☆ 4.7 Review

Enrichment driven glycoproteomics: New materials, new methods, and beyond

TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2023)

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High-throughput site-specific N-glycoproteomics reveals glyco-signatures for liver disease diagnosis

Zhenyu Sun et al.

Summary: The glycoproteome is a key target for biomarker screening due to altered glycosylation in cancer cells. A novel method combining tandem mass tag labeling and chemical labeling-assisted complementary dissociation was developed for quantitative glycoproteomics. Comprehensive site-specific and subclass-specific N-glycosylation profiling of human serum immunoglobulin G (IgG) was performed, revealing IgG1-H3N5F1 and IgG4-H4N3 as potential markers for different stages of liver diseases. The expression changes of glycosylation in liver diseases were successfully validated using targeted parallel reaction monitoring in a separate sample cohort.

NATIONAL SCIENCE REVIEW (2023)

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Article Biochemical Research Methods

Deciphering the Properties and Functions of Glycoproteins Using Quantitative Proteomics

Senhan Xu et al.

Summary: Glycosylation is a common and important protein modification that regulates the properties and functions of proteins. Aberrant glycosylation is directly related to human diseases. Recent advancements in mass spectrometry and glycoproteomic methods have allowed for comprehensive analysis of glycoproteins in complex biological samples. The use of quantitative proteomics provides valuable information on protein functions, cellular activities, and disease mechanisms.

JOURNAL OF PROTEOME RESEARCH (2023)

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Article Multidisciplinary Sciences

Identification of tagged glycans with a protein nanopore

Minmin Li et al.

Summary: The structural complexity of glycans poses a significant challenge to existing analytical methods. In this study, the authors use a glycan derivatization strategy and nanopore sensing to identify glycan isomers, glycans with varying chain lengths, and distinct branched glycans. The structural complexity of glycans arises from the diversities in composition, linage, configuration, and branching, making structural analysis complicated.

NATURE COMMUNICATIONS (2023)

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Article Multidisciplinary Sciences

Glycopeptide database search and de novo sequencing with PEAKS GlycanFinder enable highly sensitive glycoproteomics

Weiping Sun et al.

Summary: GlycanFinder is a database search and de novo sequencing tool for accurate identification of intact glycopeptides. It integrates peptide-based and glycan-based search strategies to overcome the challenge of complex fragmentation. With a deep learning model, GlycanFinder is able to sequence glycans not found in the database. Extensive analyses and benchmarking studies demonstrate its comparable performance to leading software and its capability to identify previously unknown glycopeptides.

NATURE COMMUNICATIONS (2023)

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Review Materials Science, Multidisciplinary

Hierarchically engineered nanochannel systems with pore-in/on-pore structures

Minmin Li et al.

Summary: Biological ion channels have asymmetries in structure and charge distribution, which enable them to perform diverse activities such as signal transduction and cell motility. Inspired by this, researchers have been pursuing artificial ion channels with comparable functions. However, current homogeneous nanochannels have not been able to achieve similar rewards. Hierarchically engineered heterogeneous nanochannels, on the other hand, have shown promising properties such as ion selectivity and permeability, and have found applications in selective ion transport, energy conversion, biomolecular separation, and detection. In this article, recent advances in these hierarchically engineered nanochannel systems are reviewed, with a focus on pore-on-pore and pore-in-pore structures, and their potential applications are discussed.

NPG ASIA MATERIALS (2023)

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Simultaneous analysis of cellular glycoproteome and phosphoproteome in cervical carcinoma by one-pot specific enrichment

Huimin Chu et al.

Summary: In this study, a magnetic binary metal oxide composite with the functionalization of hydrophilic tripeptide was designed and synthesized for the simultaneous enrichment of glycopeptide and phosphopeptide in cervical carcinoma cells. The composite exhibited excellent enrichment efficiency and stability, showing promising applications in the discovery and screening of cervical carcinoma.

