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)
Article
Biochemical Research Methods
Miaomiao Xin, Yintai Xu, Shanshan You, Cheng Li, Bojing Zhu, Jiechen Shen, Zexuan Chen, Wenhao Shi, Xia Xue, Juanzi Shi, Shisheng Sun
Summary: In this study, a precise site-specific N-glycoproteome map of human seminal plasma was established using a site-specific glycoproteomic approach and a glycan structure interpretation software. The results revealed a diverse range of glycoproteins in seminal plasma, which is crucial for studying the glycosylation structure and function in the male reproductive system.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Oncology
Jun Li, Ting Zhao, Jing Li, Jiechen Shen, Li Jia, Bojing Zhu, Liuyi Dang, Chen Ma, Didi Liu, Fan Mu, Liangshuo Hu, Shisheng Sun
Summary: This study identified numerous unique N-glycan structures in ICC through precision N-glycoproteomic analysis, providing a valuable resource for future research on ICC diagnostic biomarkers, therapeutic targets, and mechanism investigations.
MOLECULAR ONCOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Yang Zhao, Man Wang, Bo Meng, Ying Gao, Zhichao Xue, Minjun He, You Jiang, Xinhua Dai, Dan Yan, Xiang Fang
Summary: This study provided a comprehensive overview of molecular alterations in fasting plasma of 24 Chinese participants, including T2D patients, prediabetic subjects, and healthy controls. The research identified a diverse set of potential biomarkers for enhancing efficiency and accuracy in (pre)diabetes diagnosis. Glycoproteomic analysis revealed systemic N-glycosylation alterations in complement activation pathways in T2D patients, offering new opportunities for disease diagnosis and treatment. The results highlight the potential role of glycoproteomics in understanding (pre)diabetes and present a new direction for diabetes research.
FRONTIERS IN CHEMISTRY
(2021)
Article
Cell Biology
Piaopiao Wen, Jingru Chen, Chenyang Zuo, Xiaodong Gao, Morihisa Fujita, Ganglong Yang
Summary: STT3A and STT3B are the main catalytic subunits of the oligosaccharyltransferase complex, playing different roles in N-linked glycosylation. Deletion of the STT3A gene has a significant impact on protein expression, particularly on glycoproteins. This deletion also affects the expression of glycan-related enzymes, resulting in altered levels of mannosylated and fucosylated N-glycans. Hyperglycosylated proteins are identified in STT3A-KO cells, which are associated with endoplasmic reticulum stress and unfolded protein response.
Article
Biochemical Research Methods
H. Mehmet Kayili, Bekir Salih
Summary: This study utilized high-throughput glyco-analytical strategies to analyze the N-glycosylation sites and glycan contents of human thyroglobulin. The results revealed the presence of high-mannose type glycans at some sites and complex/hybrid type glycans at other regions, with sulfated glycoform structures detected at sites containing complex/hybrid type glycans.
JOURNAL OF PROTEOMICS
(2022)
Article
Chemistry, Analytical
Xueting Jin, Canhong Zhu, Jiani Wu, Yinghua Yan, Chuan-Fan Ding, Keqi Tang, Di Zhang
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)
Article
Biochemistry & Molecular Biology
Zhuokun Du, Qianying Yang, Yuanyuan Liu, Sijie Chen, Hongxian Zhao, Haihong Bai, Wei Shao, Yangjun Zhang, Weijie Qin
Summary: N-glycosylation and phosphorylation are important posttranslational modifications in biological processes. Simultaneous characterization of these modifications is challenging, especially for tiny amount of samples obtained in tissue biopsy. This study introduces a new strategy for the efficient tandem enrichment of N-glycopeptides and phosphopeptides using HILIC and TiO2 microparticles.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
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
Biochemistry & Molecular Biology
Cheng Ma, Hong-Yuan Tsai, Qi Zhang, Lakmini Senavirathna, Lian Li, Lih-Shen Chin, Ru Chen, Sheng Pan
Summary: In this study, the impact of the well-known glycolysis inhibitor 2-Deoxy-D-glucose (2DG) on cancer cells was investigated. The findings reveal complex changes in protein glycosylation and expression underlying the various effects of 2DG on cancer cells, providing insights for therapeutic development targeting protein glycosylation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Biochemistry & Molecular Biology
Liuyi Dang, Pengfei Li, Wei Dan, Huanhuan Liu, Jiechen Shen, Bojing Zhu, Li Jia, Shisheng Sun
Summary: The study systematically investigated the regulatory roles of bisecting N-glycans in human HK-2 cells. The results showed that bisecting N-glycans can impact the biosynthesis of N-glycans and protein expressions, and they are mainly involved in cell adhesion, extracellular matrix regulation, and cell signaling.
