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Current Glycoproteomics: Theory, Methods and Applications

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 27162

Special Issue Editors


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Guest Editor
Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud University Medical Center Geert Grooteplein Zuid 10, 6525 GA Nijmegen, The Netherlands
Interests: protein glycosylation; mitochondrial disease; proteoforms; proteomics; mass spectrometry; ion mobility
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Guest Editor
Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Univesità Cattolica del Sacro Cuore, 00168 Rome, Italy
Interests: hydrogen sulfide; metabolomics; mitochondrial biochemistry; neurodegenerative diseases; oxidative stress; proteomics; PTMs; redox dysregulation; sulfur species
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein glycosylation is a key mediator of protein biology and a major contributor to protein diversity in bacteria, archaea and eukaryota. Glycoprotein characterization by mass spectrometry has become a powerful tool to elucidate glycan structures on proteins and to investigate alterations in the glycosylation status of proteins in response to cellular changes. Aberrant protein glycosylation has been linked to various genetic and acquired human diseases which provides exciting opportunities for biomarker applications and rationale treatment strategies that modulate protein glycosylation. The glycosylation status of (poly)peptides are also important in industrial processes since protein glycosylation may impact a.o. production yields, functionality and stability of manufactured biologics (e.g. antibodies and glycoprotein conjugates), or trigger immunological responses following food intake or drug administration. Comprehensive analytical characterization of glycoproteins is therefore of great interest in (glyco)biology, healthcare and biotechnology.

Recent developments in mass-spectrometry-based glycoproteomics have enabled in-depth characterization of the glycan micro-heterogeneity (different glycan structures on a singly glycosylation site) and macro-heterogeneity (different combinations of glycan structures on a single protein molecule) for proteins in both simple and complex matrices such as biologics and blood plasma, respectively. Understanding the advantages and limitations of current mass spectrometry methods to characterize glycoproteins is essential to maximize the potential of glycoproteomics to support biological research, advance healthcare applications, and support industrial processes.

This special issue aims to provide essential background information and application examples to both glycoproteomics scientists and non-experts. We look for manuscripts to cover glycobiology, glycoproteomics technology and glycoproteomics applications in biological research, healthcare and industry. Both review and article manuscript types are welcomed that focus on any of the topics listed below. Please note that we will also accept manuscripts that make use of available (published) data to illustrate technological aspects and applications for educative purposes.

Main topics of this special issue include, but are not limited to:

Glycobiology

  • N- and O-glycosylation pathways and associated processes in human and other species (e.g. glycoprotein trafficking, glycoprotein export mechanisms, and sugar metabolism)
  • Protein glycosylation in health and disease
  • Glycoengineering

Glycoproteomics technology

  • Glycoproteomics strategies: top-down/middle-down/bottom-up workflows*
  • Sample preparation techniques
  • Analytical separation technologies (e.g. liquid chromatography and capillary electrophoresis)
  • ESI and MALDI of glycoproteins and glycopeptides
  • Analysis of glycopeptides and glycoproteins by mass spectrometry
  • Glycopeptide and glycoprotein characterization by complementary techniques (in relationship with mass spectrometry) such as ion mobility spectrometry or infrared ion spectroscopy
  • Gas phase fragmentation techniques and mechanisms
  • Interpretation of gas phase fragmentation data
  • Computational approaches to (pre-)process and analyze glycoproteomics MSn data 
  • Bioinformatics to summarize, visualize, and interpret glycoproteomics results
  • Methods to model analytical parameters of glyco(poly)peptides (e.g. chromatographic retention time, collisional cross section/ion mobility, ionization efficiency)

Glycoproteomics applications

  • Analysis of glycoproteins or glycoproteomes in health and disease
  • Biomarker discovery
  • Characterization/ QC of biologics (e.g. glycoprotein conjugates, antibodies and antibody drug conjugates)

* Note: Only approaches that use released glycan analysis to characterize purified glycoproteins will be accepted as this special issue specifically targets glycoprotein analysis in which glycan information is linked to its respective peptide- or protein-moiety.