ANALYTICA CHIMICA ACTA (2022)

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Hydrophilic arginine-functionalized mesoporous polydopamine-graphene oxide composites for glycopeptides analysis

Yu Zheng et al.

Summary: A novel hydrophilic two-dimensional composite material was used to selectively enrich glycopeptides from biological samples, showing potential application in protein post-translational modification research.

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Synergistic synthesis of hydrophilic hollow zirconium organic frameworks for simultaneous recognition and capture of phosphorylated and glycosylated peptides

Yanting He et al.

Summary: In this work, a new synergistic strategy was developed to synthesize hydrophilic hollow zirconium-organic frameworks (HHZr-MOFs) for simultaneous recognition and capture of phospho-and N-glycopeptides. The HHZr-MOFs act as a highly efficient bifunctional probe for simultaneous enrichment of phospho-and N-glycopeptides based on hydrophilic interaction chromatography (HILIC) and metal oxide affinity chromatography (MOAC). The study demonstrates the potential of HHZr-MOFs in rapid detection of clinical biomarkers and comprehensive profiling of phosphoproteomic and glycoproteomic.

ANALYTICA CHIMICA ACTA (2022)

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Selective Enrichment of Sialylglycopeptides Enabled by Click Chemistry and Dynamic Covalent Exchange

Miyang Li et al.

Summary: This study developed a novel workflow combining mild periodate oxidation, hydrazide chemistry, copper-catalyzed azide/alkyne cycl-oaddition (CuAAC) click chemistry, and dynamic covalent exchange for selective enrichment of sialylglycopeptides (SGPs). The method showed high enrichment efficiency, good reproducibility, and easily adopted procedure, making it a promising tool for broad applications in SGP analysis.

ANALYTICAL CHEMISTRY (2022)

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Review Biochemical Research Methods

Metal organic frameworks as advance d adsorb ent materials for separation and analysis of complex samples

Baichun Wang et al.

Summary: This review summarizes the recent advances in sample pre-treatment based on metal-organic frameworks (MOFs) for protein phosphorylation and glycosylation studies. The enrichment of phosphoprotein and glycoprotein overcomes the challenges of direct detection by mass spectrometry. The design and synthesis of different types of MOFs are discussed, as well as the potential problems in sample pre-treatment in proteomics.

JOURNAL OF CHROMATOGRAPHY A (2022)

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Article Multidisciplinary Sciences

Glyco-Decipher enables glycan database-independent peptide matching and in-depth characterization of site-specific N-glycosylation

Zheng Fang et al.

Summary: The traditional site-specific glycoproteomics analysis often fails to account for glycopeptides with unusual glycans or poor peptide backbone fragmentation. In this study, a glycoproteomics tool called Glyco-Decipher is developed to address these issues. Glyco-Decipher utilizes database-independent peptide matching and the fragmentation pattern of shared peptide backbones to improve spectrum interpretation. Benchmark tests demonstrate that Glyco-Decipher identifies more peptide-spectrum matches than other existing tools, resulting in a significant increase in the number of identified glycopeptide spectra. By enabling unbiased profiling of attached glycans, Glyco-Decipher enables the discovery of modified glycans in mouse tissues, including those with chemical or biological modifications. This tool holds great promise for advancing glycoproteomics analysis in biological research.

NATURE COMMUNICATIONS (2022)

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Review Chemistry, Multidisciplinary

Advances in hydrophilic metal-organic frameworks for N-linked glycopeptide enrichment

Siqi Li et al.

Summary: This review summarizes the advances of hydrophilic MOFs for N-linked glycopeptide enrichment. Categorized into three classes according to synthesis strategies, the preparation, functionality, and enrichment performance of these materials were covered. Sensitivity, selectivity, and practical application were evaluated.

FRONTIERS IN CHEMISTRY (2022)

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Review Chemistry, Analytical

Advances in the adsorption/enrichment of proteins/peptides by metal-organic frameworks-affinity adsorbents

Zhengjie Hu et al.

