Article
Biochemical Research Methods
Yuan Zhi, Li Jia, Jiechen Shen, Jun Li, Zexuan Chen, Bojing Zhu, Zhifang Hao, Yintai Xu, Shisheng Sun
Summary: Formic acid solution is commonly used for dissolving glycopeptide and glycan samples before mass spectrometry analysis. However, storing the samples in formic acid solution at -20°C can lead to an undesirable modification that affects the identification and quantification of glycans. Therefore, storing samples at -20°C should be avoided.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Christopher Burgoyne, Rob Smith
Summary: Glycans are important in biochemical processes, but the computational interpretation of glycans in mass spectrometry analysis can be challenging. The C++ implementation of the Sweet-SEQer algorithm, called C-SEQer, outperforms the original algorithm in terms of time and memory usage, making glycan analysis more efficient and effective. The implementation is freely available with an MIT license.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Stefan Gaunitz, Lars O. Tjernberg, Sophia Schedin-Weiss
Summary: Proteomics and protein glycosylation studies are crucial for understanding the roles of proteins and pathways in diseases. Important steps in the research include sample preparation, glycan release, derivatization, quantification, and advancements in mass spectrometry. Recent studies have shown altered protein glycosylation in Alzheimer's disease, providing new insights into the disease.
Article
Biochemistry & Molecular Biology
Xuyao Zeng, Milos Novotny, David E. Clemmer, Jonathan C. Trinidad
Summary: A substantial shortcoming of large-scale datasets is the difficulty in representing and visualizing key features, particularly in the study of glycopeptides and glycans. This paper presents a simple and concise graphical representation method to capture the microheterogeneity of glycan modification at specific sites, and provides visual illustrations of glycans and glycopeptides from various species.
Review
Chemistry, Multidisciplinary
Dylan Nicholas Tabang, Megan Ford, Lingjun Li
Summary: Protein modification by glycans is crucial for mediating biological functions, and mass spectrometry (MS) has become a powerful tool for glycomic and glycoproteomic analyses in various diseases. Recent advances in pancreatic disease research using MS have led to the discovery of new biomarkers and understanding of the links between glycans and disease pathology.
FRONTIERS IN CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Noortje de Haan, Maja Pucic-Bakovic, Mislav Novokmet, David Falck, Guinevere Lageveen-Kammeijer, Genadij Razdorov, Frano Vuckovic, Irena Trbojevic-Akmacic, Olga Gornik, Maja Hanic, Manfred Wuhrer, Gordan Lauc
Summary: Glycans enhance the structural complexity of proteins, and glycosylation is an important regulatory mechanism in many biological processes. Due to extensive interindividual differences in glycosylation, large studies are needed to map the structures and understand the role of glycosylation in human physiology. High-throughput glycomics methods have emerged to tackle the complexity of glycosylation and extensively characterize the human glycome in various biological samples. The ultimate goal is to gain better knowledge of the complete human glycome using easily implementable methods in biomedical research.
Article
Biochemical Research Methods
Margaret Downs, Jillian Curran, Joseph Zaia, Manveen K. Sethi
Summary: Proteoglycans are a diverse family of proteins that play various roles at the cell surface and extracellular matrix. This study presents a method combining serial proteolysis, higher-energy collisional dissociation (HCD), and electron transfer/higher-energy collisional dissociation (EThcD) to optimize protein sequence coverage and glycopeptide identification from proteoglycans. The use of EThcD allows the confident assignment of glycan compositions on multiply glycosylated peptides. The development of analytical tools for glycoproteomic similarity comparisons in biological samples is of great interest.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Zheng Fang, Hongqiang Qin, Jiawei Mao, Zhongyu Wang, Na Zhang, Yan Wang, Luyao Liu, Yongzhan Nie, Mingming Dong, Mingliang Ye
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)
Article
Biochemical Research Methods
Fanni Bugyi, Gabor Toth, Kinga Bernadett Kovacs, Laszlo Drahos, Lilla Turiak
Summary: Efficient phosphoproteomic analysis of small amounts of biological samples requires careful enrichment and purification steps. This study evaluated the performance of various self-packed and commercial centrifugal SPE cartridges/spin tips, and identified several methods that provided excellent results in terms of sample purification, reducing sample loss, and increasing the detection and recovery of phosphopeptides.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Review
Medicine, Research & Experimental
Tomislav Caval, Frederico Alisson-Silva, Flavio Schwarz
Summary: Cell surface glycosylation plays important roles in cancer, including impaired signaling, metastasis, and evading immune responses. Several glycosyltransferases, such as B3GNT3, FUT8, and B3GNT2, have been linked to reduced anti-tumor immune responses. There is a need for unbiased methods to investigate cell surface glycosylation. The field of glycoproteomics has advanced to allow large-scale profiling of intact glycopeptides for discovering new targets against cancer.