Dr. Hans J.C.T. Wessels
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Published Papers (5 papers)

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Research

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21 pages, 3461 KiB  
Article
Monitoring Human Milk β-Casein Phosphorylation and O-Glycosylation Over Lactation Reveals Distinct Differences between the Proteome and Endogenous Peptidome
by Kelly A. Dingess, Inge Gazi, Henk W. P. van den Toorn, Marko Mank, Bernd Stahl, Karli R. Reiding and Albert J. R. Heck
Int. J. Mol. Sci. 2021, 22(15), 8140; https://doi.org/10.3390/ijms22158140 - 29 Jul 2021
Cited by 23 | Viewed by 6922
Abstract
Human milk is a vital biofluid containing a myriad of molecular components to ensure an infant’s best start at a healthy life. One key component of human milk is β-casein, a protein which is not only a structural constituent of casein micelles but [...] Read more.
Human milk is a vital biofluid containing a myriad of molecular components to ensure an infant’s best start at a healthy life. One key component of human milk is β-casein, a protein which is not only a structural constituent of casein micelles but also a source of bioactive, often antimicrobial, peptides contributing to milk’s endogenous peptidome. Importantly, post-translational modifications (PTMs) like phosphorylation and glycosylation typically affect the function of proteins and peptides; however, here our understanding of β-casein is critically limited. To uncover the scope of proteoforms and endogenous peptidoforms we utilized mass spectrometry (LC-MS/MS) to achieve in-depth longitudinal profiling of β-casein from human milk, studying two donors across 16 weeks of lactation. We not only observed changes in β-casein’s known protein and endogenous peptide phosphorylation, but also in previously unexplored O-glycosylation. This newly discovered PTM of β-casein may be important as it resides on known β-casein-derived antimicrobial peptide sequences. Full article
(This article belongs to the Special Issue Current Glycoproteomics: Theory, Methods and Applications)
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15 pages, 2584 KiB  
Article
Oxonium Ion Guided Analysis of Quantitative Proteomics Data Reveals Site-Specific O-Glycosylation of Anterior Gradient Protein 2 (AGR2)
by Martina Pirro, Yassene Mohammed, Arnoud H. de Ru, George M. C. Janssen, Rayman T. N. Tjokrodirijo, Katarina Madunić, Manfred Wuhrer, Peter A. van Veelen and Paul J. Hensbergen
Int. J. Mol. Sci. 2021, 22(10), 5369; https://doi.org/10.3390/ijms22105369 - 20 May 2021
Cited by 4 | Viewed by 3376
Abstract
Developments in mass spectrometry (MS)-based analyses of glycoproteins have been important to study changes in glycosylation related to disease. Recently, the characteristic pattern of oxonium ions in glycopeptide fragmentation spectra had been used to assign different sets of glycopeptides. In particular, this was [...] Read more.
Developments in mass spectrometry (MS)-based analyses of glycoproteins have been important to study changes in glycosylation related to disease. Recently, the characteristic pattern of oxonium ions in glycopeptide fragmentation spectra had been used to assign different sets of glycopeptides. In particular, this was helpful to discriminate between O-GalNAc and O-GlcNAc. Here, we thought to investigate how such information can be used to examine quantitative proteomics data. For this purpose, we used tandem mass tag (TMT)-labeled samples from total cell lysates and secreted proteins from three different colorectal cancer cell lines. Following automated glycopeptide assignment (Byonic) and evaluation of the presence and relative intensity of oxonium ions, we observed that, in particular, the ratio of the ions at m/z 144.066 and 138.055, respectively, could be used to discriminate between O-GlcNAcylated and O-GalNAcylated peptides, with concomitant relative quantification between the different cell lines. Among the O-GalNAcylated proteins, we also observed anterior gradient protein 2 (AGR2), a protein which glycosylation site and status was hitherto not well documented. Using a combination of multiple fragmentation methods, we then not only assigned the site of modification, but also showed different glycosylation between intracellular (ER-resident) and secreted AGR2. Overall, our study shows the potential of broad application of the use of the relative intensities of oxonium ions for the confident assignment of glycopeptides, even in complex proteomics datasets. Full article
(This article belongs to the Special Issue Current Glycoproteomics: Theory, Methods and Applications)
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16 pages, 2551 KiB  
Article
Dissecting Total Plasma and Protein-Specific Glycosylation Profiles in Congenital Disorders of Glycosylation
by Agnes L. Hipgrave Ederveen, Noortje de Haan, Melissa Baerenfaenger, Dirk J. Lefeber and Manfred Wuhrer
Int. J. Mol. Sci. 2020, 21(20), 7635; https://doi.org/10.3390/ijms21207635 - 15 Oct 2020
Cited by 17 | Viewed by 3913
Abstract
Protein N-glycosylation is a multifactorial process involved in many biological processes. A broad range of congenital disorders of glycosylation (CDGs) have been described that feature defects in protein N-glycan biosynthesis. Here, we present insights into the disrupted N-glycosylation of various [...] Read more.
Protein N-glycosylation is a multifactorial process involved in many biological processes. A broad range of congenital disorders of glycosylation (CDGs) have been described that feature defects in protein N-glycan biosynthesis. Here, we present insights into the disrupted N-glycosylation of various CDG patients exhibiting defects in the transport of nucleotide sugars, Golgi glycosylation or Golgi trafficking. We studied enzymatically released N-glycans of total plasma proteins and affinity purified immunoglobulin G (IgG) from patients and healthy controls using mass spectrometry (MS). The applied method allowed the differentiation of sialic acid linkage isomers via their derivatization. Furthermore, protein-specific glycan profiles were quantified for transferrin and IgG Fc using electrospray ionization MS of intact proteins and glycopeptides, respectively. Next to the previously described glycomic effects, we report unprecedented sialic linkage-specific effects. Defects in proteins involved in Golgi trafficking (COG5-CDG) and CMP-sialic acid transport (SLC35A1-CDG) resulted in lower levels of sialylated structures on plasma proteins as compared to healthy controls. Findings for these specific CDGs include a more pronounced effect for α2,3-sialylation than for α2,6-sialylation. The diverse abnormalities in glycomic features described in this study reflect the broad range of biological mechanisms that influence protein glycosylation. Full article
(This article belongs to the Special Issue Current Glycoproteomics: Theory, Methods and Applications)
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Review