Summary: Metal-organic frameworks (MOFs) are emerging ordered porous materials composed of metal clusters and organic ligands, which exhibit efficient adsorption/enrichment capabilities in proteomic analysis. This review summarizes the functional moieties of MOFs in sample processing and their controllable integration with various protein/peptide species. It also discusses recent advances in adsorption/enrichment of proteins/peptides by MOFs-affinity adsorbents under different driving forces, as well as the challenges and perspectives of MOFs in protein/peptide enrichment.

TRAC-TRENDS IN ANALYTICAL CHEMISTRY (2022)

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Sialylated glycan-modulated biomimetic ion nanochannels driven by carbohydrate-carbohydrate interactions

Jie Xiao et al.

Summary: This study reports a biomimetic ion nanochannel device that can be precisely regulated by sialylated glycans (SGs). The device can discriminate between different types of SGs and monitor the sialylation process in real time, showing its potential in enzyme activity determination and in vitro enzyme identification.

NPG ASIA MATERIALS (2022)

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Article Biochemical Research Methods

Glycoproteomics Landscape of Asymptomatic and Symptomatic Human Alzheimer's Disease Brain

Suttipong Suttapitugsakul et al.

Summary: This study investigates the molecular changes in the brain of individuals with Alzheimer's disease (AD) using glycoproteomics analysis. The results reveal differences in the N-glycoproteomics landscape of the brain compared to other tissues, and identify glycosylation differences in different stages of AD. These findings provide insights into the progression and treatment development of AD.

MOLECULAR & CELLULAR PROTEOMICS (2022)

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Glycoproteomics

Ieva Bagdonaite et al.

Summary: This Primer provides an overview of glycoproteomic methods and their applications, including glycopeptide analysis, sample selection, and mass spectrometry techniques. It focuses on the study of N-linked and O-linked glycosylation and provides insights into future directions in the field.

NATURE REVIEWS METHODS PRIMERS (2022)

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Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry

Yao Chen et al.

Summary: The CHO-GlcNAc strategy developed in this study efficiently enriches O-GlcNAc glycopeptides and has been successfully applied to analyze O-GlcNAcylation in the nucleus of HeLa cells, identifying a large number of potential O-GlcNAcylation sites and associated proteins. This method could serve as a versatile tool for proteomic analysis of O-GlcNAcylation.

ANALYTICAL CHEMISTRY (2021)

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Article Biochemical Research Methods

Melamine foam assisted in-tip packed amine-functionalized titanium metal-organic framework for the selective enrichment of endogenous glycopeptides

Muhammad Mujahid Ali et al.

Summary: Endogenous glycopeptides play a significant role in diverse pathological and physiological systems, but their direct analysis is challenging due to low abundance and interfering species. In this study, a novel amine-functionalized titanium metal-organic framework (NH2-MIL-125(Ti)) was synthesized and utilized for efficient enrichment of glycopeptides. The designed separation media displayed high hydrophilicity and stability, allowing for excellent hydrophilic interaction chromatography (HILIC) performance. The NH2-MIL-125(Ti) crystals packed in pipette tip showed high selectivity and detection limits, offering potential for trace glycopeptide biomarker enrichment from biological fluids.

JOURNAL OF CHROMATOGRAPHY A (2021)

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Editorial Material Biochemical Research Methods

Glycoproteomics

Arunima Singh

Summary: Glycoproteomics has matured, thanks to advancements in instrumentation, experimental methodologies, and computational search algorithms.

NATURE METHODS (2021)

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Editorial Material Multidisciplinary Sciences

Glycomic profiling and the mammalian brain

Jennyfer Tena et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Biochemical Research Methods

Precise, fast and comprehensive analysis of intact glycopeptides and modified glycans with pGlyco3

Wen-Feng Zeng et al.

