Pub Date : 2026-03-23DOI: 10.1021/acs.analchem.5c05356
Yu Deng,Xiaoyuan Zhen,Ruocheng Xia,Ruxin Zhu,Gongying Zhang,Pengyu Chen,Jianghua Lai,Ruiyang Tao
Body fluid identification (BFID) and estimation of time since deposition (TsD) are valuable yet challenging in forensic practice. Previous studies have demonstrated that integrating microbial and metabolomic profiles provides complementary biological insights. Therefore, this study performed untargeted metabolomic profiling and full-length 16S rRNA sequencing on fresh saliva (SA), semen (SE), vaginal secretions (VF), and their mixtures (SA-VF and SE-VF), with additional microbial analysis after 15 and 30 days of indoor exposure. Results showed the single-fluid samples exhibited specific dominant bacterial taxa, whereas the two mixture samples contained detectable bacterial signatures from both constituent fluids. Untargeted UHPLC-QTOF/MS analysis revealed unique metabolic signatures for each body fluid, enriched in biologically relevant pathways like steroid and bile acid metabolism. Moreover, we putatively identified characteristic metabolites, including α-solanine, candicidin, and megalomicin C1, some of which are rare microbial antibiotics. Owing to the exploratory nature and associated constraints of nontargeted approaches, these results serve as a provisional reference for identifying potential candidates. Integration of metabolomic and microbiome data uncovered strong metabolite-microbe correlations, highlighting microbially influenced metabolic networks unique to each body fluid type. Using differential microbes and metabolites individually as input features, the random forest model achieved BFID accuracies of 80 and 83.1%, respectively; however, integrating both sets of features increased accuracy to 100%. In contrast, microbial-based TsD prediction performed well for single-fluid samples but showed reduced effectiveness for mixed samples. Overall, our research highlights the powerful predictive potential and improved predictive accuracy of the integration of microbiome and metabolome data in BFID.
{"title":"Integrated Microbiome and Metabolome Analysis for Characterization and Discrimination of Saliva, Semen, Vaginal Secretions, and Their Mixtures.","authors":"Yu Deng,Xiaoyuan Zhen,Ruocheng Xia,Ruxin Zhu,Gongying Zhang,Pengyu Chen,Jianghua Lai,Ruiyang Tao","doi":"10.1021/acs.analchem.5c05356","DOIUrl":"https://doi.org/10.1021/acs.analchem.5c05356","url":null,"abstract":"Body fluid identification (BFID) and estimation of time since deposition (TsD) are valuable yet challenging in forensic practice. Previous studies have demonstrated that integrating microbial and metabolomic profiles provides complementary biological insights. Therefore, this study performed untargeted metabolomic profiling and full-length 16S rRNA sequencing on fresh saliva (SA), semen (SE), vaginal secretions (VF), and their mixtures (SA-VF and SE-VF), with additional microbial analysis after 15 and 30 days of indoor exposure. Results showed the single-fluid samples exhibited specific dominant bacterial taxa, whereas the two mixture samples contained detectable bacterial signatures from both constituent fluids. Untargeted UHPLC-QTOF/MS analysis revealed unique metabolic signatures for each body fluid, enriched in biologically relevant pathways like steroid and bile acid metabolism. Moreover, we putatively identified characteristic metabolites, including α-solanine, candicidin, and megalomicin C1, some of which are rare microbial antibiotics. Owing to the exploratory nature and associated constraints of nontargeted approaches, these results serve as a provisional reference for identifying potential candidates. Integration of metabolomic and microbiome data uncovered strong metabolite-microbe correlations, highlighting microbially influenced metabolic networks unique to each body fluid type. Using differential microbes and metabolites individually as input features, the random forest model achieved BFID accuracies of 80 and 83.1%, respectively; however, integrating both sets of features increased accuracy to 100%. In contrast, microbial-based TsD prediction performed well for single-fluid samples but showed reduced effectiveness for mixed samples. Overall, our research highlights the powerful predictive potential and improved predictive accuracy of the integration of microbiome and metabolome data in BFID.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"15 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147495061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-23DOI: 10.1021/acs.analchem.6c00623
Ye Tian,Xinxi Li,Jingdong Tang,Lei Zhang,Shuai Jiang,Halimulati Muertizha,Zhenwei Yang
Diabetic foot ulcer (DFU), a severe complication of diabetes, necessitates sensitive detection of pathogenic microRNAs (miRNAs) as emerging diagnostic biomarkers. The exponential amplification reaction (EXPAR) offers high efficiency and rapid kinetics for miRNA detection, but its application is limited by persistent nonspecific amplification arising from spurious template-template interactions and interference from partially complementary sequences in complex samples. To address this, we present an integrated strategy combining a blocking probe prehybridized to the EXPAR template to sterically hinder nonspecific hybridization, magnetic bead-based isolation of target-bound probes to remove interferents, and a self-priming mechanism that regenerates the EXPAR primer only upon target recognition. This design ensures high specificity and minimizes primer-independent amplification. Coupling this optimized EXPAR platform with a G-quadruplex-based signal transduction system enables facile colorimetric readout for instrument-free visual detection. The method achieves a detection limit of 41.4 aM across a dynamic range of 100 aM to 50 pM for DFU-associated miRNAs, with excellent selectivity against nontarget miRNAs and consistent reproducibility in fibroblasts and serum. This work provides a generalizable solution to the specificity issue in EXPAR and delivers a reliable, sensitive platform for miRNA profiling in clinical and point-of-care settings.
