Analytical Chemistry最新文献

{"title":"Discovery of an Enzyme-Activated Fluorogenic Probe for In Vivo Profiling of Acylaminoacyl-Peptide Hydrolase","authors":"Shi-Yu Liu, Huiling Wang, Yue-Yang Zhang, Le-Yu Huang","doi":"10.1021/acs.analchem.4c05192","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c05192","url":null,"abstract":"Acylaminoacyl-peptide hydrolase (APEH), a serine peptidase that belongs to the prolyl oligopeptidase (POP) family, catalyzes removal of N-terminal acetylated amino acid residues from peptides. As a key regulator of protein N-terminal acetylation, APEH was involved in many important physiological processes while its aberrant expression was correlated with progression of various diseases such as inflammation, diabetics, Alzheimer’s disease (AD), and cancers. However, while emerging attention has been attracted in APEH-related disease diagnosis and drug discovery, the mechanisms behind APEH and related disease progression are still unclear; thus, further investigating the physiological role and function of APEH is of great importance. To date, enzyme-activated fluorescent probes targeting POPs have been extensively reported and adopted in relevant medical research and applications. Nevertheless, as an important member of the POP family, APEH was rarely referred in the field of bioimaging while the fluorescent probe for <i>in vivo</i> sensing of APEH activity has not been reported yet. Thus, acquiring an efficient APEH-targeted probe is in urgent need. Herein, an enzyme-activated fluorogenic probe for <i>in vivo</i> profiling of APEH was first discovered via a substrate mimic-based strategy. By combination of stimulated molecular docking-based preliminary screening and experiment-based secondary screening, the optimal probe (named as <b>TMN-AcA</b>), which displayed high binding affinity, sensitivity, and specificity toward APEH, was screened out. Owing to the superior properties of <b>TMN-AcA</b>, endogenous APEH activity in various cell lines and transplanted tumor could be visualized while tissue distribution of APEH was revealed. Most importantly, APEH was first demonstrated to be a potential biomarker of multiple-organ injury via <b>TMN-AcA</b>-based bioimaging and immunohistochemistry (IHC) analysis while the newly developed probe could serve as a vital tool for APEH-related disease diagnosis and biological function study.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"20 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031167","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}

{"title":"Sialic Acid-Modified NIR-II Fluorophore with Enhanced Brightness and Photoconversion Capability for Targeted Lymphoma Phototheranostics","authors":"Fang Nan, Zhongxin Zhou, Qian Bai, Kai Chen, Yu Liu, Shuqi Wu","doi":"10.1021/acs.analchem.4c06424","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c06424","url":null,"abstract":"Lymphoma is a malignant cancer characterized by a rapidly increasing incidence, complex etiology, and lack of obvious early symptoms. Efficient theranostics of lymphoma is of great significance in improving patient outcomes, empowering informed decision-making, and driving medical innovation. Herein, we developed a multifunctional nanoplatform for precise optical imaging and therapy of lymphoma based on a new photosensitizer (1-oxo-1<i>H</i>-benzoo[de]anthracene-2,3-dicarbonitrile-triphenylamine (OBADC-TPA)). OBADC-TPA is a donor–acceptor (D–A) molecule characterized by a novel small coplanar and strong electron-withdrawing acceptor skeleton, while the OBADC moiety facilitates strong intramolecular charge transfer. OBADC-TPA-based nanoparticles (NPs) were prepared through encapsulation with an amphiphilic polymer and subsequent modification with sialic acid (SA). Both in vitro and in vivo studies demonstrated that NPs-SA possessed good biocompatibility, effective tumor accumulation, high photoacoustic (PA) contrast, bright second near-infrared (NIR-II) fluorescence emission, and efficient photothermal/photodynamic conversion capabilities, which can serve as a multifunctional nanocomposite for targeted PA/NIR-II fluorescence imaging-guided synergistic type I/II photodynamic and photothermal therapy (PDT/PTT) of lymphoma. This work not only provides a new NIR-II fluorophore with a novel acceptor moiety but also offers a new, accurate, and effective approach for the targeted diagnosis and treatment of lymphoma, holding promising prospects for clinical application.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"15 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031168","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}

