Analytical Chemistry最新文献

{"title":"Atmospheric Pressure Laser Ionization Mass Spectrometry with Tunable UV Wavelength Utilizing an Optical Parametric Oscillator","authors":"Fabian Etscheidt, Christopher P. Rüger, Carolin Schwarz, Ole Tiemann, Anika Neumann, Helly J. Hansen, Thorsten Streibel, Sven Ehlert, Ralf Zimmermann","doi":"10.1021/acs.analchem.4c05040","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c05040","url":null,"abstract":"To our knowledge, this study presents the first implementation of wavelength-resolved resonance-enhanced multiphoton ionization (REMPI) spectroscopy under atmospheric pressure ionization conditions using a high-resolution mass spectrometric system. Atmospheric pressure laser ionization MS spectroscopic measurements were conducted on over 70 different polycyclic aromatic hydrocarbons (PAHs) and hetero-PAHs (N, S, and O) in standard solutions, as well as three complex PAH-containing samples. The results demonstrate the successful transfer of REMPI spectroscopy from vacuum to atmospheric pressure conditions, maintaining spectral integrity without significant band broadening. The obtained spectral data add an orthogonal dimension to mass spectrometry, providing structural insights into aromatic core motifs and enabling isomeric differentiation. This differentiation is further enhanced by linear regression algorithms, which allow for the semiquantitative analysis of isomer mixtures. Comparison between standard spectra and complex sample spectra reveals high correlation values for certain peaks, strongly indicating the presence of specific PAHs and distinguishing between phenanthrene and anthracene in fossil- and biobased samples.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"92 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873987","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-Enabled Rapid Metabolic Decoding of Small Extracellular Vesicles via Dual-Use Mass Spectroscopy Chip Array","authors":"Chenyu Yang, He Chen, Yun Wu, Xiangguo Shen, Hongchun Liu, Taotao Liu, Xizhong Shen, Ruyi Xue, Nianrong Sun, Chunhui Deng","doi":"10.1021/acs.analchem.4c04106","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c04106","url":null,"abstract":"The increasing focus of small extracellular vesicles (sEVs) in liquid biopsy has created a significant demand for streamlined improvements in sEV isolation methods, efficient collection of high-quality sEV data, and powerful rapid analysis of large data sets. Herein, we develop a high-throughput dual-use mass spectroscopic chip array (DUMSCA) for the rapid isolation and detection of plasma sEVs. The DUMSCA realizes more than a 50% increase in speed compared to traditional method and confirms proficiency in robust storage, reuse, high-efficiency desorption/ionization, and metabolite quantification. With the collected metabolic data matrix of sEVs, a deep learning model achieves high-performance diagnosis of Crohn’s disease. Furthermore, discovered biomarkers by feature sparsification and tandem mass spectrometry experiments also exhibited remarkable performance in diagnosis. This work demonstrates the rapidity and validity of DUMSCA for disease diagnosis, enabling the diagnosis of diseases without the necessity for prior knowledge and providing a high-throughput technology for sEV-based liquid biopsy that will empower its vigorous development.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"83 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142874105","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":"Utilization of Liquid Chromatography–Mass Spectrometry and High-Resolution Ion Mobility–Mass Spectrometry to Characterize Therapeutically Relevant Peptides with Asparagine Deamidation and Isoaspartate","authors":"Andrew B. Dykstra, Thomas G. Lubinsky, Heidi Vitrac, Iain D. G. Campuzano, Pavel V. Bondarenko, Ashli R. Simone","doi":"10.1021/acs.analchem.4c05246","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c05246","url":null,"abstract":"Rapid identification of asparagine (Asn) deamidation and isoaspartate (<i>iso</i>Asp) in proteins remains a challenging analytical task during the development of biological therapeutics. For this study, 46 therapeutically relevant peptides corresponding to 13 peptide families (13 unmodified peptides and 33 modified peptides) were obtained; modified peptides included Asn deamidation and isoAsp. The peptide families were characterized by three methods: reversed-phase ultrahigh performance liquid chromatography–mass spectrometry (RP-UHPLC-MS); flow injection analysis high-resolution ion mobility–mass spectrometry (FIA-HRIM-MS); and shortened gradient RP-UHPLC-HRIM-MS. UHPLC-MS data acquisition was 2 h per injection, in contrast to high-throughput 1 min data acquisition of the FIA-HRIM-MS technique. A rapid 2D peptide map has been demonstrated by combining shortened gradient RP-UHPLC with HRIM, to optimize the resolution of the Asn-, Asp-, and isoAsp-containing peptides, increasing the likelihood of detecting peptides containing these quality attributes with expedited data acquisition. Additionally, this paper provides an ion mobility calibration data set for therapeutically relevant peptides (unmodified and modified) over an ion-neutral collisional cross-section range of 300–800 Ų.