{"title":"Development of a High-Fidelity EXPAR Platform and Its Application for Ultrasensitive Detection of Diabetic Foot Ulcer-Associated MicroRNAs.","authors":"Ye Tian,Xinxi Li,Jingdong Tang,Lei Zhang,Shuai Jiang,Halimulati Muertizha,Zhenwei Yang","doi":"10.1021/acs.analchem.6c00623","DOIUrl":"https://doi.org/10.1021/acs.analchem.6c00623","url":null,"abstract":"Diabetic foot ulcer (DFU), a severe complication of diabetes, necessitates sensitive detection of pathogenic microRNAs (miRNAs) as emerging diagnostic biomarkers. The exponential amplification reaction (EXPAR) offers high efficiency and rapid kinetics for miRNA detection, but its application is limited by persistent nonspecific amplification arising from spurious template-template interactions and interference from partially complementary sequences in complex samples. To address this, we present an integrated strategy combining a blocking probe prehybridized to the EXPAR template to sterically hinder nonspecific hybridization, magnetic bead-based isolation of target-bound probes to remove interferents, and a self-priming mechanism that regenerates the EXPAR primer only upon target recognition. This design ensures high specificity and minimizes primer-independent amplification. Coupling this optimized EXPAR platform with a G-quadruplex-based signal transduction system enables facile colorimetric readout for instrument-free visual detection. The method achieves a detection limit of 41.4 aM across a dynamic range of 100 aM to 50 pM for DFU-associated miRNAs, with excellent selectivity against nontarget miRNAs and consistent reproducibility in fibroblasts and serum. This work provides a generalizable solution to the specificity issue in EXPAR and delivers a reliable, sensitive platform for miRNA profiling in clinical and point-of-care settings.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"11 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147502179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isothermal amplification techniques, such as helicase-dependent amplification (HDA) combined with CRISPR, are cutting-edge approaches for nucleic acid detection. In this work, we developed a novel ultrashort mesophilic HDA (termed usHDA) for rapid, highly sensitive nucleic acid amplification at 37 °C and constructed a one-pot usHDA-CRISPR/Cas12 assay. The usHDA is specifically designed for rapid amplification of ultrashort sequences (about 40 nt) at 37 °C within 30 min. This usHDA-CRISPR/Cas12a detection can be completed within 1 h, achieving a limit of detection (LOD) of 5 aM. When tested on 58 clinical specimens from patients infected with respiratory pathogens, this assay identified 41 positive and 17 negative samples for influenza A virus. This assay achieved 100% sensitivity, 100% specificity, and a perfect receiver operating characteristic curve (area under the curve value = 1.00; n = 58) compared with PCR analysis. Furthermore, 24 samples of Staphylococcus infection were detected using usHDA-CRISPR/Cas12a, and the same 100% sensitivity and specificity were achieved. These findings highlighted the strong applicability of our proposed assay for universal nucleic acid detection.