CARBOHYDRATE RESEARCH
(2023)
Article
Biochemical Research Methods
Wenbo Dong, Lin Chen, Li Jia, Zexuan Chen, Jiechen Shen, Pengfei Li, Shisheng Sun
Summary: The low abundance and heterogeneity of N-glycosylation at the peptide level poses a great challenge in the field of glycobiology. In this study, different combinations of desalting and enrichment columns were compared for the enrichment of intact N-glycopeptides from mouse brain tissues. Results showed that the C18 column was slightly superior to the HLB column, and the use of both MAX and HILIC columns complemented each other in the enrichment of intact N-glycopeptides. Based on these findings, sequential enrichment of glycopeptides using HILIC and then MAX columns is recommended for in-depth analysis of site-specific glycoproteome.
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)
Review
Biochemical Research Methods
Shulei Liu, Edward D. Kerr, Cassandra L. Pegg, Benjamin L. Schulz
Summary: This article reviews recent studies on proteomic and glycoproteomic analyses of beer and wine. Many grape and yeast proteins are glycosylated, while barley proteins can be glycated during the beer making process. The use of high-resolution mass spectrometry allows for the identification, quantification, and characterization of the glyco/proteomes of fermented beverages, which helps in controlling the quality of the final products.
Article
Multidisciplinary Sciences
Hooman H. Rashidi, John Pepper, Taylor Howard, Karina Klein, Larissa May, Samer Albahra, Brett Phinney, Michelle R. Salemi, Nam K. Tran
Summary: The study aims to compare the performance of two commercial automated machine learning platforms in COVID-19 mass spectrometry analysis. The results demonstrate the robustness of machine learning models against SARS-CoV-2 variants on different platforms and highlight similarities and differences in producing predictive algorithms.
Article
Oncology
Prabhakar Bastola, Gary S. Leiserowitz, Jeremy Chien
Summary: The increased dependency of cancer cells on protein homeostasis creates a vulnerability that can be exploited using protein homeostasis inhibiting drugs. Recently, valosin-containing protein has emerged as a key component of the pathway and a novel therapeutic target for cancer treatment. Our results indicate that VCP inhibitors can be combined with other endoplasmic reticulum stress-inducing agents to produce synergistic cytotoxicity in ovarian cancer cells.
Article
Medical Laboratory Technology
Nico P. M. Smit, Fred P. H. T. M. Romijn, Vanessa J. J. van Ham, Esther Reijnders, Christa M. Cobbaert, L. Renee Ruhaak
Summary: Plasma anticoagulants affect the results of quantitative protein mass-spectrometry (QPMS) analysis of apolipoproteins. Heparin plasma shows comparable results to serum, whereas citrate plasma shows reduced concentrations that can be explained by dilution. EDTA-plasma shows reduced recovery due to altered proteolytic digestion efficiency.
CLINICAL CHEMISTRY AND LABORATORY MEDICINE
(2023)
Article
Cell Biology
Jingyue Jia, Fulong Wang, Zambarlal Bhujabal, Ryan Peters, Michal Mudd, Thabata Duque, Lee Allers, Ruheena Javed, Michelle Salemi, Christian Behrends, Brett Phinney, Terje Johansen, Vojo Deretic
Summary: Lysosomal damage induces the formation of stress granules and coordinates mTOR inactivation through the process of membrane atg8ylation. This process is effective against various lysosomal damaging agents.
