{"title":"Metabolomics for clinical applications","authors":"Yu Bai, Anna Laura Capriotti","doi":"10.1007/s00216-025-05867-3","DOIUrl":"10.1007/s00216-025-05867-3","url":null,"abstract":"","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":"417 13","pages":"2751 - 2752"},"PeriodicalIF":3.8,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143904802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jinkai Wang, Xiangzhuo Han, Yingzhe Wang, Zhanchen Cui, Zuosen Shi
{"title":"Polymer optical waveguide recoverable evanescent field nitroaromatics sensor based on D-π-A chromophore.","authors":"Jinkai Wang, Xiangzhuo Han, Yingzhe Wang, Zhanchen Cui, Zuosen Shi","doi":"10.1007/s00216-025-05769-4","DOIUrl":"10.1007/s00216-025-05769-4","url":null,"abstract":"<p><p>Nitroaromatics are a significant concern due to their high explosiveness and potential for water pollution. Optical waveguide sensing technology has been employed in the detection of nitroaromatics, leveraging its advantages of affordability, high sensitivity, reusability, and effective detection results. However, most current optical waveguide sensors operate on the principle of cumulative refractive index change, which necessitates extended detection times. Additionally, although many optical waveguide sensors are reusable, they often require complex and time-consuming post-processing steps for device recovery, and their detection performance significantly degrades after multiple uses, thus limiting their practical applications. In this work, we developed an evanescent field optical waveguide sensor for the detection of nitroaromatics in water, utilizing polymeric optical waveguide materials and D-π-A chromophore molecule. We integrated the sensing molecules into the hydrophobic fluorosilicone resin upper cladding material and employed the evanescent field principle to monitor changes in the optical properties of the surface sensing molecules following their interaction with nitroaromatics. This approach not only prevented contaminant penetration into the sensor, allowing for rapid device recovery, but also facilitated quick quantitative detection. Our sensor demonstrates a detection time of approximately 5 s, a recovery time of about 3 s, and achieves a detection limit of 0.11 ppm, with performance remaining largely intact after several detection cycles.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"1885-1895"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Impact of NH<sub>4</sub><sup>+</sup> on the catalytic activity of G-quadruplex/hemin DNAzyme for chemiluminescent sensing.","authors":"Xinyu Zhang, Chenxi Zhu, Yanying Wang, Yi Zhao, Honghu Tang, Xianming Li, Peng Wu","doi":"10.1007/s00216-025-05842-y","DOIUrl":"https://doi.org/10.1007/s00216-025-05842-y","url":null,"abstract":"<p><p>G-quadruplex/hemin DNAzyme, a versatile tool for biosensing, is challenged by its low peroxidase-mimic activities. The addition of NH<sub>4</sub><sup>+</sup> may offer an efficient approach to improve its activity. However, the detailed impact of NH<sub>4</sub><sup>+</sup> on its catalytic activity remains unclear, confusing the selection of appropriate DNAzymes for biosensing applications. Here, we conducted a comprehensive examination of the influence of NH<sub>4</sub><sup>+</sup> on G-quadruplex/hemin DNAzyme. The results revealed that all DNAzymes with different G-quadruplex topologies exhibited increased catalytic activities in the presence of NH<sub>4</sub><sup>+</sup> relative to K<sup>+</sup>, followed by the subsequent activity order: parallel > hybrid > antiparallel. Further investigations indicated that the increased catalytic activity can be ascribed to the increased stability of the G-quadruplex/hemin complex, elevated reaction velocity, and improved substrate affinity. Leveraging the significant disparity in enzymatic activity between parallel and antiparallel G-quadruplexes, an allosteric sensor based on the Pb<sup>2+</sup>-induced topological conformation was developed for sensitive detection of Pb<sup>2+</sup> in the NH<sub>4</sub><sup>+</sup>-boosted G-quadruplex/hemin DNAzyme system (LOD, 1.56 nM), indicating potential for practical applications. Our discovery improves the understanding of NH<sub>4</sub><sup>+</sup>-boosted G-quadruplex/hemin DNAzyme and may facilitate the development of biosensors.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":""},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wenbo Ma, Mengyang Song, Zhenyang Ji, Yiping Liu, Pengjun Na, Yuze Li, Zongxiu Nie