{"title":"One-Pot CRISPR/Cas12a Assay Based on Ultrashort HDA for Ultrasensitive and Universal Nucleic Acid Detection.","authors":"Huimin Liao,Huiyun Xie,Hengming Ye,Xiaoying Liu,Yuanhao Chen,Ruofu Zhong,Suhui He,Xiang Xiao,Zhaoyang Xie,Zheng Shao,Luxin Yu,Zhangquan Chen","doi":"10.1021/acs.analchem.5c08249","DOIUrl":"https://doi.org/10.1021/acs.analchem.5c08249","url":null,"abstract":"Isothermal amplification techniques, such as helicase-dependent amplification (HDA) combined with CRISPR, are cutting-edge approaches for nucleic acid detection. In this work, we developed a novel ultrashort mesophilic HDA (termed usHDA) for rapid, highly sensitive nucleic acid amplification at 37 °C and constructed a one-pot usHDA-CRISPR/Cas12 assay. The usHDA is specifically designed for rapid amplification of ultrashort sequences (about 40 nt) at 37 °C within 30 min. This usHDA-CRISPR/Cas12a detection can be completed within 1 h, achieving a limit of detection (LOD) of 5 aM. When tested on 58 clinical specimens from patients infected with respiratory pathogens, this assay identified 41 positive and 17 negative samples for influenza A virus. This assay achieved 100% sensitivity, 100% specificity, and a perfect receiver operating characteristic curve (area under the curve value = 1.00; n = 58) compared with PCR analysis. Furthermore, 24 samples of Staphylococcus infection were detected using usHDA-CRISPR/Cas12a, and the same 100% sensitivity and specificity were achieved. These findings highlighted the strong applicability of our proposed assay for universal nucleic acid detection.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"265 1 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147502182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-23DOI: 10.1021/acs.analchem.6c00448
Limin Yang,Huilin Tan,Yujue Wang,Jingang Zhang,Xiangyu Meng,Xiaojuan Liu,Ting Hou,Weiqi Chen,Feng Li
Accurate identification and profiling of multiple protein biomarkers on tumor-derived extracellular vesicles (tEVs) are crucial for noninvasive cancer subtyping diagnosis but remain technically challenging due to their high heterogeneity, low abundance in biofluids, and preisolation/purification processes. Herein, we developed a homogeneous electrochemical biosensor empowered by fluidly confined CRISPR-magnetic microbots for the amplified detection and sensitive discrimination of tEV subtypes. The CRISPR-magnetic microbots were constructed by engineering CRISPR/Cas12a and DNA icosahedra/doxorubicin (DNA-ICOS/DOX) on intracellularly gelated magnetic cells (IGMCs). Benefiting from the synergistic effects of spatial confinement and membrane fluidity to elevate the local concentration and collision efficiency, the activity of CRISPR/Cas12a was found to be greatly enhanced on IGMCs. For selective sorting of tEVs, a logic-gated aptamer system was used to orthogonally label tEV subpopulations, which further triggers the trans-cleavage activity of CRISPR/Cas12a, resulting in the release of massive DNA-ICOS/DOX into solution. After magnetic separation, the liberated DOX molecules generate a strong electrochemical signal. Particularly, the CRISPR-magnetic microbots could efficiently reduce the background signal, endowing a significantly improved signal-to-noise ratio. Therefore, by combining the CRISPR-magnetic microbots with the dual-target-guided orthogonal barcoding strategy in a homogeneous electrochemical biosensor, precise identification and sensitive detection of tEVs were successfully achieved. More significantly, this assay achieves accurate cancer subtyping in clinical samples, demonstrating its potential as a robust, noninvasive tool for high-accuracy disease screening, classification, and progression monitoring.