Summary: The study introduces a new glycan-first glycopeptide search engine, pGlyco3, which can comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with modified saccharide units, in a fast and accurate manner.

NATURE METHODS (2021)

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Article Chemistry, Analytical

Bowl-like mesoporous polydopamine with size exclusion for highly selective recognition of endogenous glycopeptides

Yuyan Yan et al.

Summary: The study introduced a novel bowl-like mesoporous polydopamine nanoparticle modified by carrageenan for high specificity enrichment of endogenous glycopeptides. The nanoparticle exhibited prominent performance in enriching N-linked glycopeptides from complex biological samples, showcasing great potential for glycopeptidome analysis.

TALANTA (2021)

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Article Chemistry, Analytical

Effective Enrichment Strategy Using Boronic Acid-Functionalized Mesoporous Graphene-Silica Composites for Intact N- and O-Linked Glycopeptide Analysis in Human Serum

Siyuan Kong et al.

Summary: A new enrichment strategy using a boronic acid-functionalized mesoporous graphene-silica composite is proposed for isolating intact glycopeptides, showing effectiveness and specificity in glycosylation analysis.

ANALYTICAL CHEMISTRY (2021)

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Article Chemistry, Analytical

Hydrophilic carrageenan functionalized magnetic carbon-based framework linked by silane coupling agent for the enrichment of N-glycopeptides from human saliva

Xueting Jin et al.

Summary: By modifying a magnetic graphene material, a hydrophilic nanocomposite material with good enrichment effect and stability was successfully prepared. It exhibits high selectivity and sensitivity for glycopeptide enrichment, showing potential for application in enriching N-glycopeptides from complex biological samples.

JOURNAL OF SEPARATION SCIENCE (2021)

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Article Biochemical Research Methods

In-depth Site-specific Analysis of N-glycoproteome in Human Cerebrospinal Fluid and Glycosylation Landscape Changes in Alzheimer's Disease

Zhengwei Chen et al.

Summary: A novel N-glycoproteomic approach was developed in this study and successfully applied to analyze human cerebrospinal fluid samples, identifying a large number of intact N-glycopeptides and providing a molecular basis for understanding the structure-function relationships and disease mechanisms related to glycoproteins in cerebrospinal fluid. Additionally, a comparative in-depth N-glycoproteomic analysis of cerebrospinal fluid samples from healthy controls and Alzheimer's disease patients revealed altered glycosylation patterns for several N-glycoproteins, suggesting potential targets for further studies on glycosylation-based Alzheimer's disease research.

MOLECULAR & CELLULAR PROTEOMICS (2021)

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Article Biochemistry & Molecular Biology

Glycoproteomics: growing up fast

David R. Thomas et al.

Summary: Glycoproteomics is a rapidly growing field that aims to identify and characterize glycosylation events at a proteome scale. Recent advancements in mass spectrometry instrumentation and enrichment approaches have allowed for the identification and quantification of hundreds to thousands of glycosylation sites. The field is now moving towards studying specific mechanisms and disease states rather than simply identifying glycosylated substrates.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2021)

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StrucGP: de novo structural sequencing of site-specific N-glycan on glycoproteins using a modularization strategy

Jiechen Shen et al.

Summary: This study introduces a modularization strategy and an algorithm named StrucGP for automated interpretation of N-glycan structures using tandem mass spectrometry, enabling detailed glycan structure determination on thousands of glycosites. The approach aids in identifying rare/new glycan structures and facilitates in-depth structural and functional study of glycoproteins in the biomedical research field. StrucGP offers a novel de novo glycan mapping method for determining detailed N-glycan structures at the site-specific level.

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Hanqing Zhang et al.

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Hydrophilic maltose-modified magnetic metal-organic framework for highly efficient enrichment of N-linked glycopeptides

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Bifunctional Magnetic Supramolecular-Organic Framework: A Nanoprobe for Simultaneous Enrichment of Glycosylated and Phosphorylated Peptides

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Qi Lu et al.

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