{"title":"Rapid metabolic profiling and authentication of Cordyceps using ambient ionization mass spectrometry and machine learning.","authors":"Wenbo Ma, Mengyang Song, Zhenyang Ji, Yiping Liu, Pengjun Na, Yuze Li, Zongxiu Nie","doi":"10.1007/s00216-025-05776-5","DOIUrl":"10.1007/s00216-025-05776-5","url":null,"abstract":"<p><p>Cordyceps sinensis, a symbiotic organism formed between a fungus and an insect, is celebrated for its substantial medicinal benefits and economic significance in traditional Chinese medicine. However, the market for Cordyceps sinensis is rife with counterfeits, where numerous types of Cordyceps frequently pose as the genuine species, leading to financial losses for consumers. Here, we developed an ambient ionization mass spectrometry for the metabolic analysis of four kinds of Cordyceps. We tentatively identified a total of 81 metabolites, revealing significant differences between wild-type Cordyceps sinensis and its counterfeit counterparts. The heterogeneous distribution of metabolites was also examined. Notably, ergothioneine, an antioxidant, and its precursor hercynine were found to be more abundant in the stroma compared to other sections. Then, a neural network was employed to distinguish between different Cordyceps, achieving an average classification accuracy of 90.3% in blind tests. We demonstrate the potential for on-site detection of Cordyceps using a handheld nano-electrospray ionization source in conjunction with a miniature mass spectrometer, yielding mass spectral profiles comparable to those obtained with a benchtop system.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"1935-1945"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pengyu Hong, Chaoshuang Xia, Yang Tang, Juan Wei, Cheng Lin
{"title":"Glycan mixture analysis by kernel component composition for matrix factorization.","authors":"Pengyu Hong, Chaoshuang Xia, Yang Tang, Juan Wei, Cheng Lin","doi":"10.1007/s00216-025-05777-4","DOIUrl":"10.1007/s00216-025-05777-4","url":null,"abstract":"<p><p>A major challenge in structural glycomics is the presence of isomeric glycan structures, which may not be fully resolved by separation techniques such as liquid chromatography (LC) and ion mobility spectrometry (IMS). Tandem mass spectrometry (MS/MS) can be employed following on-line separation to distinguish unresolved features, as the temporal profiles of various fragment ions reflect different combinations of those from their respective precursor ions. However, traditional principal component analysis can produce negative signals that are unrealistic for real data, and classic non-negative matrix factorization (NMF) methods may result in factors that include contributions from multiple components. This paper introduces a new variation of NMF, termed kernel component composition (KCC), which enables users to impose domain-specific prior knowledge about the components as parametric kernels. These kernel parameters are then learned directly from the data. We developed a theoretically guaranteed algorithm based on proximal gradient descent to solve the optimization problem posed by KCC and derived detailed parameter update rules when using Gaussian kernels. The effectiveness of the KCC algorithm is demonstrated through simulation tests and its application to deconvoluting chemical datasets, including LC- and IM-MS/MS analysis of isomeric glycan mixtures.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"1975-1984"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143405004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Recent advances in analytical methods and bioinformatic tools for quantitative glycomics.","authors":"Jihong Lu, Shuhong Guo, Qiannan Liu, Nafisa Tursumamat, Shengyang Liu, Shuye Wu, Heming Li, Juan Wei","doi":"10.1007/s00216-025-05778-3","DOIUrl":"10.1007/s00216-025-05778-3","url":null,"abstract":"<p><p>The significance of glycans in various biological processes has been widely acknowledged. Quantitative glycomics is emerging as an important addition to clinical biomarker discovery, as it helps uncover disease-associated glycosylation patterns that are valuable for diagnosis, prognosis, and treatment evaluation. Compared to glycoproteomics and other established omics approaches, quantitative glycomics exhibits greater methodological diversity and it encounters various challenges in automation and standardization. Nonetheless, numerous advancements have been made in this field over the past 5 years. Here, we have reviewed recent progress in analytical methods and software to improve mass spectrometry-based quantitative glycomics primarily on N- and O-glycosylation. The discussion is organized into four sections: stable isotopic labeling, isobaric labeling, label-free, and fluorescence labeling strategies, with a particular emphasis on quantitative data interpretation. Novel derivatization methods and advanced techniques have been developed for high-throughput and highly sensitive glycan quantification with high accuracy. However, due to variations in glycan derivatization and difficulties in structural identification, most glycomic quantification methods are tailored to specific applications, and manual inspection is frequently necessary for precise data interpretation. Therefore, further advancements in glycan sample preparation, structural characterization, and automated data interpretation are essential to facilitate comprehensive and accurate quantification across a wide array of glycans.