{"title":"Fluidly Confined CRISPR-Magnetic Microbots Empowered Homogeneous Electrochemical Biosensor for Amplified Detection and Discrimination of Cancer-Derived Extracellular Vesicle Subtypes.","authors":"Limin Yang,Huilin Tan,Yujue Wang,Jingang Zhang,Xiangyu Meng,Xiaojuan Liu,Ting Hou,Weiqi Chen,Feng Li","doi":"10.1021/acs.analchem.6c00448","DOIUrl":"https://doi.org/10.1021/acs.analchem.6c00448","url":null,"abstract":"Accurate identification and profiling of multiple protein biomarkers on tumor-derived extracellular vesicles (tEVs) are crucial for noninvasive cancer subtyping diagnosis but remain technically challenging due to their high heterogeneity, low abundance in biofluids, and preisolation/purification processes. Herein, we developed a homogeneous electrochemical biosensor empowered by fluidly confined CRISPR-magnetic microbots for the amplified detection and sensitive discrimination of tEV subtypes. The CRISPR-magnetic microbots were constructed by engineering CRISPR/Cas12a and DNA icosahedra/doxorubicin (DNA-ICOS/DOX) on intracellularly gelated magnetic cells (IGMCs). Benefiting from the synergistic effects of spatial confinement and membrane fluidity to elevate the local concentration and collision efficiency, the activity of CRISPR/Cas12a was found to be greatly enhanced on IGMCs. For selective sorting of tEVs, a logic-gated aptamer system was used to orthogonally label tEV subpopulations, which further triggers the trans-cleavage activity of CRISPR/Cas12a, resulting in the release of massive DNA-ICOS/DOX into solution. After magnetic separation, the liberated DOX molecules generate a strong electrochemical signal. Particularly, the CRISPR-magnetic microbots could efficiently reduce the background signal, endowing a significantly improved signal-to-noise ratio. Therefore, by combining the CRISPR-magnetic microbots with the dual-target-guided orthogonal barcoding strategy in a homogeneous electrochemical biosensor, precise identification and sensitive detection of tEVs were successfully achieved. More significantly, this assay achieves accurate cancer subtyping in clinical samples, demonstrating its potential as a robust, noninvasive tool for high-accuracy disease screening, classification, and progression monitoring.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"13 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147495097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dimethyl carbonate (DMC), the primary component of lithium-ion battery (LIBs) electrolytes, is volatile at room temperature and can serve as a key indicator for detecting electrolyte leakage. In this work, leaf-like Cs3Sb2Cl9 was synthesized via a single solvent solubility difference method, with its surface exhibiting strong orientation on the (110) crystal plane. The sensor demonstrated excellent gas-sensing performance toward detecting DMC (50 ppm of DMC of 3.94), with relatively short response and recovery times of 104 and 66 s, respectively (when tested 25 ppm of DMC), and a low detection limit of 100 ppb. In situ infrared spectroscopy first revealed that Cs3Sb2Cl9 catalyzes the decomposition of DMC into the byproduct methanol during the adsorption process. Density functional theory (DFT) calculations further elucidated the adsorption behavior of DMC on different active sites of the Cs3Sb2Cl9 (110) plane, indicating that the Sb site possesses a stronger adsorption affinity for DMC. Provides strong evidence that the B site of the perovskite serves as a highly active site. This study not only presents a preliminary exploration of Cs3Sb2Cl9 in gas sensing but also provides valuable insights into the sensing mechanisms of lead-free halide perovskites.
{"title":"Gas Sensing Performance of Lead-Free Perovskite Cs3Sb2Cl9 for Monitoring Typical Electrolyte (DMC) Leakage in Lithium-Ion Batteries.","authors":"Chaofan Ma,Huiyu Su,Yazhou Yang,Chaoqi Zhu,Jiahong Tang,Kechen Zhou,Dawen Zeng","doi":"10.1021/acs.analchem.6c00432","DOIUrl":"https://doi.org/10.1021/acs.analchem.6c00432","url":null,"abstract":"Dimethyl carbonate (DMC), the primary component of lithium-ion battery (LIBs) electrolytes, is volatile at room temperature and can serve as a key indicator for detecting electrolyte leakage. In this work, leaf-like Cs3Sb2Cl9 was synthesized via a single solvent solubility difference method, with its surface exhibiting strong orientation on the (110) crystal plane. The sensor demonstrated excellent gas-sensing performance toward detecting DMC (50 ppm of DMC of 3.94), with relatively short response and recovery times of 104 and 66 s, respectively (when tested 25 ppm of DMC), and a low detection limit of 100 ppb. In situ infrared spectroscopy first revealed that Cs3Sb2Cl9 catalyzes the decomposition of DMC into the byproduct methanol during the adsorption process. Density functional theory (DFT) calculations further elucidated the adsorption behavior of DMC on different active sites of the Cs3Sb2Cl9 (110) plane, indicating that the Sb site possesses a stronger adsorption affinity for DMC. Provides strong evidence that the B site of the perovskite serves as a highly active site. This study not only presents a preliminary exploration of Cs3Sb2Cl9 in gas sensing but also provides valuable insights into the sensing mechanisms of lead-free halide perovskites.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"19 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147502181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We developed a novel two-color digital immunoassay platform for the simultaneous detection of neurodegenerative disease protein biomarkers (neurofilament light chain (NfL) and interleukin-6 (IL-6)) in a homogeneous, wash-free format. This multiplex approach employs two antibody pairs: capture antibodies conjugated with porphyrin-metal organic framework (pMOF) as singlet oxygen (1O2) nanogenerators, and detection antibodies functionalized with spectrally distinct upconversion nanoparticles (UCNPs) serving as nanoreporters─specifically BHQ2-modified Er3+-doped UCNPs for NfL detection and dabsyl-modified Tm3+-doped UCNPs for IL-6 detection, both with luminescence caged by 1O2-cleavable quenchers. Antigen binding formed immunocomplexes between nanoprobe pairs, triggering specific luminescence activation in distinct channels: green emission at 540 nm for NfL and blue emission at 475 nm for IL-6. The spatially restricted diffusion radius of pMOF-generated 1O2 ensured the selective cleavage of proximal quenchers, enabling digital quantification via single-molecule fluorescence imaging. The platform demonstrated exceptional sensitivity with cross-talk-free performance, achieving detection limits of 25 aM for NfL and 11 aM for IL-6. Serum analysis confirmed the biosensor's potential for comprehensive neurological biomarker detection, establishing its utility for large-scale neurodegenerative disease screening.