Article
Oncology
Michael Russelle Alvarez, Qingwen Zhou, Jennyfer Tena, Mariana Barboza, Maurice Wong, Yixuan Xie, Carlito B. Lebrilla, Michelle Cabanatan, Ma. Teresa Barzaga, Nelia Tan-Liu, Francisco M. Heralde, Luster Serrano, Ruel C. Nacario, Gladys Cherisse Completo
Summary: Protein glycosylation is a modification that affects a protein's function and has been correlated with cancer progression. This study aims to find unique protein glycosylation cancer biomarkers in a Philippine population, as previous research has focused on Caucasian populations. Lung cancer, particularly NSCLC, is a major cause of cancer death, and identifying potential biomarkers is crucial for diagnosis. The study analyzed the glycosylation patterns and protein expression profiles of Filipino lung cancer patients, and found specific trends that support the role of aberrant glycosylation in cancer progression.
Review
Spectroscopy
Guinevere S. M. Lageveen-Kammeijer, Bernhard Kuster, Dietmar Reusch, Manfred Wuhrer
Summary: This review evaluates mass spectrometric workflows and detection methods for glycans and glycoproteins, highlighting glycomic methodologies and innovations tailored for high sensitivity analysis. The discussion focuses on analyzing mammalian N-linked and GalNAc-type O-linked glycans.
MASS SPECTROMETRY REVIEWS
(2022)
Article
Chemistry, Analytical
Qianying Sheng, Junyan Li, Yingxin Chen, Xinmiao Liang, Minbo Lan
Summary: The researchers synthesized a new hydrophilic composite by introducing cationic cellulose, which can efficiently enrich N-glycopeptides, thus improving the detection sensitivity of human serum immunoglobulin G (IgG).
Article
Biochemical Research Methods
Daniel G. Delafield, Hannah N. Miles, Yuan Liu, William A. Ricke, Lingjun Li
Summary: Continual developments in instrumental and analytical techniques have established connections between protein glycosylation and human illness. Porous graphitic carbon (PGC) chromatography has gained considerable interest in glycomics research due to its flexibility and improved structural elucidation. Comparative analysis of single and biphasic separation regimes at different column temperatures demonstrated complementary advantages for each method. Utilizing multiple separation regimes and column temperatures can aid in profiling the glycoproteome in tumorigenic cells.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Review
Chemistry, Analytical
Yuting Xiong, Minmin Li, Yunhai Liu, Xinmiao Liang, Guangyan Qing
Summary: Glycoproteomics is a rapidly growing field that aims to identify and characterize protein glycosylation events at a system level. This review summarizes novel glycopeptide enrichment materials and approaches, and discusses the application of glycoproteomics in both the functional analysis of glycoproteins and the study of human diseases.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Biochemical Research Methods
Kaitlyn B. Donohoo, Junyao Wang, Mona Goli, Aiying Yu, Wenjing Peng, Md Abdul Hakim, Yehia Mechref
Summary: This review focuses on recent advances in MS-based techniques for glycomic analysis over the last 5 years, addressing topics such as glycan release, purification, derivatization, separation, ionization, tandem MS, and biocomputing tools for glycan analysis.