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29 pages, 2652 KiB  
Review
Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics
by Xing Li, Zhijue Xu, Xiaokun Hong, Yan Zhang and Xia Zou
Int. J. Mol. Sci. 2020, 21(18), 6727; https://doi.org/10.3390/ijms21186727 - 14 Sep 2020
Cited by 19 | Viewed by 5296
Abstract
Glycosylation plays critical roles in various biological processes and is closely related to diseases. Deciphering the glycocode in diverse cells and tissues offers opportunities to develop new disease biomarkers and more effective recombinant therapeutics. In the past few decades, with the development of [...] Read more.
Glycosylation plays critical roles in various biological processes and is closely related to diseases. Deciphering the glycocode in diverse cells and tissues offers opportunities to develop new disease biomarkers and more effective recombinant therapeutics. In the past few decades, with the development of glycobiology, glycomics, and glycoproteomics technologies, a large amount of glycoscience data has been generated. Subsequently, a number of glycobiology databases covering glycan structure, the glycosylation sites, the protein scaffolds, and related glycogenes have been developed to store, analyze, and integrate these data. However, these databases and tools are not well known or widely used by the public, including clinicians and other researchers who are not in the field of glycobiology, but are interested in glycoproteins. In this study, the representative databases of glycan structure, glycoprotein, glycan–protein interactions, glycogenes, and the newly developed bioinformatic tools and integrated portal for glycoproteomics are reviewed. We hope this overview could assist readers in searching for information on glycoproteins of interest, and promote further clinical application of glycobiology. Full article
(This article belongs to the Special Issue Current Glycoproteomics: Theory, Methods and Applications)
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29 pages, 2311 KiB  
Review
Sugary Logistics Gone Wrong: Membrane Trafficking and Congenital Disorders of Glycosylation
by Peter T. A. Linders, Ella Peters, Martin ter Beest, Dirk J. Lefeber and Geert van den Bogaart
Int. J. Mol. Sci. 2020, 21(13), 4654; https://doi.org/10.3390/ijms21134654 - 30 Jun 2020
Cited by 22 | Viewed by 6258
Abstract
Glycosylation is an important post-translational modification for both intracellular and secreted proteins. For glycosylation to occur, cargo must be transported after synthesis through the different compartments of the Golgi apparatus where distinct monosaccharides are sequentially bound and trimmed, resulting in increasingly complex branched [...] Read more.
Glycosylation is an important post-translational modification for both intracellular and secreted proteins. For glycosylation to occur, cargo must be transported after synthesis through the different compartments of the Golgi apparatus where distinct monosaccharides are sequentially bound and trimmed, resulting in increasingly complex branched glycan structures. Of utmost importance for this process is the intraorganellar environment of the Golgi. Each Golgi compartment has a distinct pH, which is maintained by the vacuolar H+-ATPase (V-ATPase). Moreover, tethering factors such as Golgins and the conserved oligomeric Golgi (COG) complex, in concert with coatomer (COPI) and soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-mediated membrane fusion, efficiently deliver glycosylation enzymes to the right Golgi compartment. Together, these factors maintain intra-Golgi trafficking of proteins involved in glycosylation and thereby enable proper glycosylation. However, pathogenic mutations in these factors can cause defective glycosylation and lead to diseases with a wide variety of symptoms such as liver dysfunction and skin and bone disorders. Collectively, this group of disorders is known as congenital disorders of glycosylation (CDG). Recent technological advances have enabled the robust identification of novel CDGs related to membrane trafficking components. In this review, we highlight differences and similarities between membrane trafficking-related CDGs. Full article
(This article belongs to the Special Issue Current Glycoproteomics: Theory, Methods and Applications)
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