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"48 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873988","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":"Millisecond Label-Free Single Peptide Detection and Identification Using Nanoscale Electrochromatography and Resistive Pulse Sensing","authors":"Maximillian Chibuike, Chathurika Rathnayaka, Suresh Shivanka, Junseo Choi, Matthew Verber, Sunggook Park, Steven A. Soper","doi":"10.1021/acs.analchem.4c04542","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c04542","url":null,"abstract":"We are developing a unique protein identification method that consists of generating peptides proteolytically from a single protein molecule (i.e., peptide fingerprints) with peptide detection and identification carried out using nanoscale electrochromatography and label-free resistive pulse sensing (RPS). As a step in realizing this technology, we report herein the nanoscale electrochromatography of model peptides using thermoplastic columns with surfaces engineered to identify peptides via their molecularly dependent mobility (i.e., time-of-flight, ToF). ToFs were elucidated using a dual in-plane nanopore sensor, which consisted of two in-plane nanopores placed on either end of the nanoelectrochromatography column. The surface of the nanocolumn, which consisted of poly(methyl methacrylate) (PMMA), was activated with an O₂ plasma, creating surface carboxylic acid groups (−COOH) inducing a surface charge on the column wall as well as affecting its hydrophilicity. To understand scaling effects, we carried out microchip and nanochannel electrochromatography of the peptides labeled with an ATTO 532 reporter to allow for single-molecule tracking. Our results indicated that the apparent mobilities of the model peptides did not allow for their separation in a microchannel, but when performed in a nanocolumn, clear differences in their apparent mobilities could be observed especially when operated at high electric field strengths. We next performed label-free detection of peptides using the dual in-plane nanopore sensor with the two pores separated by a 5 μm (length) column with a 50 nm width and depth. When a single peptide molecule passed through an in-plane nanopore, the sensor read a pair of resistive pulses with a time difference equivalent to ToF. We identified the peptides by evaluating their ToF, normalized RPS current transient amplitude (Δ<i>I</i>/<i>I</i>₀), and RPS peak dwell time (<i>t</i>_d). We could identify the model peptides with nearly 100% classification accuracy at the single-molecule level using machine learning with a single molecule measurement requiring &lt;10 ms.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"53 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873986","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":"Full Spectral Overlap to Enhanced Fluorescence Quenching Ability by Using Covalent Organic Frameworks as a Springboard of Quencher for the Turn-on Fluorescence Immunoassay","authors":"Yuanyuan Cheng, Xiaomin Li, Shouyu Xue, Xuechi Yin, Yuechun Li, Jianlong Wang, Daohong Zhang","doi":"10.1021/acs.analchem.4c03915","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c03915","url":null,"abstract":"According to the fluorescence internal filtering effect (IFE), the more the absorption spectrum of the quencher overlaps with the excitation and emission spectra of the fluorescent substance, the better the quenching effect and, correspondingly, the more significant and sensitive the contrast becomes when the fluorescence is turned on. Thus, in the competitive fluorescence-quenching lateral flow immunoassays (FQ-LFIAs), the fluorescence quencher with an outstanding optical property is of great importance. Herein, gold nanoparticles (AuNPs) and polydopamine (PDA) coengineered covalent organic frameworks (COF/Au@PDA) were synthesized as a fluorescence quencher to increase spectral overlap. Thanks to the excellent visible light absorption of COF with donor–acceptor (D-A) structure, the localized surface plasmon resonance (LSPR) capability of AuNPs, and the broad light absorption of the PDA layer, the COF/Au@PDA exhibits intense absorption and a full spectral overlap toward aggregation-induced emission luminous (AIE) dots. Thereafter, COF/Au@PDA, with its immense potential to completely quench the fluorescence of AIE dots through primary IFE and secondary IFE, was applied to a bimodal LFIA platform for verification with a nitrofurazone metabolite as a model analyte. As expected, the detection sensitivity of the COF/Au@PDA-based FQ-LFIA (turn-on) is improved by 6-fold compared with that of the colorimetric (CM)-LFIA (turn-off). Further, ChatGpt was used to improve the assay accuracy and sensitivity, utilizing its high sensitivity to subtle changes in LFIA signals, especially for weak signals that are indeterminate with the naked eye. This work offers a potential approach for building a high-performance fluorescence quencher in the FQ-LFIA and indicates the potential for the application of artificial intelligence in highly sensitive LFIAs.