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"1947-1959"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143412662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Cost-effective in-house-made whole blood materials for internal quality control in clinical flow cytometry analysis.","authors":"Hui-Min Chong, Zhao-Wei Zhang, Jin-Mi Li, Xiao-Dong Ren, Chun-Mei Gong, Zhi-Xian Zhu, Nan Xiang, Zhong-Hua Ni, Qing Huang","doi":"10.1007/s00216-025-05801-7","DOIUrl":"10.1007/s00216-025-05801-7","url":null,"abstract":"<p><p>Internal quality control (IQC) is essential for ensuring the accuracy of results in clinical trials. However, there is a significant shortage of commercial quality control materials for IQC in flow cytometry. This study aimed to develop cost-effective in-house-made whole blood materials from clinically discarded samples to serve as IQC in clinical flow cytometry analysis. Discarded clinical whole blood samples were collected to prepare red blood cell (RBC) suspensions through density centrifugation. White blood cell (WBC) suspensions were prepared using made in-house (MiH) lysing buffer, followed by fixation with the MiH fixative solution. The in-house-made whole blood materials were then prepared by mixing the RBC and WBC suspensions. These mixtures were stored under controlled temperature conditions to ensure long-term stability. These materials are intended for use in internal quality control (IQC) for clinical flow cytometry analysis. The recovery rate of RBC suspensions achieved through density centrifugation was 95%. Different blood type RBC suspensions were effectively preserved in Alsever's solution via plasma washing and re-mixing. The average viability of MiH WBC suspensions was 97%, with a recovery rate of 84%, both significantly higher than those observed with ACK (p < 0.001). Among the in-house-made whole blood material samples, sample a1-which included plasma, Alsever's solution, RBC suspension, WBC suspension, and Proclin 300-exhibited the best stability in flow cytometry, demonstrating stable expression of cell antigens for over 5 months. The in-house-made whole blood materials proved to be cost-effective and suitable for use in IQC for clinical flow cytometry analysis.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"2121-2132"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143447676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jon R Sobus, Nickolas A Sayre-Smith, Alex Chao, Troy M Ferland, Jeffrey M Minucci, E Tyler Carr, Laura D Brunelle, Angela L Batt, Heather D Whitehead, Tommy Cathey, Matthew Boyce, Elin M Ulrich, James P McCord, Antony J Williams
{"title":"Automated QA/QC reporting for non-targeted analysis: a demonstration of \"INTERPRET NTA\" with de facto water reuse data.","authors":"Jon R Sobus, Nickolas A Sayre-Smith, Alex Chao, Troy M Ferland, Jeffrey M Minucci, E Tyler Carr, Laura D Brunelle, Angela L Batt, Heather D Whitehead, Tommy Cathey, Matthew Boyce, Elin M Ulrich, James P McCord, Antony J Williams","doi":"10.1007/s00216-025-05771-w","DOIUrl":"10.1007/s00216-025-05771-w","url":null,"abstract":"<p><p>The US Environmental Protection Agency (EPA) uses non-targeted analysis (NTA) to characterize potential risks associated with environmental pollutants and anthropogenic materials. NTA is used throughout EPA's Office of Research and Development (ORD) to support the needs of states, tribes, EPA regions, EPA program offices, and other outside partners. NTA methods are complex and conducted via myriad instrumental platforms and software products. Comprehensive standards do not yet exist to guide NTA quality assurance/quality control (QA/QC) procedures. Furthermore, no single software tool meets EPA's needs for QA/QC review and documentation. Considering these factors, ORD developed \"INTERPRET NTA\" (Interface for Processing, Reviewing, and Translating NTA data) to support liquid chromatography (LC) high-resolution mass spectrometry (HRMS) NTA experiments. For purposes of NTA QA/QC, INTERPRET NTA (1) calculates data quality statistics related to accuracy, precision, and reproducibility; (2) produces interactive visualizations to facilitate quality threshold optimization; and (3) outputs comprehensive documentation for inclusion in official reports and research publications. INTERPRET NTA has additional functionality to facilitate rapid chemical identification and risk-based prioritization. The current article describes only the QA/QC elements of INTERPRET NTA's MS<sup>1</sup> workflow, which are demonstrated using published data from a de facto water reuse study. INTERPRET NTA, in its current form, exists primarily to meet the needs of EPA and its partners, but a public release is planned. Workflows, terminology, and outputs of INTERPRET NTA provide a focal point for necessary discussions on the harmonization of NTA QA/QC practices.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"1897-1914"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143424698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shirley Pu, James P McCord, Rebecca A Dickman, Nickolas A Sayresmith, Helen Sepman, Anneli Kruve, Diana S Aga, Jon R Sobus