{"title":"Two-Color Digital Immunoassay for Simultaneous Detection of Low-Abundance Neurodegenerative Disease Protein Biomarkers.","authors":"Ruiying Peng,Daian Chen,Ting Deng,Jishan Li,Jian-Hui Jiang","doi":"10.1021/acs.analchem.5c06815","DOIUrl":"https://doi.org/10.1021/acs.analchem.5c06815","url":null,"abstract":"We developed a novel two-color digital immunoassay platform for the simultaneous detection of neurodegenerative disease protein biomarkers (neurofilament light chain (NfL) and interleukin-6 (IL-6)) in a homogeneous, wash-free format. This multiplex approach employs two antibody pairs: capture antibodies conjugated with porphyrin-metal organic framework (pMOF) as singlet oxygen (1O2) nanogenerators, and detection antibodies functionalized with spectrally distinct upconversion nanoparticles (UCNPs) serving as nanoreporters─specifically BHQ2-modified Er3+-doped UCNPs for NfL detection and dabsyl-modified Tm3+-doped UCNPs for IL-6 detection, both with luminescence caged by 1O2-cleavable quenchers. Antigen binding formed immunocomplexes between nanoprobe pairs, triggering specific luminescence activation in distinct channels: green emission at 540 nm for NfL and blue emission at 475 nm for IL-6. The spatially restricted diffusion radius of pMOF-generated 1O2 ensured the selective cleavage of proximal quenchers, enabling digital quantification via single-molecule fluorescence imaging. The platform demonstrated exceptional sensitivity with cross-talk-free performance, achieving detection limits of 25 aM for NfL and 11 aM for IL-6. Serum analysis confirmed the biosensor's potential for comprehensive neurological biomarker detection, establishing its utility for large-scale neurodegenerative disease screening.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"25 3 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147495067","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Biological matrix data are essential for computational analysis, providing a structured framework to identify patterns and relationships in biological systems. Many other biological data types, including sequences, networks, and images, can be transformed into matrix representations through feature extraction and encoding. However, their high dimensionality complicates analysis, leading to increased computational complexity and the risk of overfitting, known as the curse of dimensionality. To address these challenges, we developed SIBioX, a matrix-based bioinformatics tool powered by swarm intelligence algorithms. It integrates 54 swarm intelligence methods, 5 conventional feature selection techniques, and 17 machine learning models, enabling comprehensive analysis of biological matrix data. With a user-friendly graphical interface, it supports operations such as feature normalization, selection, classification, clustering, statistical analysis, and data visualization. Additionally, it converts nonmatrix biological data, like gene and protein sequences, into matrix formats for further study. Experimental results demonstrate that SIBioX not only attains high accuracy in feature selection but also effectively reduces dimensionality, thereby streamlining bioinformatics workflows and promoting greater efficiency in biomedical research.
