Untargeted Spatial Metabolomics and Spatial Proteomics on the Same Tissue Section.

An increasing number of spatial multiomic workflows have recently been developed. Some of these approaches have leveraged initial mass spectrometry imaging (MSI)-based spatial metabolomics to inform the region of interest (ROI) selection for downstream spatial proteomics. However, these workflows have been limited by varied substrate requirements between modalities or have required analyzing serial sections (i.

Intrinsic Chirality Modulation and Biosensing Application of Helical Gold Nanorods by Anisotropic Etching.

The investigation of plasmonic chirality is a profound and intriguing topic, and the distinctive morphology of intrinsically chiral nanoparticles has prompted significant interest in the structure-activity relationship between particle morphology and chirality. In this work, the anisotropic etching of chiral helical gold nanorods (HGNRs) by a cetyltrimethylammonium bromide (CTAB)-HAuCl complex was observed with an interesting bidirectional variation of intrinsic chirality that initially enhanced and subsequently weakened, which was related with the diversity in CTAB distribution. In addition, an ultrasensitive and convenient sensing platform for acetylcholinesterase was developed based on the circular dichroism signal recovery of HGNRs caused by the dual inhibition of HGNR etching.

Measurement of Bacterial Headspaces by FT-IR Spectroscopy Reveals Distinct Volatile Organic Compound Signatures.

Ensuring prompt and precise identification of bacterial pathogens is essential for initiating appropriate antibiotic therapy and combating severe bacterial infections effectively. Traditional microbiological diagnostics, involving initial culturing and subsequent pathogen detection, are often laborious and time-consuming. Even though modern techniques such as Raman spectroscopy, MALDI-TOF, and 16S rRNA PCR have significantly expedited this process, new methods are required for the accurate and fast detection of bacterial pathogens.

Glycosylase Pretreatment with Chemical Labeling-Assisted HPLC-MS/MS: An Ultrasensitive and Reliable Strategy for Quantification of 8-Oxo-7,8-dihydro-2'-deoxyguanosine in Genomic DNA.

8-Oxo-7,8-dihydro-2'-deoxyguanosine (dOG), the dominant oxidative product of 2'-deoxyguanosine (dG) under high levels of reactive oxygen species, usually serves as a biomarker for oxidative stress and a risk assessment factor for various diseases. Due to the extremely low abundance of dOG and the susceptibility of dOG detection to the interference of spurious oxidation, research on related biological processes is limited by insufficient sensitivity and specificity. In this work, an ultrasensitive and reliable approach for genome-wide dOG quantification was developed through chemical labeling-assisted high-performance liquid chromatography-tandem mass spectrometry with the introduction of glycosylase pretreatment.

Development and Comprehensive Evaluation of Culture-Independent, Long Amplicon-Based Targeted Next-Generation Sequencing Methods for Predicting Antimicrobial Resistance in Tuberculosis.

The great variety of antimicrobial resistance (AMR) profiles among tuberculosis (TB) patients necessitates a comprehensive detection method. This study developed culture-independent, long amplicon-based targeted next-generation sequencing (tNGS) methods for predicting AMR across 16 drugs within the complex (MTBC). Multiplex PCR amplification was employed to enrich 20 gene regions, with sequencing performed on either the Oxford Nanopore Technologies (ONT) or Illumina platforms.

Near-Infrared Light-Activated DNA Nanodevice for Spatiotemporal In Vivo Fluorescence Imaging of Messenger RNA.

Real-time visualization of messenger RNA (mRNA) is essential for tumor classification, grading, and staging. However, the low signal-to-background ratios and nonspatiotemporal specific signal amplification restricted the in vivo imaging of mRNA. In this study, a near-infrared (NIR) light-activated DNA nanodevice (DND) was developed for spatiotemporal in vivo fluorescence imaging of mRNA.

Single-Cell Mass Spectrometry Studies of Secondary Drug Resistance of Tumor Cells.

Patients with epidermal growth factor receptor mutant nonsmall cell lung cancer (NSCLC) often fail to treat gefitinib because of secondary drug resistance. The development of tumor drug resistance is closely related to variations in cancer cell metabolism. Single-cell metabolomics analysis can provide unique information about tumor drug resistance.

Top-Down Computational Design of Molecule Recognition Peptides (MRPs) for Enzyme-Peptide Self-Assembly and Chemiluminescent Biosensing.

The recognition of small molecules plays a crucial role in disease diagnosis, environmental assessment, and food safety. Currently, their recognition elements predominantly rely on antibodies and aptamers while suffering from a limitation of the complex screening process due to the low immunogenicity of small molecules. Herein, we present a top-down computational design strategy for molecule recognition peptides (MRPs) for enzyme-peptide self-assembly and chemiluminescence biosensing.