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"24 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873992","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":"LRET-Based Simultaneous Detection of Dual miRNAs via Multitrap Optical Tweezers Assisted Suspension Array Tagged by Two Different Luminescent Quenchable UCNPs Combining CRISPR/Cas12a Amplification","authors":"He Yu, Peng-Fei Xu, Yang Liu, Zeng-Shuai Jia, Yu-Yao Li, Hong-Wu Tang","doi":"10.1021/acs.analchem.4c04895","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c04895","url":null,"abstract":"Nowadays, optical tweezers play a vital role not only in optical manipulation but also in bioassay. As principal optical trapping objects, microbeads can combine optical tweezers with suspension array technology, with amply focused laser beams and adequately concentrated tags contributing to highly sensitive detection. In view of the inefficiency of conventional single-trap optical tweezers, multitrap systems are developed. Here, green- and blue-emitting core–shell–shell upconversion nanoparticles (UCNPs) are adopted to encode microbeads and determine dual miRNAs, with the internal shells leading the luminescence process to facilitate quenching through luminescence resonance energy transfer (LRET). Utilizing the trans cleavage of CRISPR/Cas12a, quenched luminescence signals are recovered and amplified, causing further enhanced detection sensitivity. Ultimately, limits of detection (LOD) of 17 and 22 aM are obtained with excellent specificities verified. Furthermore, dual miRNAs from MCF-7, A549, and MCF-10A cells are extracted and detected, with results consistent with those obtained by PCR. Notably, miR-155 in MCF-7 and A549 cells is detectable at the single-cell level. Thus, the differences in the measured miRNA levels between MCF-7 and MCF-10A cells imply the potential of this method to discriminate breast cancer cells from epithelial cells despite the difficulty in distinguishing different cancer cells due to similar miRNA levels.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"14 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873995","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":"LipoCLEAN: A Machine Learning Filter to Improve Untargeted Lipid Identification Confidence","authors":"Steven L. Tavis, Matthew J. Keller, Andrew J. Stai, Tomás A. Rush, Robert L. Hettich","doi":"10.1021/acs.analchem.4c04040","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c04040","url":null,"abstract":"In untargeted lipidomics experiments, putative lipid identifications generated by automated analysis software require substantial manual filtering to arrive at usable high-confidence data. However, identification software tools do not make full use of the available data to assess the quality of lipid identifications. Here, we present a machine-learning-based model to provide coherent, holistic quality scores based on multiple lines of evidence. Underutilized metrics such as isotope ratios and chromatographic behavior allow for much higher accuracy of identification confidence. We find that approximately 50% of tandem mass spectrometry-based automated lipid identifications are incorrect but that multidimensional rescoring reduces false discoveries to only 7% while retaining 80% of true positives. Our method works with most chromatography methods and is generalized across a family of MS instruments. LipoCLEAN is available at https://github.com/stavis1/LipoCLEAN.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"60 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873991","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":"Active-Targeted ICG for Surgical Navigation and Fluorescence-Guided Laparoscopic Photothermal Ablation in Pancreatic Ductal Adenocarcinoma","authors":"Lei Zhou, Manxiong Dai, Jiahao Zhou, Xingyang Zhao, Zixiong Liu, Hao Bu, Yang Zhou, Yan Liao, Hongwen Liu, Wei Cheng, Kang Chen","doi":"10.1021/acs.analchem.4c04575","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c04575","url":null,"abstract":"Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy, but there is limited improvement in its treatment. Near-infrared fluorescence (NIRF) imaging could potentially address the clinical challenges of PDAC. Indocyanine green (ICG) has been widely used in clinical practice; however, its short half-life and lack of active targeting greatly limit its application in pancreatic surgery. In this study, the active targeting peptide KTLLPTP (which actively recognizes PDAC cell surface overexpression Plectin-1) was modified to the ICG to create the novel contrast agent ICG-PTP, which actively targets PDAC cells. It was successfully applied to the NIRF imaging of the PDAC orthotopic mice model, achieving an improved tumor signal background ratio (T/N ratio) of 4.28, compared to 2.34 in the free ICG group. Next, Fluorescence-guided excision of subcutaneous/orthotopic PDAC using ICG-PTP was performed, accurately identifying the tumor margin and significantly facilitating resection efficiency. Finally, PDAC metastases were identified, and interventional photothermal ablation (iPTA) was performed under fluorescence laparoscope guidance. ICG-PTP exhibits good biosafety and clinical transitional potential. Thus, they can provide surgeons with efficient real-time tumor information and offer new treatment strategies for metastases. Accordingly, modification of probes for clinical use and adaptation studies of current equipment are the current focus.