Yukui Zhang
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View article: Dissecting <i>In Vivo</i> Cross-Linker Performance: Insights into Structural Dynamics and Molecular Rigidity
Dissecting <i>In Vivo</i> Cross-Linker Performance: Insights into Structural Dynamics and Molecular Rigidity Open
Understanding protein structure and dynamics is crucial to elucidating their biological functions. Recent advancements in experimental techniques and AI-driven predictions, such as AlphaFold, have significantly enhanced our ability to dete…
View article: Exosome separation and enrichment technologies and their applications in disease diagnosis and treatment
Exosome separation and enrichment technologies and their applications in disease diagnosis and treatment Open
Exosomes are nanoscale vesicles wrapped in lipid bilayers that are secreted by cells and carry a variety of proteins, lipids, nucleic acids, and metabolites. Exosomes are widely present in various bodily fluids and mediate intercellular co…
View article: Utilizing a Negative Enrichment Strategy to Profile Protein Methylation, Leveraging the Orthogonality of LysargiNase and Trypsin
Utilizing a Negative Enrichment Strategy to Profile Protein Methylation, Leveraging the Orthogonality of LysargiNase and Trypsin Open
View article: Electrostatic assembly-derived β-ketoenamine covalent organic framework/polyacrylonitrile composite nanofiltration membrane for efficient removal of emerging contaminants
Electrostatic assembly-derived β-ketoenamine covalent organic framework/polyacrylonitrile composite nanofiltration membrane for efficient removal of emerging contaminants Open
View article: Electrostatic assembly-derived β-ketoenamine covalent organic framework/polyacrylonitrile composite nanofiltration membrane for efficient removal of emerging contaminants
Electrostatic assembly-derived β-ketoenamine covalent organic framework/polyacrylonitrile composite nanofiltration membrane for efficient removal of emerging contaminants Open
View article: Deciphering the endogenous SUMO-1 landscape: a novel combinatorial peptide enrichment strategy for global profiling and disease association
Deciphering the endogenous SUMO-1 landscape: a novel combinatorial peptide enrichment strategy for global profiling and disease association Open
Using a “dual-hook fishing” approach, this method selectively captures two C-terminal regions of SUMO-1 remnants, enabling an unprecedented and comprehensive landscape of SUMO-1 modifications across species.
View article: Toward molecular diagnosis of major depressive disorder by plasma peptides using a deep learning approach
Toward molecular diagnosis of major depressive disorder by plasma peptides using a deep learning approach Open
Major depressive disorder (MDD) is a severe psychiatric disorder that currently lacks any objective diagnostic markers. Here, we develop a deep learning approach to discover the mass spectrometric features that can discriminate MDD patient…
View article: Targeted Analysis of Mitochondrial Protein Conformations and Interactions by Endogenous ROS‐Triggered Cross‐Linker Release
Targeted Analysis of Mitochondrial Protein Conformations and Interactions by Endogenous ROS‐Triggered Cross‐Linker Release Open
The study of in situ conformations and interactions of mitochondrial proteins plays a crucial role in understanding their biological functions. Current chemical cross‐linking mass spectrometry (CX‐MS) has difficulty in achieving in‐depth a…
View article: Progress in enrichment methods for protein &lt;italic&gt;N&lt;/italic&gt;-phosphorylation
Progress in enrichment methods for protein <italic>N</italic>-phosphorylation Open
Protein phosphorylation is one of the most common and important post-translational modifications that regulates almost all life processes. In particular, protein phosphorylation regulates the development of major diseases such as tumors, n…
View article: Golgi apparatus proteome deciphering in living cells enabled by aggregation-induced emission luminogen-mediated photocatalytic proximity labeling (AIE-PhoPL)
Golgi apparatus proteome deciphering in living cells enabled by aggregation-induced emission luminogen-mediated photocatalytic proximity labeling (AIE-PhoPL) Open
As a central platform of proteins sorting and signal docking, in situ Golgi apparatus (GA) proteome mapping is critical for elucidating relevant biological events. However, chemical proteomic dissection of GA is poorly studied owing to the…
View article: Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology
Progress, Challenges and Opportunities of NMR and XL-MS for Cellular Structural Biology Open
The validity of protein structures and interactions, whether determined under ideal laboratory conditions or predicted by AI tools such as Alphafold2, to precisely reflect those found in living cells remains to be examined. Moreover, under…