Umbrella Sampling MD Simulations for Retention Prediction in Peptide Reversed-phase Liquid Chromatography.

Reversed-phase liquid chromatography (RPLC) is an essential tool for separating complex mixtures such as proteolytic digests in bottom-up proteomics. There is growing interest in methods that can predict the RPLC retention behavior of peptides and other analytes. Already, existing algorithms provide excellent performance based on empirical rules or large sets of RPLC training data.

In Situ and In Vivo Evaluation of Multiplex Protein-Specific Glycosylation of Tumors with a Dual-SERS Encoding Strategy.

A dual-SERS encoding strategy was designed for in situ and in vivo evaluation of multiplex protein-specific glycosylation of tumors. The dual-SERS encoding strategy consisted of two pairs of dual gold nanoprobes with different diameters of 10 and 30 nm, which were encoded with four different and distinguishable Raman signal molecules. The 10 and 30 nm gold nanoprobes (Au10 and Au30 probes, respectively) were further modified with lectins and aptamers to recognize the target glycans and proteins, respectively.

miR-Cabiner: A Universal microRNA Sensing Platform Based on Self-Stacking Cascaded Bicyclic DNA Circuit-Mediated CRISPR/Cas12a.

CRISPR/Cas12a-based diagnostics have great potential for sensing nucleic acids, but their application is limited by the sequence-dependent property. A platform termed miR-Cabiner (a universal NA sensing platform based on self-stacking scaded cyclic DA circuit-mdiated CISPR/Cas12a) is demonstrated herein that is sensitive and universal for analyzing miRNAs. This platform combines catalytic hairpin assembly (CHA) and hybrid chain reaction (HCR) into a unified circuit and finally cascades to CRISPR/Cas12a.

A Modern Framework for Analytical Procedure Development and Lifecycle Management Based on ICH Q14 Principles.

This paper explores the current analytical method validation practices, mainly derived from the International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) Q2(R1) guidelines (2005) and presents a strategy for adopting the latest guidelines for analytical chemistry in the pharmaceutical industry (ICH Q14/Q2(R2), USP ⟨1220⟩). These documents emphasize a lifecycle approach to method development, qualification, and validation, aligning with the holistic, risk-based control strategy central to future submission dossier structures. Key elements of the enhanced approach described in ICH Q14, including Analytical Target Profile (ATP), Knowledge Management, Analytical Risk Assessment, and Performance Monitoring, are discussed and integrated into a clear Analytical Quality by Design (AQbD) framework for analytical procedure development and lifecycle management.

Raman Spectral Feature Enhancement Framework for Complex Multiclassification Tasks.

Raman spectroscopy enables label-free clinical diagnosis in a single step. However, identifying an individual carrying a specific disease from people with a multi-disease background is challenging. To address this, we developed a Raman spectral implicit feature augmentation with a Raman Intersection, Union, and Subtraction augmentation strategy (RIUS).

Advanced Mass-Spectra-Based Machine Learning for Predicting the Toxicity of Traditional Chinese Medicines.

Traditional Chinese medicine (TCM) has been a cornerstone of health care for centuries, valued for its preventive and therapeutic properties. However, recent decades have revealed significant toxicological concerns associated with TCMs due to their complex chemical compositions. Traditional QSAR (quantitative structure-activity relationships) models, which predict toxicity based on chemical structures, face challenges with the intricate nature of TCM compounds.

TG-MS Analysis for Elemental Composition of Organic Matters and Their Structural Properties.

A novel approach for determining the elemental content of organic matter through thermal gravimetric analysis coupled online with a mass spectrometer (TG-MS) is disclosed. This method not only yields results equivalent to ASTM analysis but also provides insight into the covalent bond structure within the sample. The principle of this technique consists of the combustion of organic matter in an oxygen-enriched environment within the thermogravimetric (TG) system.

Microneedle-Based Electrochemical Array Patch for Ultra-Antifouling and Ultra-Anti-Interference Monitoring of Subcutaneous Oxygen.

Oxygen saturation is a crucial indicator in the management of various diseases and in preoperative diagnosis, and the detection of oxygen content is valuable in guiding clinical treatment. However, as the classical and dominant oxygen detection strategies, current photoelectric oximeters and electrochemical-based blood gas analyzers often suffer from significant interindividual variation and poor compliance, respectively. In recent years, wearable microneedles (MNs) for analyzing biomarkers in interstitial fluid (ISF) have received great attention and recognition mainly for the reason that the content of the substances distributed in ISF has a better correlation with that in blood circulation compared with other body fluids such as sweat and saliva.