{"title":"Deep-Learning-Assisted Digital Fluorescence Immunoassay on Magnetic Beads for Ultrasensitive Determination of Protein Biomarkers","authors":"Jian Zhang, Wenshuai Zhou, Honglan Qi, Xiaowei He","doi":"10.1021/acs.analchem.4c05877","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c05877","url":null,"abstract":"Digital fluorescence immunoassay (DFI) based on random dispersion magnetic beads (MBs) is one of the powerful methods for ultrasensitive determination of protein biomarkers. However, in the DFI, improving the limit of detection (LOD) is challenging since the ratio of signal-to-background and the speed of manual counting beads are low. Herein, we developed a deep-learning network (ATTBeadNet) by utilizing a new hybrid attention mechanism within a UNet3+ framework for accurately and fast counting the MBs and proposed a DFI using CdS quantum dots (QDs) with narrow peak and optical stability as reported at first time. The developed ATTBeadNet was applied to counting the MBs, resulting in the F1 score (95.91%) being higher than those of other methods (ImageJ, 68.33%; computer vision-based, 92.99%; fully convolutional network, 75.00%; mask region-based convolutional neural network, 70.34%). On principle-on-proof, a sandwich MB-based DFI was proposed, in which human interleukin-6 (IL-6) was taken as a model protein biomarker, while antibody-bound streptavidin-coated MBs were used as capture MBs and antibody-HRP-tyramide-functionalized CdS QDs were used as the binding reporter. When the developed ATTBeadNet was applied to the MB-based DFI of IL-6 (20 μL), the linear range from 5 to 100 fM and an LOD of 3.1 fM were achieved, which are better than those using the ImageJ method (linear range from 30 to 100 fM and LOD of 20 fM). This work demonstrates that the integration of the deep-learning network with DFI is a promising strategy for the highly sensitive and accurate determination of protein biomarkers.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"9 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027032","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}

{"title":"Suppression of Collision-Induced Dissociation in a Supersonically Expanding Gas","authors":"Uma Namangalam, Salvi Mohandas, Hemanth Dinesan, Sunil Kumar S.","doi":"10.1021/acs.analchem.4c06342","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c06342","url":null,"abstract":"In high-resolution mass spectrometry, an electrospray ionization source is often paired with an ion-funnel to enhance ion transmission. Although it is established that ions experience collision-induced dissociation as they pass through this device, the impact of gas-flow dynamics on ion fragmentation remains unexplored. The present work demonstrates that the gas-flow dynamics from the capillary interface of an electrospray ionization source into an ion-funnel significantly reduces ion fragmentation. This reduction stems from the substantial decrease in the rate of increase in the internal energy of the ions, resulting from the collisions with a supersonically expanding gas. The results of this study have significant consequences for systems that employ electrospray mass spectrometry and ion-mobility spectrometry as well as in interdisciplinary fields involving ion transport through a gaseous medium.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"49 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027030","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}

{"title":"Energy Resolved Mass Spectrometry Data from Surfaced Induced Dissociation Improves Prediction of Protein Complex Structure","authors":"Robert M. Bolz, Justin T. Seffernick, Zachary C. Drake, Sophie R. Harvey, Vicki H. Wysocki, Steffen Lindert","doi":"10.1021/acs.analchem.4c05837","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c05837","url":null,"abstract":"Native Mass Spectrometry (nMS) is a versatile technique for elucidating protein structure. Surface-Induced Dissociation (SID) is an activation method in tandem MS predominantly employed for determining protein complex stoichiometry alongside information about interface strengths. SID-nMS data can be collected over a range of acceleration energies, yielding Energy Resolved Mass Spectrometry (ERMS) data. Previous work demonstrated that the onset and appearance energy from SID-nMS can be used in integrative computational and experimental modeling to guide multimeric structure determination in some cases. However, the appearance energy is a single data point, while the ERMS data provide a full pattern of interface breakage. We hypothesized that incorporation of ERMS data into multimeric protein structure prediction would significantly outperform appearance energy. To test this hypothesis, we generated models of 20 protein complexes with RosettaDock using subunits generated from AlphaFold2. We simulated the ERMS data for each predicted model and rescored based on its agreement to experimental ERMS data. We demonstrated that more accurately predicted models exhibited simulated ERMS data in better agreement with the experimental data. As part of our ERMS-based rescoring, we matched or improved the RMSD of the best scoring model compared to Rosetta in 16 out of 20 cases, with 4 out of 20 cases improving to become a highly accurate (below 5 Å) structure. Finally, we benchmarked our method against our previously published appearance energy-based rescoring and showed improvement in 14 out of 20 cases, with 6 out of 20 becoming a highly accurate (below 5 Å) model. Our method is freely available through Rosetta Commons, with a usage tutorial and test files provided in the Supporting Information.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"120 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031170","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}