Review
Spectroscopy
Wenjing Peng, Cristian D. Gutierrez Reyes, Sakshi Gautam, Aiying Yu, Byeong Gwan Cho, Mona Goli, Kaitlyn Donohoo, Stefania Mondello, Firas Kobeissy, Yehia Mechref
Summary: Glycosylation is a significant posttranslational modification in mammalian cells, involved in various biofunctions and diseases. Mass spectrometry is a powerful tool for glycan and glycopeptide isomeric analysis, but its comprehensive characterization remains a challenge. Separation methods and bioinformatic tools are applied to address this challenge.
MASS SPECTROMETRY REVIEWS
(2023)
Review
Biochemical Research Methods
Cristian D. Gutierrez-Reyes, Peilin Jiang, Mojgan Atashi, Andrew Bennett, Aiying Yu, Wenjing Peng, Jieqiang Zhong, Yehia Mechref
Summary: Protein glycosylation is essential in various biological processes and its aberrant forms are associated with diseases. Researchers have developed different methods and technologies to achieve quantitative and qualitative analysis of glycoproteins.
Review
Cell Biology
Firas Kobeissy, Abir Kobaisi, Wenjing Peng, Chloe Barsa, Mona Goli, Ahmad Sibahi, Samer El Hayek, Samar Abdelhady, Muhammad Ali Haidar, Mirna Sabra, Matej Oresic, Giancarlo Logroscino, Stefania Mondello, Ali H. Eid, Yehia Mechref
Summary: Proteomic analysis has revolutionized our understanding of protein expression patterns and post-translational modifications, such as glycosylation. This review provides an overview of glycosylation processes and their role in gene and pathway regulation. It also explores the association between glycosylation and neuropsychiatric disorders, as well as neurodegenerative diseases.
Article
Biochemistry & Molecular Biology
Muhammad Ali Haidar, Zaynab Shakkour, Chloe Barsa, Maha Tabet, Sarin Mekhjian, Hala Darwish, Mona Goli, Deborah Shear, Jignesh D. Pandya, Yehia Mechref, Riyad El Khoury, Kevin Wang, Firas Kobeissy
Summary: This study investigated the protective effects of MitoQ in traumatic brain injury using a mouse model. The results showed that MitoQ improved neurological and cognitive functions, reduced inflammation, and prevented axonal injury.
Article
Biochemistry & Molecular Biology
Akeem Sanni, Mona Goli, Jingfu Zhao, Junyao Wang, Chloe Barsa, Samer El Hayek, Farid Talih, Bartolo Lanuzza, Firas Kobeissy, Giuseppe Plazzi, Monica Moresco, Stefania Mondello, Raffaele Ferri, Yehia Mechref
Summary: This study aimed to identify potential serum biomarkers for narcolepsy type 1 (NT1), a life-threatening disorder characterized by a sleep-wake cycle disorder. A proteomics analysis was conducted, which revealed 36 differentially expressed proteins associated with NT1. These findings provide insights into the pathophysiological effects and important biochemical pathways involved in NT1.
Article
Chemistry, Multidisciplinary
Yifei Tan, Jianhui Zhu, Cristian D. Gutierrez Reyes, Yu Lin, Zhijing Tan, Zuowei Wu, Jie Zhang, Alva Cano, Sara Verschleisser, Yehia Mechref, Amit G. Singal, Neehar D. Parikh, David M. Lubman
Summary: Aberrant changes in site-specific core fucosylation (CF) of serum proteins can serve as potential diagnostic markers of tumors. A study employed an optimized data-dependent acquisition (DDA) workflow to identify CF of serum proteins in patients with nonalcoholic steatohepatitis-related cirrhosis and hepatocellular carcinoma. The study found significant changes in CF peptides between cirrhosis and HCC, with one peptide showing the best diagnostic performance in discriminating HCC from cirrhosis.