View article: Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers
Enhancing protein dynamics analysis with hydrophilic polyethylene glycol cross-linkers Open
Cross-linkers play a critical role in capturing protein dynamics in chemical cross-linking mass spectrometry techniques. Various types of cross-linkers with different backbone features are widely used in the study of proteins. However, it …
View article: A Self-Calibrating Ratiometric Fluorescence Sensor with Photonic Crystal-Based Signal Amplification for the Detection of Tetracycline in Food
A Self-Calibrating Ratiometric Fluorescence Sensor with Photonic Crystal-Based Signal Amplification for the Detection of Tetracycline in Food Open
View article: Non-Tandem Enzymatic Modules-Encapsulated Metal-Organic Framework Cubes: Mutual-Validated Operation for Dual-Modal Competitive Immunoassay of Antibiotics
Non-Tandem Enzymatic Modules-Encapsulated Metal-Organic Framework Cubes: Mutual-Validated Operation for Dual-Modal Competitive Immunoassay of Antibiotics Open
View article: Site-Specific Identification and Quantitation of Endogenous Sumoylation Based on Sumo-Specific Protease and Strong Anion Exchange Chromatography
Site-Specific Identification and Quantitation of Endogenous Sumoylation Based on Sumo-Specific Protease and Strong Anion Exchange Chromatography Open
View article: High-throughput and in-depth analysis of plasma proteome by UV-assisted protein digestion, 5-plex labeling and MS-based high abundance protein removal method
High-throughput and in-depth analysis of plasma proteome by UV-assisted protein digestion, 5-plex labeling and MS-based high abundance protein removal method Open
Human plasma contains various proteins, some of which reflect individuals’ physiological health state or predict diseases. Therefore, plasma analysis can provide a wealth of information on novel biomarkers for clinical diagnosis and progno…
View article: Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria
Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria Open
View article: Biomaterials promote in vivo generation and immunotherapy of CAR-T cells
Biomaterials promote in vivo generation and immunotherapy of CAR-T cells Open
Chimeric antigen receptor-T (CAR-T) cell therapy based on functional immune cell transfer is showing a booming situation. However, complex manufacturing processes, high costs, and disappointing results in the treatment of solid tumors have…
View article: A hierarchical strategy to decipher protein dynamics<i>in vivo</i>with chemical cross-linking mass spectrometry
A hierarchical strategy to decipher protein dynamics<i>in vivo</i>with chemical cross-linking mass spectrometry Open
Protein dynamics are essential for their various functions. Meanwhile, the intracellular environment would affect protein structural dynamics, especially for the intrinsically disordered proteins (IDPs). Chemical cross-linking mass spectro…
View article: ComMap: a software to perform large-scale structure-based mapping for cross-linking mass spectrometry
ComMap: a software to perform large-scale structure-based mapping for cross-linking mass spectrometry Open
Motivation Chemical cross-linking combined with mass spectrometry (CXMS) is now a well-established method for profiling existing protein–protein interactions (PPIs) with partially known structures. It is expected to map the results of CXMS…
View article: An Aptamer-Functionalized Photonic Crystal Sensor for Ultrasensitive and Label-Free Detection of Aflatoxin B1
An Aptamer-Functionalized Photonic Crystal Sensor for Ultrasensitive and Label-Free Detection of Aflatoxin B1 Open
View article: A facile strategy for comprehensive proteome analysis of urine using ultracentrifugation fractionation, solid-phase alkylation based sample preparation and liquid chromatography-mass spectrometry
A facile strategy for comprehensive proteome analysis of urine using ultracentrifugation fractionation, solid-phase alkylation based sample preparation and liquid chromatography-mass spectrometry Open
In this work, a facile strategy with combination of ultracentrifugation fraction, solid-phase alkylation sample preparation and liquid chromatography-mass spectrometry (LC-MS) was developed to achieve comprehensive proteome profiling of ur…
View article: On-capillary alkylation micro-reactor: a facile strategy for proteo-metabolome profiling in the same single cells
On-capillary alkylation micro-reactor: a facile strategy for proteo-metabolome profiling in the same single cells Open
An on-capillary alkylation micro-reactor (OCAM) was developed for parallel measurement of proteome and metabolome in the same single cells, providing a new avenue for studying system biology at single-cell level.