{"title":"Silver Microdisc Array Electrode Chip for Urea Detection in Saliva Samples from Patients with Chronic Nephritis","authors":"Xingyu Meng, Bingbing Pan, Hongyi Tong, Yaojin Xu, Meihong Peng, Qiongjing Yuan, Jiao Quan, Sijue Zou, Baisheng Wang, Zhangzhe Peng, Yi-Ge Zhou","doi":"10.1021/acs.analchem.4c05823","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c05823","url":null,"abstract":"Urea is an important biomarker for diagnosing various kidney and liver disorders. However, many existing methods rely on invasive blood sampling, which can potentially harm patients. Saliva has been recently recognized as a noninvasive and easily collectible alternative to blood for urea quantification. Electrochemical urea detection in saliva remains limited, with catalytic materials typically applied to the electrode surface via drop casting. This results in a random distribution of materials and potential aggregation on the electrode, which inevitably hinders the efficient mass transport of analytes, reducing both detection sensitivity and the utilization of catalytic materials. In this work, a silver nanoparticle (AgNP)-integrated microdisc array electrode chip was fabricated through the in situ growth of AgNPs on polydopamine (PDA) arrays, which were patterned using the microcontact printing (μCP) technique on an indium tin oxide (ITO) glassy substrate. The resulting AgNP microdisc array chip sensor exhibited much higher sensitivity toward urea sensing and greater material utilization as compared to traditional drop-cast electrodes, due to the enhanced mass transfer. Furthermore, the chip sensors demonstrated superior selectivity when challenged with potential interferences. More importantly, reliable urea quantification was achieved in clinical saliva samples from nephritis patients. These results indicate that the current sensor presents great opportunities for developing a noninvasive and sensitive liquid biopsy platform for urea determination in clinical diagnosis applications.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"2 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027029","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}

{"title":"Amplification Bias-Free Sequence-Generic Exponential Amplification Reaction","authors":"Xinrong Yan, Qingyuan Wang, Peiru Yang, Yuan Liu, Bin Liu, Tian Wang, Dehui Qiu, Shijiong Wei, Desheng Chen, Jun Zhou, Chenghui Liu, Xiaobo Zhang","doi":"10.1021/acs.analchem.4c05633","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c05633","url":null,"abstract":"Despite the unique advantage of the isothermal exponential amplification reaction (EXPAR) for the rapid detection of short nucleic acids, it severely suffers from the drawback of sequence-dependent amplification bias, mainly arising from the secondary structures of the EXPAR template under the commonly used reaction temperature (55 °C). As such, the limits of detection (LOD) for different target sequences may vary considerably from aM to nM. Here we report a sequence-generic exponential amplification reaction (SG-EXPAR) that eliminates sequence-dependent amplification bias and achieves similar amplification performance for different targets with generally sub-fM LODs. The assay innovatively employs a thermophilic nicking enzyme that allows SG-EXPAR to work efficiently at higher temperatures (60–70 °C) while eliminating the secondary structures of the templates, which is the basis for eliminating the amplification bias. Furthermore, we increased the probability of trigger/template binding through rational modification of the locked nucleic acids and template optimization, further ensuring the high amplification efficiency for various targets. According to these critical principles, we have developed an automated design platform that allows nonspecialists to obtain the optimal SG-EXPAR template for any desired sequence. The robust performance of the proposed methodology was demonstrated by quantifying microRNA, SARS-CoV-2, monkeypox virus, and HPV B19 at the 1 fM level without sequence screening. SG-EXPAR significantly expands the potential applications of EXPAR and facilitates the development of reliable point-of-care nucleic acid assays.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"6 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031169","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}