{"title":"SIBioX: A Matrix Based Bioinformatics Analysis Tool Based on Swarm Intelligence Algorithm.","authors":"Zhaomin Yao,Haonan Shangguan,Weiming Xie,Jingwei Too,Chen Yang,Gancheng Zhu,Ying Zhan,Xiaodan Wu,Yingxin Dai,Yusong Pei,Guoxu Zhang,Zhiguo Wang","doi":"10.1021/acs.analchem.5c07841","DOIUrl":"https://doi.org/10.1021/acs.analchem.5c07841","url":null,"abstract":"Biological matrix data are essential for computational analysis, providing a structured framework to identify patterns and relationships in biological systems. Many other biological data types, including sequences, networks, and images, can be transformed into matrix representations through feature extraction and encoding. However, their high dimensionality complicates analysis, leading to increased computational complexity and the risk of overfitting, known as the curse of dimensionality. To address these challenges, we developed SIBioX, a matrix-based bioinformatics tool powered by swarm intelligence algorithms. It integrates 54 swarm intelligence methods, 5 conventional feature selection techniques, and 17 machine learning models, enabling comprehensive analysis of biological matrix data. With a user-friendly graphical interface, it supports operations such as feature normalization, selection, classification, clustering, statistical analysis, and data visualization. Additionally, it converts nonmatrix biological data, like gene and protein sequences, into matrix formats for further study. Experimental results demonstrate that SIBioX not only attains high accuracy in feature selection but also effectively reduces dimensionality, thereby streamlining bioinformatics workflows and promoting greater efficiency in biomedical research.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"3 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147495095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this study, a wireless passive radio frequency identification (RFID) integrated sensor was proposed for on-site rapid detection of Pb2+ in soil, eliminating the need for intricate detection circuits or high-cost equipment (e.g., vector network analyzer (VNA)). The RFID-integrated sensor comprised an RF chip, a tag antenna, and an rGO/LISM chemiresistive sensing unit, with a modular design (reusable housing/peripherals, clamp-connected replaceable sensing unit) to curtail long-term detection costs. Moreover, a detection method based on impedance mismatch was developed, using an experimental setup that captured changes in the minimum response power (MRP) of the RFID-integrated sensor. Specifically, Pb2+ in soil extracts selectively permeated through the LISM and underwent specific chemisorption with oxygen-containing functional groups on rGO, which altered the hole carrier concentration of the sensing unit, increased its resistance, and further modified the impedance of the tag antenna. This alteration induced impedance mismatch between the RF chip and the tag antenna, where varying degrees of impedance mismatch directly modulated the MRP. Validated via simulations and testing, the RFID-integrated sensor achieved rapid detection (<2 min) of Pb2+ in real soil samples, with RMSEs < 0.30 mg/kg, relative errors <15%, and recovery rates of 85.23%-107.14%, supporting it as an economical and rapid solution for Pb2+ detection. This method additionally offered an efficient and straightforward approach for the on-site rapid detection of heavy metals in soil, boasting practical application prospects.
{"title":"A Wireless Passive RFID-Integrated Sensor for the Detection of Pb2+ in Soil: An Innovative Method Using Impedance Mismatch for On-Site Detection of Heavy Metals.","authors":"Zuozheng Ding,Chengjie Gu,Lingling Yang,Junchao Zhang,Yihan Yao,Guowei Fan,Guo Zhao","doi":"10.1021/acs.analchem.5c07268","DOIUrl":"https://doi.org/10.1021/acs.analchem.5c07268","url":null,"abstract":"In this study, a wireless passive radio frequency identification (RFID) integrated sensor was proposed for on-site rapid detection of Pb2+ in soil, eliminating the need for intricate detection circuits or high-cost equipment (e.g., vector network analyzer (VNA)). The RFID-integrated sensor comprised an RF chip, a tag antenna, and an rGO/LISM chemiresistive sensing unit, with a modular design (reusable housing/peripherals, clamp-connected replaceable sensing unit) to curtail long-term detection costs. Moreover, a detection method based on impedance mismatch was developed, using an experimental setup that captured changes in the minimum response power (MRP) of the RFID-integrated sensor. Specifically, Pb2+ in soil extracts selectively permeated through the LISM and underwent specific chemisorption with oxygen-containing functional groups on rGO, which altered the hole carrier concentration of the sensing unit, increased its resistance, and further modified the impedance of the tag antenna. This alteration induced impedance mismatch between the RF chip and the tag antenna, where varying degrees of impedance mismatch directly modulated the MRP. Validated via simulations and testing, the RFID-integrated sensor achieved rapid detection (<2 min) of Pb2+ in real soil samples, with RMSEs < 0.30 mg/kg, relative errors <15%, and recovery rates of 85.23%-107.14%, supporting it as an economical and rapid solution for Pb2+ detection. This method additionally offered an efficient and straightforward approach for the on-site rapid detection of heavy metals in soil, boasting practical application prospects.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"15 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147495064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-21DOI: 10.1021/acs.analchem.5c07111
