsp;Qiong Wang,&nbsp;Fang Huang,&nbsp;Jingjing Li,&nbsp;Lintao Han","doi":"10.1002/rcm.9939","DOIUrl":"10.1002/rcm.9939","url":null,"abstract":"<div>\u0000 \u0000 <section>\u0000 \u0000 <h3> Rationale</h3>\u0000 \u0000 <p>Ulcerative colitis (UC) is a chronic inflammatory gastrointestinal disease typically coexisting with intestinal microbiota dysbiosis, oxidative stress, and an inflammatory response. Although its underlying mechanism of action is unclear, Ma-Mu-Ran Antidiarrheal Capsules (MMRAC) have demonstrated significant therapeutic efficacy for UC.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>The mechanism of action of MMRAC in the treatment of UC model was investigated by combining metabolomics, transcriptomics, and intestinal microbiota detection techniques.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>The high-dose group of MMRAC was determined as the best therapeutic dose by pathological changes and biochemical indexes. Transcriptome analysis revealed that 360 genes were differentially altered after MMRAC treatment. Metabolomic analysis using colon tissue yielded 14 colon tissue metabolites with significant differences. Intestinal flora analysis showed that 26 major microorganisms were identified at the genus level.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>Based on a thorough multi-omics analysis of transcriptomics, metabolomics, and gut flora, it was determined that MMRAC regulated cysteine and methionine metabolism, arginine biosynthesis, and sphingolipid metabolism and their respective genes BHMT, PHGDH, iNOS, and SPHK1, which in turn served to inhibit UC-generated inflammatory responses and oxidative stress. Additionally, MMRAC regulated the abundance of Coprococcus, Helicobacter, Sutterella, Paraprevotella, and Roseburia in the intestinal tracts of UC mice, which was regulated toward normal levels, thereby restoring normal intestinal function.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery and Characterization of Unusual O-Linked Glycosylation of IgG4 Antibody Using LC-MS","authors":"Dariusz J. Janecki,&nbsp;Chi-Ya Kao-Scharf,&nbsp;Andreas Hoffmann","doi":"10.1002/rcm.9969","DOIUrl":"10.1002/rcm.9969","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <h3> Background</h3>\u0000 \u0000 <p>Consensus is that immunoglobulin IgG4 contains only N-linked glycosylation. The analysis of several batches of commercial biopharmaceutical product Dupixent using top-down intact mass spectrometry revealed that this IgG4 features a small amount of O-linked glycosylation in the Fab region. This is the first report of an O-linked glycosylation in an IgG4 antibody.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Methods</h3>\u0000 \u0000 <p>Monoclonal antibody solutions were subjected to cation exchange (CEX) and reverse phase (RP) chromatography and/or additional preconcentration/fractionation methods to prepare samples for subsequent analysis. Advanced MS analysis and fragmentation techniques (HCD, ETD, and EThcD) were employed to localize the O-linked glycosylation as well as elucidate the structure of the glycan(s).</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Results</h3>\u0000 \u0000 <p>O-linked glycosylation in the IgG4 dupilumab was discovered by intact-MS. The probable location was narrowed down to four sites in the CH1 domain, and the structure of the O-linked glycan was determined to be of Core 1 type. The relative quantities of the modifications were low, but the glycosylation was consistently detected in several batches of Dupixent.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Conclusions</h3>\u0000 \u0000 <p>We discovered a rare glycosylation modification on dupilumab, an IgG4 antibody. The O-linked glycosylation was characterized and localized in the Fab region.</p>\u0000 </section>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11635057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142811415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Adaptive Multicore Dual-Path Fusion Multimodel Extraction of Heterogeneous Features for FAIMS Spectral Analysis","authors":"Ruilong Zhang,&nbsp;Xiaoxia Du,&nbsp;Wenxiang Xiao,&nbsp;Hua Li","doi":"10.1002/rcm.9967","DOIUrl":"10.1002/rcm.9967","url":null,"abstract":"<div>\u0000 \u0000 <p>With the increasing application scenarios and detection needs of high-field asymmetric waveform ion mobility spectrometry (FAIMS) analysis, deep learning–assisted spectral analysis has become an important method to improve the analytical effect and work efficiency. However, a single model has limitations in generalizing to different types of tasks, and a model trained from one batch of spectral data is difficult to achieve good results on another task with large differences. To address this problem, this study proposes an adaptive multicore dual-path fusion multimodel extraction of heterogeneous features for FAIMS spectral analysis model in conjunction with FAIMS small-sample data analysis scenarios. Multinetwork complementarity is achieved through multimodel feature extraction, adaptive feature fusion module adjusts feature size and dimension fusion to heterogeneous features, and multicore dual-path fusion can capture and integrate information at all scales and levels. The model's performance improves dramatically when performing complex mixture multiclassification tasks: accuracy, precision, recall, f1-score, and micro-AUC reach 98.11%, 98.66%, 98.33%, 98.30%, and 98.98%. The metrics for the generalization test using the untrained xylene isomer data were 96.42%, 96.66%, 96.96%, 96.65%, and 97.60%. The model not only exhibits excellent analytical results on preexisting data but also demonstrates good generalization ability on untrained data.</p>\u0000 </div>","PeriodicalId":225,"journal":{"name":"Rapid Communications in Mass Spectrometry","volume":"39 5","pages":""},"PeriodicalIF":1.8,"publicationDate":"2024-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}