Article
Chemistry, Analytical
Peilin Jiang, Wenjing Peng, Jingfu Zhao, Mona Goli, Yifan Huang, Yunxiang Li, Yehia Mechref
Summary: The complexity and heterogeneity of protein glycosylation present challenges in characterization and quantitation. This study introduces a metabolic isotope labeling strategy called GlyProSILC, which can label both the glycan motif and peptide backbone in the same batch of cells. It provides an accurate and effective quantitation approach for glycomics, proteomics, and glycoproteomics in a cell culture system.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Chirine El-Baba, Zeinab Ayache, Mona Goli, Berthe Hayar, Zeinab Kawtharani, Claudio Pisano, Firas Kobeissy, Yehia Mechref, Nadine Darwiche
Summary: The study shows that ST1926 is effective in reducing cell viability and inducing apoptosis in GBM cells, and it also reduces the level of POLA1 protein. Additionally, proteomics analysis reveals that ST1926 affects multiple cellular processes related to GBM cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Junyao Wang, Aiying Yu, Byeong Gwan Cho, Yehia Mechref
Summary: Retention time is a crucial parameter in liquid chromatography (LC) for demonstrating separation results. However, it can vary when samples are tested with different instruments and labs, making it difficult to compare data from different LC systems. To address this issue, a hydrophobicity index was introduced to normalize the retention time of glycopeptides separated by reversed-phase LC (RPLC). Tandem MS was used for glycopeptide detection and identification.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Biochemical Research Methods
Oluwatosin Daramola, Cristian D. Gutierrez-Reyes, Junyao Wang, Judith Nwaiwu, Sherifdeen Onigbinde, Mojibola Fowowe, Michael Dominguez, Yehia Mechref
Summary: Changes in glycan expression play a role in the development of diseases. Analyzing isomeric N-glycans using LC-MS/MS is challenging due to the large number of possible conformations. Derivatization of glycans is commonly used but time-consuming. This study focuses on efficient isomeric separation of native N-glycans using a nano ZIC-HILIC column. The stability and reproducibility of the column were confirmed.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Biochemistry & Molecular Biology
Sherifdeen Onigbinde, Cristian D. Gutierrez Reyes, Mojibola Fowowe, Oluwatosin Daramola, Mojgan Atashi, Andrew I. Bennett, Yehia Mechref
Summary: The differences in glycosylation patterns on the spike protein of SARS-CoV-2 variants influence immune evasion, infectivity, and transmission. O-micron variant has the highest number of O-glycosylation sites and the highest level of sialylation on the S1 subunit.
Article
Biology
Gerardo Alejo-Jacuinde, Hector-Rogelio Najera-Gonzalez, Ricardo A. Chavez A. Montes, Cristian D. Gutierrez D. Reyes, Alfonso Carlos Barragan-Rosillo, Benjamin Perez Sanchez, Yehia Mechref, Damar Lopez-Arredondo, Lenin Yong-Villalobos, Luis Herrera-Estrella
Summary: This study presents a chromosome-level reference genome for chia and analyzes the transcriptome, proteome, and metabolome to uncover the molecular basis of the unique characteristics of chia seeds. Chia is an emerging crop with functional food properties, but the genetic basis for traits like seed mucilage and polyphenol content remains unclear.
COMMUNICATIONS BIOLOGY
(2023)
Review
Oncology
Reem Halabi, Fatima Dakroub, Mohammad Z. Haider, Stuti Patel, Nayef A. Amhaz, Mohammad A. Reslan, Ali H. Eid, Yehia Mechref, Nadine Darwiche, Firas Kobeissy, Ibrahim Omeis, Abdullah A. Shaito
Summary: This review discusses the genetic and epigenetic abnormalities in meningiomas, with a focus on neurofibromatosis type 2 and non-NF2 mutations. It also explores novel biomarkers for meningioma diagnosis and prognosis, including epigenetic-, RNA-, metabolomics-, and protein-based markers. Additionally, the available meningioma-specific animal models are overviewed.
Article
Chemistry, Analytical
Junyao Wang, Xue Dong, Aiying Yu, Yifan Huang, Wenjing Peng, Yehia Mechref
Summary: This study focuses on the separation of glycan isomers using reversed-phase liquid chromatography (RPLC) and permethylated glycans. Different LC conditions were optimized to achieve separations of glycan standards and model glycoproteins. The reproducibility and stability of the RPLC C18 column were also tested, and the approach was successfully applied to separate glycan isomers from complex biological samples.