JOURNAL OF CELL BIOLOGY
(2022)
Editorial Material
Cell Biology
Jingyue Jia, Fulong Wang, Zambarlal Bhujabal, Ryan Peters, Michal Mudd, Thabata Duque, Lee Allers, Ruheena Javed, Michelle Salemi, Christian Behrends, Brett Phinney, Terje Johansen, Vojo Deretic
Summary: The functions of mammalian Atg8 proteins (mATG8s) go beyond autophagy and also include Atg8ylation. Lysosomal damage induces stress granules (SGs) that inhibit protein translation via EIF2A/eIF2 alpha phosphorylation and promote ATF4-dependent stress response. GABARAPs interact with NUFIP2 and G3BP1, and Atg8ylation is required for their recruitment to damaged lysosomes. The roles of NUFIP2 and G3BP1 in SG formation and MTOR activation are regulated by GABARAP and Atg8ylation.
Article
Medical Laboratory Technology
L. Renee Ruhaak, Fred P. H. T. M. Romijn, Ilijana Begcevic Brkovic, Zsusanna Kuklenyik, Julia Dittrich, Uta Ceglarek, Andrew N. Hoofnagle, Harald Althaus, Eduardo Angles-Cano, Stefan Coassin, Vincent Delatour, Liesbet Deprez, Ioannis Dikaios, Gerhard M. Kostner, Florian Kronenberg, Alicia Lyle, Urban Prinzing, Hubert W. Vesper, Christa M. Cobbaert, Int Federation Clinical Chem Lab Med Working Grp Apolipoproteins Mass Spect
Summary: In order to ensure the accuracy and reliability of medical results from in vitro diagnostic and in-house tests, a higher order reference measurement system traceable to endorsed reference measurement procedures and reference materials is needed. A candidate reference measurement procedure for serum apolipoprotein(a) [apo(a)] based on mass spectrometry was developed and provisionally validated. The method demonstrated accurate quantitation of serum apo(a) and fulfilled predefined analytical performance specifications.
CLINICAL CHEMISTRY
(2023)
Article
Ophthalmology
Iman Jalilian, Santoshi Muppala, Maryam Ali, Johnathon D. Anderson, Brett Phinney, Michelle Salemi, Phillip A. Wilmarth, Christopher J. Murphy, Sara M. Thomasy, VijayKrishna Raghunathan
Summary: This study investigates the effects of TGF-beta and ascorbic acid (AA) on the composition and stiffness of the extracellular matrix (ECM) secreted by corneal endothelial cells (CECs). It finds that TGF-beta decreases matrix stiffness while AA modulates the oxidative stress pathway in the matrix. These findings provide insights into the molecular mechanisms of Fuchs endothelial corneal dystrophy (FECD).
EXPERIMENTAL EYE RESEARCH
(2023)
Review
Medical Laboratory Technology
Nina M. M. Diederiks, Yuri E. M. van der Burgt, L. Renee Ruhaak, Christa M. M. Cobbaert
Summary: In the past decade, there has been a significant resurgence of interest in serum/plasma lipoprotein(a) (Lp(a)) as an independent risk factor for cardiovascular disease (CVD). Updated evidence has been published supporting a causal association between Lp(a) concentrations and cardiovascular outcomes in different ethnic groups. The development of new Lp(a)-lowering drugs has also contributed to the growing interest in measuring Lp(a) levels. The accuracy and standardization of Lp(a) tests are crucial for identifying high-risk individuals and evaluating the effectiveness of Lp(a)-lowering medication.
