Article
Chemistry, Applied
Eshani Nandita, Nikita P. Bacalzo, Christopher L. Ranque, Matthew J. Amicucci, Ace Galermo, Carlito B. Lebrilla
Summary: A new method was proposed in this study to depolymerize polysaccharides into oligosaccharide markers for rapid identification of food polysaccharides using HPLC-QTOF MS. The method showed high repeatability and validation, as confirmed by experimental results.
CARBOHYDRATE POLYMERS
(2021)
Article
Biochemistry & Molecular Biology
Junyao Wang, Wenjing Peng, Aiying Yu, Mohamed Fokar, Yehia Mechref
Summary: This study investigated the glycan expression changes in breast cancer and brain cancer cell lines cultivated in a complex physiological culture medium (Plasmax) compared to commercial media. The results showed significant differences in glycosylation patterns, providing valuable information for in vitro cancer cell glycomics studies and media selection.
Article
Biochemistry & Molecular Biology
Byeong Gwan Cho, Cristian D. Gutierrez Reyes, Yehia Mechref
Summary: The study investigated different N-glycan sample preparation approaches and found that increasing the amount of buffer solution led to higher intensity, indicating better efficiency in N-glycan release compared to a previously published method and FANGS.
Article
Chemistry, Applied
Lianwu Xie, Qiachi Fu, Shuyun Shi, Jiawei Li, Xinji Zhou
Summary: A new analytical strategy was proposed to identify 33 bioactive compounds from Buddleja Flos, with six flavonoid aglycones showing excellent alpha-glucosidase inhibitory activities. The results demonstrate the high efficiency of the proposed strategy in profiling bioactive compounds from natural products.
Article
Biochemical Research Methods
Qianru Ma, Wentao Wang, Xu Yang, Yunhong Chen, Yan Liu, Hongxu Chen, Yufen Zhao
Summary: This study developed a novel glycan labelling reagent, P(4)HZD, for mass spectrometry analysis of oligosaccharides. The reagent with a permanent positive charge enhanced the MS signal intensity of oligosaccharides. Compared with a commercialized oligosaccharide tag, P(4)HZD more effectively enhanced the signal of oligosaccharides in the middle or higher mass range using both ESI and MALDI ion sources. P(4)HZD showed good efficacy for the detection of oligosaccharides in complex biological samples.
JOURNAL OF CHROMATOGRAPHY A
(2022)
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
Immunology
Laudine M. C. Petralia, Angela van Diepen, Dieu-Linh Nguyen, Lena A. Lokker, Erliyani Sartono, Sasisekhar Bennuru, Thomas B. Nutman, Kenneth Pfarr, Achim Hoerauf, Samuel Wanji, Jeremy M. Foster, Cornelis H. Hokke
Summary: Parasitic nematodes cause chronic disablement in humans worldwide. Current diagnostics for surveillance of filarial diseases have limitations, and improved assays are needed. We studied the glycan antigens of the parasite Brugia malayi and found that they triggered IgG responses. Our findings suggest potential for developing disease-specific diagnostics for filarial disease control.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Neurosciences
Wenjing Peng, Firas Kobeissy, Stefania Mondello, Chloe Barsa, Yehia Mechref
Summary: Neurological diseases have a significant impact on millions of people worldwide, and their prevalence is increasing due to global aging. Glycosylation, a post-translational modification, has been found to play a vital role in neurological diseases and can provide novel biomarkers and information for disease pathology. Mass spectrometry is considered the most powerful tool for glycan analysis, and various techniques and strategies have been developed to enhance its identification and quantitation in neurological samples.