View article: Enhanced protein–protein interaction network construction promoted by in vivo cross-linking with acid-cleavable click-chemistry enrichment
Enhanced protein–protein interaction network construction promoted by in vivo cross-linking with acid-cleavable click-chemistry enrichment Open
Chemical cross-linking coupled with mass spectrometry has emerged as a powerful strategy which enables global profiling of protein interactome with direct interaction interfaces in complex biological systems. The alkyne-tagged enrichable c…
View article: Segmented MS/MS acquisition of a1 ion-based strategy for in-depth proteome quantitation
Segmented MS/MS acquisition of a1 ion-based strategy for in-depth proteome quantitation Open
In-depth proteome quantitation is of great significance for understanding protein functions, advancing biological, medical, environmental and metabolic engineering research. Herein, benefiting from the high formation efficiencies and inten…
View article: Covalent Organic Framework/Polyacrylonitrile Electrospun Nanofiber for Dispersive Solid-Phase Extraction of Trace Quinolones in Food Samples
Covalent Organic Framework/Polyacrylonitrile Electrospun Nanofiber for Dispersive Solid-Phase Extraction of Trace Quinolones in Food Samples Open
The extraction of quinolone antibiotics (QAs) is crucial for the environment and human health. In this work, polyacrylonitrile (PAN)/covalent organic framework TpPa–1 nanofiber was prepared by an electrospinning technique and used as an ad…
View article: Erratum to “Fully automated sample treatment method for high throughput proteome analysis”
Erratum to “Fully automated sample treatment method for high throughput proteome analysis” Open
View article: C18-Functionalized Amine-Bridged Hybrid Monoliths for Mass Spectrometry-Friendly Peptide Separation and Highly Sensitive Proteomic Analysis
C18-Functionalized Amine-Bridged Hybrid Monoliths for Mass Spectrometry-Friendly Peptide Separation and Highly Sensitive Proteomic Analysis Open
For proteomic analysis based on mass spectrometry (MS), high-performance peptide separation under MS-friendly conditions is of importance. To this end, a novel kind of amine-bridged hybrid monolith was developed by the sol-gel reaction of …
View article: Improving the Identification Coverage of Protein Interactome by Enhancing the Click Chemistry-based Cross-linking Enrichment Efficiency
Improving the Identification Coverage of Protein Interactome by Enhancing the Click Chemistry-based Cross-linking Enrichment Efficiency Open
Chemical cross-linking coupled with mass spectrometry has emerged as a powerful strategy which enables global profiling of protein interactome with direct interaction interfaces in complex biological systems. The alkyne-tagged enrichable c…
View article: SpotLink enables sensitive and precise identification of site non-specific cross-links at the proteome scale
SpotLink enables sensitive and precise identification of site non-specific cross-links at the proteome scale Open
We developed SpotLink software for identifying site non-specific cross-links at the proteome scale. Contributed by the dual pointer dynamic pruning (DPDP) algorithm and the quality control of cross-linking sites, SpotLink identified more t…