CRITICAL REVIEWS IN CLINICAL LABORATORY SCIENCES
(2023)
Article
Cell Biology
Fulong Wang, Einar S. Trosdal, Masroor Ahmad Paddar, Thabata L. A. Duque, Lee Allers, Michal Mudd, Prithvi R. Akepati, Ruheena Javed, Jingyue Jia, Michelle Salemi, Brett Phinney, Vojo Deretic
Summary: ATG5 plays a crucial role in membrane Atg8ylation and has negative effects on tuberculosis in myeloid cells. The absence of ATG5 leads to a lysosomal hypersensitivity phenotype in endolysosomal organelles, partially due to compromised recruitment of ESCRT proteins for lysosomal repair. This finding is of significance for understanding tuberculosis pathogenesis.
Article
Reproductive Biology
Jessica A. Kinkade, Arun S. Seetharam, Shrikesh Sachdev, Nathan J. Bivens, Brett S. Phinney, Gabriela Grigorean, R. Michael Roberts, Geetu Tuteja, Cheryl S. Rosenfeld
Summary: The fetal brain of the mouse relies on the placenta for serotonin and other factors, and this study suggests that placental extracellular vesicles (EV) may transport these factors to the developing brain. Analysis of EV from trophoblast cells in mice revealed high levels of serotonin, as well as dopamine and norepinephrine. Additionally, EV from different sources contained different types of small RNA. Furthermore, exposure to EV led to changes in the transcriptome profiles of neural progenitor cells, particularly affecting transcripts enriched in neural tissues.
BIOLOGY OF REPRODUCTION
(2023)
Article
Medical Laboratory Technology
Tirsa T. van Duijl, Esther N. M. de Rooij, Maxim M. Treep, Marte E. Koelemaij, Fred P. H. T. M. Romijn, Ellen K. Hoogeveen, L. Renee Ruhaak, Saskia le Cessie, Johan W. de Fijter, Christa M. Cobbaert
Summary: This study explored the potential of emerging and conventional urinary kidney injury biomarkers in different populations using LC-MS/MS analysis. The results showed that kidney injury biomarkers were increased in kidney transplant recipients with ischemia-reperfusion injury. NGAL and B2M showed the strongest response.
CLINICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Marwa Zafarullah, Jie Li, Michelle R. Salemi, Brett S. Phinney, Blythe P. Durbin-Johnson, Randi Hagerman, David Hessl, Susan M. Rivera, Flora Tassone
Summary: FXTAS is a neurodegenerative disorder associated with the FMR1 premutation. By analyzing the proteome of premutation carriers, researchers have identified differentially expressed proteins and dysregulated metabolic pathways associated with FXTAS. This provides clues for early diagnosis, development, and progression of FXTAS, as well as the study of related pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Rasheed O. Sule, Brett S. Phinney, Michelle R. Salemi, Aldrin V. Gomes
Summary: Prometryn, a widely used herbicide, has been found to have effects on the cardiac system. Proteomic profiling revealed that prometryn may induce mitochondrial dysfunction and alter signaling pathways related to energy metabolism, protein degradation, and fatty acid metabolism in the heart.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Toxicology
Lo-Wei Lin, Blythe P. Durbin-Johnson, David M. Rocke, Michelle Salemi, Brett S. Phinney, Robert H. Rice
Summary: This study focuses on the effects of environmental pro-oxidants on the formation and protein composition of epidermal cornified envelopes (CEs). The results show that pro-oxidants can alter the CE proteome and that the cellular redox state plays an important role in CE formation.
TOXICOLOGICAL SCIENCES
(2023)
Article
Medical Laboratory Technology
Tirsa T. van Duijl, L. Renee Ruhaak, Cees van Kooten, Johan W. de Fijter, Christa M. Cobbaert
Summary: This study explored the potential of LC-MS/MS as a next-generation technology for multiplex urinary protein measurement. It overcomes nonselectivity and lack of standardization by directly measuring well-defined molecular proteins.
JOURNAL OF APPLIED LABORATORY MEDICINE
(2022)