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"36 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873993","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":"Immunoaffinity Intact Top-Down Mass Spectrometry for Quantification of Neuron-Specific Enolase Gamma, a Low-Abundance Protein Biomarker","authors":"Sebastian A. H. van den Wildenberg, Sylvia A. A. M. Genet, Maarten A. C. Broeren, Joost L. J. van Dongen, Maxime C.M. van den Oetelaar, Luc Brunsveld, Volkher Scharnhorst, Daan van de Kerkhof","doi":"10.1021/acs.analchem.4c04677","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c04677","url":null,"abstract":"Quantification of intact proteins in serum by liquid chromatography high-resolution mass spectrometry (HRMS) may be a useful alternative to bottom-up LC-MS or conventional ligand binding assays, due to reduced assay complexity and by providing additional information, such as isoform differentiation or detection of post-translational modifications. The 47.2 kDa lung cancer tumor marker neuron-specific enolase γ (NSEγ) was quantified in a clinically relevant concentration range of 6.25 to 100 ng/mL in NSE-depleted human serum using magnetic bead immunoprecipitation coupled to LC-high-resolution quadrupole-time-of-flight MS. The novelty of the described approach is in the combined setup of immunoaffinity extraction and the use of a full-length NSEγ calibrator and labeled NSEγ internal standard (IS) to reliably quantify the post-translationally acetylated form of this protein tumor marker in a top-down proteomics workflow. Isolation parameters and quantification using deconvolution and reconstructed extracted ion chromatograms were evaluated, and the development of a suitable liquid chromatography method was demonstrated. Various validation parameters were determined using both quantification methods, both showing acceptable performance. Additionally, deconvolution-based quantification enabled an accurate mass determination. The developed method was compared to a commercially available ECLIA and showed good correlation in sera of patients suspected of lung cancer. This assay may form the starting point for the development of a reference method for the standardization of immunoassays.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"38 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873994","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":"Glycosylation-Targeting Aptamer for the Feasible Construction of a Dual Aptamer-Based Plasmonic Immunosandwich Assay in Cancer Diagnostics","authors":"Junyang Chen, Pengfei Ma, Jiayu Xu, Mingxi Zang, Wei Li","doi":"10.1021/acs.analchem.4c03770","DOIUrl":"https://doi.org/10.1021/acs.analchem.4c03770","url":null,"abstract":"Fibroblast activation protein (FAP) is an important antigen in the tumor microenvironment, which plays a crucial role in promoting extracellular matrix remodeling and tumor cell metastasis. A circulating form of soluble FAP has also been identified in the serum, becoming a biomarker for pan-cancer diagnosis and prognosis. However, the current peptide substrate-based enzymatic activity detection or antibody-dependent detection methods have been hindered by insufficient selectivity and complex operations, so it is valuable to develop effective nucleic acid aptamers as FAP affinity ligands. In order to deeply explore the biomimetic recognition technology, this study proposed an elaborate aptamer screening strategy for targeting the protein characteristic structure. Taking the glycosylation of the FAP protein as a target, four FAP-specific aptamers with high performance were successfully generated. Further, using the champion aptamer as a recognition tool and combining it with ultrasensitive detection technology-surface enhanced Raman scattering (SERS), a novel dual aptamer-based sandwich sensor was constructed for the rapid determination of FAP. Due to the dual-specific recognition of the orthogonal aptamer pair, the sandwich method obviously improved the selectivity to FAP protein, with a maximum cross-reactivity of less than 8% and a quantitation limit of 100 pg/mL. It was conveniently applied in high-sensitive and high-selective detection of serum FAP in cancer patient samples. Therefore, the research of this study not only opens new access for the selection of antiglycan aptamers but also boosts the application of the FAP aptamer as a recognition tool in cancer diagnostics.","PeriodicalId":27,"journal":{"name":"Analytical Chemistry","volume":"107 1","pages":""},"PeriodicalIF":7.4,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142873990","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}