Hugo G. Machado, Elliott P. Mueller, Júlio C. O. Ribeiro, Giovanni B. Bevilaqua, Gabriel F. dos Santos, Alexandre A. Ferreira, Ygor S. Rocha, Surjyendu Bhattacharjee, John M. Eiler, Boniek Gontijo
Stable isotope analysis is a vital tool across chemistry, geology, and environmental science, but conventional Isotope Ratio Mass Spectrometry (IRMS) techniques have limited capabilities for site-specific or multiply substituted (“clumped”) isotope analyses, and are particularly limited for analyses of complex mixtures without prior analyte purification. This study addresses this gap by employing a high-resolution Orbitrap mass spectrometer to directly measure the 13C/12C ratio in a model naphthenic acid (1,2,3,4-tetrahydro-2-naphthoic acid, THN) within complex organic matrices. We applied a “zero-enrichment” experimental design to evaluate accuracy and precision by comparing pure standards to the same compound in synthetic samples resembling natural waters. Complementary experiments using low-molecular-weight organic acids and natural rumen fluid were conducted to define the method’s limits under controlled and severe ion-suppression conditions. The results demonstrated that matrix effects and ion statistics can substantially degrade both accuracy and precision under certain conditions. At very low analyte concentrations, incomplete ion accumulation led to heightened δ13C variability, a condition analogous to a “blank effect”. Paradoxically, adding 1% NH4OH improved the precision of 13C/12C measurements (reducing the relative standard error from ∼0.80‰ to ∼0.63‰ at 0.1 μM THN), despite a reduced signal, by promoting more stable deprotonation and minimizing ion suppression. We also identified that coaccumulated ions, even when baseline-resolved, such as a matrix-derived fragment at m/z 177, degrade precision by perturbing the space-charge balance. Removing this interference fully restored precision, underscoring the need to control coaccumulating ions. Crucially, experiments with small organic acids demonstrated that moderate ion suppression does not lead to isotopic bias, which emerges only when severe suppression reduces analyte ion counts below a critical statistical threshold. Finally, we identified an “isotopic stability plateau”─an optimal signal range where δ13C measurements are most precise and accurate, poised between noise-dominated and space-charge-distorted regimes. This work demonstrates that Orbitrap-MS can perform reliable isotope analysis in complex organic mixtures when instrumental and chemical parameters are carefully optimized, opening new applications in petroleum geochemistry, environmental forensics, and other topics.
{"title":"Lessons Learned in Orbitrap MS-Based Isotope Ratio Analysis of Organic Acid Mixtures","authors":"Hugo G. Machado, Elliott P. Mueller, Júlio C. O. Ribeiro, Giovanni B. Bevilaqua, Gabriel F. dos Santos, Alexandre A. Ferreira, Ygor S. Rocha, Surjyendu Bhattacharjee, John M. Eiler, Boniek Gontijo","doi":"10.1021/acs.analchem.5c07111","DOIUrl":"https://doi.org/10.1021/acs.analchem.5c07111","url":null,"abstract":"Stable isotope analysis is a vital tool across chemistry, geology, and environmental science, but conventional Isotope Ratio Mass Spectrometry (IRMS) techniques have limited capabilities for site-specific or multiply substituted (“clumped”) isotope analyses, and are particularly limited for analyses of complex mixtures without prior analyte purification. This study addresses this gap by employing a high-resolution Orbitrap mass spectrometer to directly measure the <sup>13</sup>C/<sup>12</sup>C ratio in a model naphthenic acid (1,2,3,4-tetrahydro-2-naphthoic acid, THN) within complex organic matrices. We applied a “zero-enrichment” experimental design to evaluate accuracy and precision by comparing pure standards to the same compound in synthetic samples resembling natural waters. Complementary experiments using low-molecular-weight organic acids and natural rumen fluid were conducted to define the method’s limits under controlled and severe ion-suppression conditions. The results demonstrated that matrix effects and ion statistics can substantially degrade both accuracy and precision under certain conditions. At very low analyte concentrations, incomplete ion accumulation led to heightened δ<sup>13</sup>C variability, a condition analogous to a “blank effect”. Paradoxically, adding 1% NH<sub>4</sub>OH improved the precision of <sup>13</sup>C/<sup>12</sup>C measurements (reducing