CRISPR/Cas12a-Enabled Amplification-Free Colorimetric Visual Sensing Strategy for Point-of-Care Diagnostics of Biomarkers.

CRISPR/Cas12a-based biosensors have garnered significant attention in the field of point-of-care testing (POCT), yet the majority of the CRISPR-based POCT methods employ fluorescent systems as report probes. Herein, we report a new CRISPR/Cas12a-enabled multicolor visual biosensing strategy for the rapid detection of disease biomarkers. The proposed assay provided vivid color responses to enhance the accuracy of visual detection.

A-D-A Molecular Design Strategy Enabling Ultrasensitive NIR Vapor Sensing.

Thin-film fluorescent chemosensors, characterized by their tunable design, high selectivity, and exceptional sensitivity, hold significant promise for gas detection applications. However, the simultaneous realization of the 3S attributes (sensitivity, selectivity, and stability) remains a formidable challenge, particularly in the underexplored field of near-infrared (NIR) gas detection. In this work, we employ an acceptor-donor-acceptor (A-D-A) molecular design strategy to drive the development of an organic semiconductor fluorescent material with a progressive red shift in the emission wavelength.

Electrochemiluminescence Detecting and Imaging of Yeast Metabolism Indicated by Endogenetic Co-reactant.

Glycolysis, a pivotal step in yeast metabolism, plays an indispensable role as a carbohydrate utilization process crucial for cellular survival. Developing advanced technologies to elucidate this fundamental physiological process holds significant scientific implications. Electrochemiluminescence (ECL) imaging exhibits the advantage of negligible background interference and facilitates straightforward visualization, thereby conferring significant value in biomolecular observation.

MWFormer: Estimation of Molecular Weights from Electron Ionization Mass Spectra for Improved Library Searching.

Molecular weight (MW) is a crucial property to improve the accuracy of multidimensional compound identification. In this study, we have developed MWFormer, a novel method that predicts MWs solely from spectra of electron ionization mass spectrometry (EI-MS) based on a Transformer encoder. MWFormer achieves a mean absolute error (MAE) of 6.

Polyvalent Aptamers Structure-Mediated Fluorescent Aptasensor for the Early Diagnosis of Alzheimer's Disease by Coupling with HCR and CRISPR-Cas System.

The early diagnosis of Alzheimer's disease (AD) plays a vital role in slowing the progression of AD and improving the quality of human life. However, it is still a challenge in the medical field. Herein, an ultrasensitive fluorescent aptasensor was designed for the detection of special phosphorylated tau181 (P-tau181) by coupling with polyvalent aptamers (PAs) structure, hybridization chain reaction (HCR), and the CRISPR-Cas system.

Introducing "Identification Probability" for Automated and Transferable Assessment of Metabolite Identification Confidence in Metabolomics and Related Studies.

Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence─the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies.

Electric Field Distribution in Bipolar Electrochemical Cells: Effects on the Wirefree Electrodeposition of Conducting Polymer Films.

Wirefree, or bipolar electrochemistry, is advancing key fields, including (nano)materials, human health, and energy. Central to these applications is an understanding of the potential distribution induced in the bipolar electrode, BPE. Here, the impact of the electric field distribution is reported for the wirefree deposition of the conducting polymer, poly(3,4-ethylenedioxythiophene), PEDOT, in the absence of deliberately added electrolytes.

Aptamer-Based Activatable Tyramide Signal Amplification for Low-Background Detection of SARS-CoV-2 Nucleocapsid Protein.

As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection posed a significant threat to public health and the global economy, in vitro diagnosis of the SARS-CoV-2 nucleocapsid protein proved to be an effective way for SARS-CoV-2 infection control in the past years. Tyramide signal amplification (TSA) has been extensively utilized in tissue imaging and pathological diagnosis owing to the powerful signal enhancement. However, the elevated "ALWAYS ON" fluorescence background limited the accuracy and sensitivity of the conventional TSA assay.

An Entropy-Driven Multipedal DNA Walker Microsensor for In Situ Electrochemical Detection of ATP.

Microelectrode- and nanoelectrode-based electrochemistry has become a powerful tool for the in situ monitoring of various biomolecules in vivo. However, two challenges limit the application of micro- and nanoelectrodes: the difficulty of highly sensitive detection of nonelectroactive molecules and the specific detection of target molecules in complex biological environments. Herein, we propose an electrochemical microsensor based on an entropy-driven multipedal DNA walker for the highly sensitive and selective detection of ATP.