FRONTIERS IN NEUROSCIENCE
(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)
Article
Chemistry, Applied
Haci Mehmet Kayili, Nazire Barlas, Deniz Baran Demirhan, Mehmet Emrah Yaman, Mehmet Atakay, Ulku Guler, Mustafa Kara, Kadir Serafettin Tekgunduz, Bekir Salih
Summary: This study analyzed the N-glycome of milk whey glycoproteins from different sources using MALDI-MS. The results showed that the N-glycan profiles mostly overlapped between bovine and buffalo whey, while donkey whey had a unique acetylated N-glycan. Human milk whey had the highest amount of a2,6-linked NeuAc, while goat whey had the highest amount of a2,3-linked NeuGc.
Article
Food Science & Technology
Yu-Ping Huang, Randall C. Robinson, Fernanda Furlan Goncalves Dias, Juliana Maria Leite Nobrega de Moura Bell, Daniela Barile
Summary: This study evaluated different SPE approaches and found that mixed-mode SPE is more suitable than conventional reverse-phase SPE in improving LC-MS/MS analysis of both oligosaccharides and peptides simultaneously.
Article
Chemistry, Analytical
Noortje de Haan, Yoshiki Narimatsu, Mikkel Koed Moller Aasted, Ida S. B. Larsen, Irina N. Marinova, Sally Dabelsteen, Sergey Y. Vakhrushev, Hans H. Wandall
Summary: In this study, a high-throughput sample preparation method was developed for the nonreductive release and characterization of O-glycans from human cell materials. By using reducing-end labeling and mass spectrometry analysis, O-glycan structural isomers in complex mixtures were efficiently separated and detected. This method provides an opportunity to study glycomic changes in human tissue and disease models using mainstream analytical equipment.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Shuying Mao, Wei Jin, Sisi Fu, Keanqi Liu, Feng Xu, Linlin Wu, Yexin Xu, Huizhu Yang, Huafang Liu, Guangji Wang, Yan Liang
Summary: This study developed a systematic analytical strategy and technical platform for the composition and pharmacokinetics study of protein hydrolysates (PHs). The qualitative and quantitative analysis methods were successfully applied to LPs distribution study in mice, providing valuable information for the profile and pharmacokinetics analysis of peptides in various PHs.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Xinhua Zhou, Xu Chen, Xiaomeng Yin, Mingyang Wang, Juanjuan Zhao, Yan Ren
Summary: In this study, a comprehensive method combining full scan (FS)-parent ions list (PIL)-higher energy collision induced dissociation (HCD)-MS/MS was used for the chemical profiling of flavonoids in Scutellaria barbata. The integration of mass defect filtering (MDF) and diagnostic product ions (DPIs) into the screening and identification strategy improved the subtype classification and structural confirmation. The study identified or tentatively characterized 127 target flavonoids and provided a novel approach for the systematic characterization of complex components in herbal medicines.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Biochemical Research Methods
Zhi-Rong Cui, Yi Li, Meng-Ling Zhao, Rong Xu, Meng-Han Chen, Shan Li, Fa-Liang An, Pan-Pan Zhang, Ling-Yi Kong, Jun Luo
Summary: This study developed an efficient method for the analysis of minor limonoids in Melia toosendan fruits using solid-phase extraction with high-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry. Thirteen limonoids, including four new ones, were identified in total, marking a significant progress in the identification of limonoids and opening up potential for further research in other plant species.
PHYTOCHEMICAL ANALYSIS
(2021)
Article
Chemistry, Multidisciplinary
Mina Ghanimi Fard, Zahra Khabir, Philipp Reineck, Nicole M. Cordina, Hiroshi Abe, Takeshi Ohshima, Sagar Dalal, Brant C. Gibson, Nicolle H. Packer, Lindsay M. Parker
Summary: This study developed a novel method to target glycan receptors in different brain cell types using lectin-conjugated nanodiamonds. The results demonstrate that the uptake of lectin-conjugated nanodiamonds varies across different types of brain cells.
NANOSCALE ADVANCES
(2022)
Article
Chemistry, Analytical
Yueying Cao, Jiehua Wu, Xianlin Zheng, Yanling Lu, James A. Piper, Yiqing Lu, Nicolle H. Packer
Summary: A systematic approach was introduced to quantitatively evaluate the biological activity of antibody-conjugated UCNPs. An optimal antibody conjugation efficiency of approximately 70% was determined under specific conditions, providing a practical guideline for future studies on functionalized UCNPs.