the relative standard error from ∼0.80‰ to ∼0.63‰ at 0.1 μM THN), despite a reduced signal, by promoting more stable deprotonation and minimizing ion suppression. We also identified that coaccumulated ions, even when baseline-resolved, such as a matrix-derived fragment at <i>m</i>/<i>z</i> 177, degrade precision by perturbing the space-charge balance. Removing this interference fully restored precision, underscoring the need to control coaccumulating ions. Crucially, experiments with small organic acids demonstrated that moderate ion suppression does not lead to isotopic bias, which emerges only when severe suppression reduces analyte ion counts below a critical statistical threshold. Finally, we identified an “isotopic stability plateau”─an optimal signal range where δ<sup>13</sup>C measurements are most precise and accurate, poised between noise-dominated and space-charge-distorted regimes. This work demonstrates that Orbitrap-MS can perform reliable isotope analysis in complex organic mixtures when instrumental and chemical parameters are carefully optimized, opening new applications in petroleum geochemistry, environmental forensics, and other topics.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"14 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147492701","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
As an abundant, renewable aromatic resource, lignin remains underutilized due to its complex and recalcitrant structure. Molecular-level elucidation of liquid-phase catalytic depolymerization of technical lignin is further hindered by structural heterogeneity and limited accessibility of intermediates under high-pressure conditions. Herein, a decoupled double-bed flow-through reactor integrated with online high-resolution mass spectrometry (HRMS) is employed to investigate the catalytic depolymerization of alkali Kraft lignin. Spatial separation of thermal solvolysis and catalytic hydrogenolysis enables independent characterization of products from each bed. Online HRMS resolves thousands of molecular species from monomers to oligomers up to heptamers, revealing a pronounced shift toward lower degrees of polymerization and reduced unsaturation after catalytic hydrogenolysis. Ring and double bond equivalents-carbon number, van Krevelen, and tandem MS analyses indicate extensive hydrogenation, partial deoxygenation, and the cleavage of β-O-4 linkages, with C-C interunit linkages, either native or formed via condensation, largely preserved in the residual dimers and oligomers. Continuous online monitoring captures the evolution of individual products, highlighting progressive depolymerization and suppressed recondensation under flow-through conditions. This work demonstrates online HRMS as a powerful operando tool for resolving structure-reactivity relationships in lignin depolymerization and provides molecular-level insights relevant to catalytic biomass valorization.
{"title":"Process-Decoupled Operando Molecular Characterization of Liquid-Phase Lignin Depolymerization by Online High-Resolution Mass Spectrometry.","authors":"Zhongyue Zhou,Linyu Zhu,Xintong Xiao,Hairong Ren,Cunhao Cui,Fei Qi","doi":"10.1021/acs.analchem.6c00073","DOIUrl":"https://doi.org/10.1021/acs.analchem.6c00073","url":null,"abstract":"As an abundant, renewable aromatic resource, lignin remains underutilized due to its complex and recalcitrant structure. Molecular-level elucidation of liquid-phase catalytic depolymerization of technical lignin is further hindered by structural heterogeneity and limited accessibility of intermediates under high-pressure conditions. Herein, a decoupled double-bed flow-through reactor integrated with online high-resolution mass spectrometry (HRMS) is employed to investigate the catalytic depolymerization of alkali Kraft lignin. Spatial separation of thermal solvolysis and catalytic hydrogenolysis enables independent characterization of products from each bed. Online HRMS resolves thousands of molecular species from monomers to oligomers up to heptamers, revealing a pronounced shift toward lower degrees of polymerization and reduced unsaturation after catalytic hydrogenolysis. Ring and double bond equivalents-carbon number, van Krevelen, and tandem MS analyses indicate extensive hydrogenation, partial deoxygenation, and the cleavage of β-O-4 linkages, with C-C interunit linkages, either native or formed via condensation, largely preserved in the residual dimers and oligomers. Continuous online monitoring captures the evolution of individual products, highlighting progressive depolymerization and suppressed recondensation under flow-through conditions. This work demonstrates online HRMS as a powerful operando tool for resolving structure-reactivity relationships in lignin depolymerization and provides molecular-level insights relevant to catalytic biomass valorization.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"16 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2026-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147483369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：