{"title":"Ultrasensitive Detection of Circulating Plasma Cells Using Surface-Enhanced Raman Spectroscopy and Machine Learning for Multiple Myeloma Monitoring","authors":"Dechun Zhang, Xianling Chen, Jia Lin, Shiyan Jiang, Min Fan, Nenrong Liu, Zufang Huang, Jing Wang","doi":"10.1021/acs.analchem.4c06244","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c06244","url":null,"abstract":"Multiple myeloma is a hematologic malignancy characterized by the proliferation of abnormal plasma cells in the bone marrow. Despite therapeutic advancements, there remains a critical need for reliable, noninvasive methods to monitor multiple myeloma. Circulating plasma cells (CPCs) in peripheral blood are robust and independent prognostic markers, but their detection is challenging due to their low abundance. Next-generation flow cytometry is commonly used for CPC detection but is not performed in routine clinical practice because it requires expensive instruments, is costly, and time-consuming. This study introduces a cost-effective, rapid surface-enhanced Raman spectroscopy (SERS) assay leveraging gold-deposited magnetic nanoparticles and plasmonic nanoparticles functionalized with anti-CD138 and anti-CD38 antibodies for detecting CPCs in peripheral blood samples. A portable optical device was used for signal recording, enhancing the potential for point-of-care applications. The developed assay is highly sensitive and specific, capable of detecting as few as one or two cells. The application of machine learning algorithms to SERS signal analysis yielded area under the curve values ranging from 0.90 to 0.95, demonstrating excellent performance in differentiating multiple myeloma patients from healthy donors. This SERS method provides a sensitive and accessible way for CPC detection, showing significant potential for multiple myeloma diagnosis, treatment monitoring, and prognosis prediction.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"78 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143031171","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}

{"title":"A Fast, High-Sensitivity 96-Well Plate-Based MICROFASP Method for Processing Low Microgram Proteomics Sample within 1.5 h","authors":"Guojin Ying, Yu He, Mengqing Yang, Gang Lu, Yang Li, Wei Cui, Zhengyan Hu, Zhenbin Zhang","doi":"10.1021/acs.analchem.4c04857","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c04857","url":null,"abstract":"A rapid, sensitive, and high-throughput sample preparation method is of paramount significance for proteomics analysis. Here, we report a fast, high-sensitivity MICROFASP method that is capable of completing sample preparation within 1.5 h, enhancing the throughput by over 13 times compared to the previous reports. Protein digestion time was significantly cut from 17 h to 20 min in a limited volume. Simultaneous reduction and alkylation occurred within 30 min. The label-free quantitation intensities of proteins from the fast and conventional MICROFASP methods were highly correlated (<i>r</i> = 0.91), validating the reliability of the fast-MICROFASP method. When starting with 1 μg of K562 cell lysate, the fast-MICROFASP method identified over 6 times more protein groups and 19 times more peptides than did the iST method. A 96-well plate-based version was developed to process 8 brain tissue samples from APP/PS1 transgenic mice in parallel. Averagely, with only 1 μg of protein lysate, 2826 protein groups (<i>n</i> = 8, RSD = 0.7%) and 12,972 peptides (<i>n</i> = 8, RSD = 1.5%) were identified from each sample. Amyloid-beta protein was successfully identified as a highly expressed protein, which shows its potential for detecting diagnostic markers and proteome profiling with low-microgram samples. We anticipate the high-sensitivity 96-well plate-based fast-MICROFASP method will have wide application in high-throughput and rapid preparation of large cohorts of low-microgram samples (e.g., clinical biopsy) for comprehensive proteome profiling. Data are available via ProteomeXchange with the identifier PXD053720.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"38 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027028","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}

{"title":"Tracing of Amino Acids Dynamics in Cell Lines Based on 18O Stable Isotope Labeling","authors":"Cemil Can Eylem, İpek Baysal, Samiye Yabanoğlu Çiftçi, Emirhan Nemutlu","doi":"10.1021/acs.analchem.4c05015","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c05015","url":null,"abstract":"Metabolite levels and turnover rates are necessary to understand metabolomic dynamics in a living organism fully. Amino acids can play distinct roles in various cellular processes, and their abnormal levels are associated with pathological conditions, including cancer. Therefore, their levels, especially turnover rates, may provide enormous information about a phenotype. ¹³C- or ¹³C,¹⁵N-labeled amino acids have also been commonly used to trace amino acid metabolism. This study presented a new methodology based on ¹⁸O labeling for amino acids that relied on monitoring mass isotopologues to calculate the turnover rates of amino acids. The method optimization studies were carried over for selective amino acid monitoring. This methodology provides a rapid, robust, and simple GC-MS method for analyzing the fluxes of amino acid metabolism. The developed method was applied to fetal human colon (FHC) and human colon carcinoma (Caco-2) cell lines to determine cancer-induced shifts in the turnover rates of amino acids. These results defined metabolic reprogramming in Caco-2 cells through increased glutamate and serine turnovers and sharply decreased turnovers of aspartate, threonine, and methionine, therefore pointing to some metabolic vulnerabilities in the metabolism of cancerous cells. The simple mechanism of the developed methodology, the availability of affordable ¹⁸O-enriched water, and the ease of application can open a new arena in fluxomics analysis.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"74 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143020165","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}