ANALYTICA CHIMICA ACTA
(2022)
Article
Biochemical Research Methods
Gilbert S. Omenn, Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, Susan T. Weintraub, Sandra Orchard, Michael H. A. Roehrl, Edouard Nice, Siqi Liu, Nuno Bandeira, Yu-Ju Chen, Tiannan Guo, Ruedi Aebersold, Robert L. Moritz, Eric W. Deutsch
Summary: According to the 2022 metrics of the HUPO Human Proteome Project (HPP), protein expression has been detected for 93.2% of the predicted proteins in the human genome. The number of missing proteins has been reduced, indicating experimental progress and reclassification. Proteomics continues to yield significant findings in biological and clinical studies and integrates with other omics platforms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Medicine, Research & Experimental
Wei Zhang, Yan Yang, Liewen Lin, Jingquan He, Jingjing Dong, Bin Yan, Wanxia Cai, Yumei Chen, Lianghong Yin, Donge Tang, Fanna Liu, Yong Dai
Summary: This study characterized the ubiquitinome of CRC cells and identified abnormal ubiquitination(s) potentially affecting patient survival. The findings shed light on the functions and pathways associated with ubiquitination in CRC, as well as the potential role of FOCAD mutations in RNA localization and translation. These findings offer new opportunities for clinical treatment.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Nima Sayyadi, Irene Justiniano, Yan Wang, Xianlin Zheng, Wei Zhang, Lianmei Jiang, Dmitry M. Polikarpov, Robert D. Willows, David Gillatt, Douglas Campbell, Bradley J. Walsh, Jingli Yuan, Yiqing Lu, Nicolle H. Packer, Yuling Wang, James A. Piper
Summary: Two molecular cytology approaches, TGiA and RiA, have been developed to detect prostate cancer cells. TGiA-OSAM showed single-cell PCa detection sensitivity, while RiA had a lower limit of detection. Both assays detected low abundance PCa cells in patient urine and showed correlation with clinical data.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
The Huong Chau, Anastasia Chernykh, Rebeca Kawahara, Morten Thaysen-Andersen
Summary: N-Glycoproteomics, as a system-wide study of glycans asparagine-linked to protein carriers, has the potential to provide deep insights into the complexity and dynamics of the heterogeneous N-glyco-proteome. However, it remains challenging and restricted to specialised laboratories. This article aims to stimulate discussions on method harmonisation, data standardisation, and reporting guidelines to make N-glycoproteomics more reproducible and accessible, and to highlight practical solutions and strategies for enhancing insight into the N-glycoproteome.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Edward S. X. Moh, Andreas Zankl, Nicolle H. Packer
Summary: Skeletal dysplasias are rare genetic disorders that affect skeletal growth and development, causing physical deformities and other medical problems. High-throughput genome sequencing technologies have made it easier to identify the genotype of the disorder, but phenotypic outcomes may not always be represented. In this pilot study, we demonstrate the ability to phenotype patients with CHST3-related skeletal dysplasia by profiling glycosaminoglycans and sequentially identifying their potential protein carriers using freezer-induced patient urine sediments.
AUSTRALIAN JOURNAL OF CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Ha Na Kim, Zehra Elgundi, Xiaoting Lin, Lu Fu, Fengying Tang, Edward S. X. Moh, MoonSun Jung, Keerthana Chandrasekar, Florence Bartlett-Tomasetig, Candice Foster, Nicolle H. Packer, John M. Whitelock, Jelena Rnjak-Kovacina, Megan S. Lord
Summary: Growth factors play a crucial role in angiogenesis for tissue repair and regeneration. However, the clinical success of growth factor delivery has been limited. This study demonstrates that engineered short forms of perlecan can bind and activate angiogenic growth factors. Delivery of these engineered perlecan forms in chitosan scaffolds promotes angiogenesis, making them potential next generation angiogenic therapies.