{"title":"Examining environmental matrix effects on quantitative non-targeted analysis estimates of per- and polyfluoroalkyl substances.","authors":"Shirley Pu, James P McCord, Rebecca A Dickman, Nickolas A Sayresmith, Helen Sepman, Anneli Kruve, Diana S Aga, Jon R Sobus","doi":"10.1007/s00216-025-05796-1","DOIUrl":"10.1007/s00216-025-05796-1","url":null,"abstract":"<p><p>Non-targeted analysis (NTA) is commonly used for the detection and identification of emerging pollutants, including many per- and polyfluoroalkyl substances (PFAS). While NTA outputs are often non-quantitative, concentration estimation is now possible using quantitative non-targeted analysis (qNTA) approaches. To date, few studies have examined matrix effects on qNTA performance, and little is therefore known about the implications of matrix effects on qNTA results and interpretations. Using a set of 19 PFAS, we examined the impacts of drinking water (DW) and waste-activated sludge matrices on qNTA performance across three qNTA approaches: one structure-independent approach based on \"global\" surrogates and two structure-dependent approaches based on \"expert-selected\" surrogates and predicted ionization efficiency (IE) regression. The performance of each qNTA approach was examined separately for the PFAS prepared in pure solvent, DW extract, and sludge extract using leave-one-out modeling. Performance was evaluated using previously defined qNTA metrics that describe predictive accuracy, uncertainty, and reliability. The studied sample matrices had minimal effects on qNTA accuracy and larger effects on qNTA uncertainty and reliability. Using solvent-based surrogate data to inform matrix-based estimations yielded lower uncertainty, but also lower reliability, emphasizing that uncertainty must be considered in context of reliability. No single qNTA approach uniformly performed best across all comparisons. Since the IE regression and global surrogates approaches proved most reliable, we recommended them for future qNTA applications. This study highlights the importance of examining multiple performance metrics and utilizing matrix-matched surrogate data in qNTA studies.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"2097-2110"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Daniel Köster, Tobias Hesse, Felix Niemann, Maik A Jochmann, Torsten C Schmidt
{"title":"Alkaline persulfate oxidation as an intermediate step for the development of a wet chemical oxidation interface for compound-specific δ<sup>15</sup>N analysis by LC-IRMS.","authors":"Daniel Köster, Tobias Hesse, Felix Niemann, Maik A Jochmann, Torsten C Schmidt","doi":"10.1007/s00216-025-05795-2","DOIUrl":"10.1007/s00216-025-05795-2","url":null,"abstract":"<p><p>For the measurement of compound-specific isotope ratios by liquid chromatography isotope ratio mass spectrometry (LC-IRMS), complete mineralization of organic compounds to a single species of measurement gas is required so that isotopic fractionation can be minimized and corrected by identical treatment with standards. The established use of peroxydisulfate in an acidic environment has its limitations, especially when it comes to the complete oxidation of nitrogen-containing compounds with aromatic ring systems. Under acidic oxidation conditions, ammonium and nitrate were identified as the main nitrogen containing mineralization products of the oxidation of different model compounds. In contrast to the oxidation in an acidic environment, alkaline peroxydisulfate oxidation leads to nitrate as a final mineralization product. The concept of alkaline oxidation was transferred from large-scale batch experiments to a commercially available oxidation reactor used in LC-IRMS systems. The obtained nitrate recoveries indicate that alkaline oxidation could be a promising step towards the measurement of compound-specific nitrogen isotope ratios by LC-IMRS. In our work, we show that alkaline peroxydisulfate oxidation allows faster and more complete mineralization of nitrogen-containing compounds. For several model compounds, 63 to 100% of the initially present nitrogen was converted to nitrate within a reaction time of 43 s.</p>","PeriodicalId":462,"journal":{"name":"Analytical and Bioanalytical Chemistry","volume":" ","pages":"2085-2096"},"PeriodicalIF":3.8,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961470/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}