JOURNAL OF CONTROLLED RELEASE
(2023)
Article
Multidisciplinary Sciences
Qiaochu Liang, Caixia Ma, Shauna M. Crowley, Joannie M. Allaire, Xiao Han, Raymond W. W. Chong, Nicolle H. Packer, Hong Bing Yu, Bruce A. Vallance
Summary: Enteric bacterial pathogens, such as Citrobacter rodentium, are able to adapt to the host's intestinal environment through metabolizing sialic acid derived from mucins and utilizing it as a carbon source for growth. The bacteria also sense and display chemotactic activity toward sialic acid. Sialic acid induces the secretion of autotransporter proteins, Pic and EspC, which enhance the bacteria's ability to degrade intestinal mucus and adhere to epithelial cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Immunology
Hayley Goodson, Rebeca Kawahara, Sayantani Chatterjee, Gabriel Goncalves, Joshua Fehring, Anthony W. Purcell, Nathan P. Croft, Morten Thaysen-Andersen
Summary: Immunopeptidomics study reveals that N-glycan modifications are prevalent in MHC-II immunopeptides, but the complex/hybrid-type N-glycan modifications are rare compared to the cellular glycoproteome.
FRONTIERS IN IMMUNOLOGY
(2023)
Meeting Abstract
Cardiac & Cardiovascular Systems
Benjamin J. Pullen, Achini K. Vidanapathirana, Lauren Sandeman, Arun Everest-Dass, Daniel Kolarich, Joanne T. Tan, Peter Psaltis, Stephen Nicholls, Nicolle H. Packer, Christina A. Bursill
Review
Multidisciplinary Sciences
Ieva Bagdonaite, Stacy A. Malaker, Daniel A. Polasky, Nicholas M. Riley, Katrine Schjoldager, Sergey Y. Vakhrushev, Adnan Halim, Kiyoko F. Aoki-Kinoshita, Alexey I. Nesvizhskii, Carolyn R. Bertozzi, Hans H. Wandall, Benjamin L. Parker, Morten Thaysen-Andersen, Nichollas E. Scott
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)
Article
Chemistry, Analytical
Wei Zhang, Ling Wang, Dan Li, Douglas H. Campbell, Bradley J. Walsh, Nicolle H. Packer, Qing Dong, Erkang Wang, Yuling Wang
Summary: Circulating sEVs derived from PDAC cells have potential applications in cancer diagnosis. The phenotype of sEVs is closely associated with the presence and progression of PDAC, and can be validated through various imaging techniques. The proposed SERS assay enables simultaneous detection of multiple surface membrane proteins on sEVs, providing a potential method for PDAC diagnosis and early cancer stage prediction.
ANALYTICAL METHODS
(2022)
Article
Biochemistry & Molecular Biology
Zeynep Sumer-Bayraktar, Christopher M. Fife, Frances L. Byrne, Maria Kavallaris, Nicolle H. Packer
Summary: This study provides a comprehensive protein glycome profiling of neuroblastoma cells with varying invasiveness and migratory potential, and reveals distinct membrane glycan features of cells grown under 2D vs 3D culture conditions.
Article
Biochemistry & Molecular Biology
Edward S. X. Moh, Krishnatej Nishtala, Sameera Iqbal, Vasiliki Staikopoulos, Dilip Kapur, Mark R. Hutchinson, Nicolle H. Packer
Summary: The use of opioids for persistent pain treatment has increased, but it has not improved pain management outcomes. This study investigated the molecular mechanisms of opioids by analyzing proteomics and multiglycomics of cerebral spinal fluid samples from patients receiving long-term intrathecal morphine or baclofen. The study found significant differences in polysialic acid, heparan sulfate glycosaminoglycan, and O-glycan profiles between the two treatment groups, revealing previously undescribed molecular effects of opioid administration and pain management.