1
|
Aryal RP, Noel M, Zeng J, Matsumoto Y, Sinard R, Waki H, Erger F, Reusch B, Beck BB, Cummings RD. Cosmc regulates O-glycan extension in murine hepatocytes. Glycobiology 2024; 34:cwae069. [PMID: 39216105 PMCID: PMC11398974 DOI: 10.1093/glycob/cwae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/20/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024] Open
Abstract
Hepatocytes synthesize a vast number of glycoproteins found in their membranes and secretions, many of which contain O-glycans linked to Ser/Thr residues. As the functions and distribution of O-glycans on hepatocyte-derived membrane glycoproteins and blood glycoproteins are not well understood, we generated mice with a targeted deletion of Cosmc (C1Galt1c1) in hepatocytes. Liver glycoproteins in WT mice express typical sialylated core 1 O-glycans (T antigen/CD176) (Galβ1-3GalNAcα1-O-Ser/Thr), whereas the Cosmc knockout hepatocytes (HEP-Cosmc-KO) lack extended O-glycans and express the Tn antigen (CD175) (GalNAcα1-O-Ser/Thr). Tn-containing glycoproteins occur in the sera of HEP-Cosmc-KO mice but not in WT mice. The LDL-receptor (LDLR), a well-studied O-glycosylated glycoprotein in hepatocytes, behaves as a ∼145kD glycoprotein in WT liver lysates, whereas it is reduced to ∼120 kDa in lysates from HEP-Cosmc-KO mice. Interestingly, the expression of the LDLR, as well as HMG-CoA reductase, which is typically altered in response to dysregulated cholesterol metabolism, are similar between WT and HEP-Cosmc-KO mice, indicating no significant effect by Cosmc deletion on either LDLR stability or cholesterol metabolism. Consistent with this, we observed no detectable phenotype in the HEP-Cosmc-KO mice regarding development, appearance or aging compared to WT. These results provide surprising, novel information about the pathway of O-glycosylation in the liver.
Collapse
Affiliation(s)
- Rajindra P Aryal
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, United States
| | - Maxence Noel
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, United States
| | - Junwei Zeng
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, United States
| | - Yasuyuki Matsumoto
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, United States
| | - Rachael Sinard
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, United States
| | - Hannah Waki
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, United States
| | - Florian Erger
- Institute of Human Genetics, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpenerstr. 34, Cologne 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, Cologne 50931, Germany
| | - Björn Reusch
- Institute of Human Genetics, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpenerstr. 34, Cologne 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, Cologne 50931, Germany
| | - Bodo B Beck
- Institute of Human Genetics, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpenerstr. 34, Cologne 50931, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch-Str. 21, Cologne 50931, Germany
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, United States
| |
Collapse
|
2
|
Ortega-Rodriguez U, Bettinger JQ, Zou G, Falkowski VM, Lehtimaki M, Matthews AM, Biel TG, Pritts JD, Wu WW, Shen RF, Agarabi C, Rao VA, Xie H, Ju T. A chemoenzymatic method for simultaneous profiling N- and O-glycans on glycoproteins using one-pot format. CELL REPORTS METHODS 2024; 4:100834. [PMID: 39116882 PMCID: PMC11384086 DOI: 10.1016/j.crmeth.2024.100834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 05/10/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
Glycosylation is generally characterized and controlled as a critical quality attribute for therapeutic glycoproteins because glycans can impact protein drug-product efficacy, half-life, stability, and safety. Analytical procedures to characterize N-glycans are relatively well established, but the characterization of O-glycans is challenging due to the complex workflows and lack of enzymatic tools. Here, we present a simplified chemoenzymatic method to simultaneously profile N- and O-glycans from the same sample using a one-pot format by mass spectrometry (MS). N-glycans were first released by PNGase F, followed by O-glycopeptide generation by proteinase K, selective N-glycan reduction, and O-glycan release by β-elimination during permethylation of both N- and O-glycans. Glycan structural assignments and determination of N- to O-glycan ratio was obtained from the one-pot mass spectra. The streamlined, one-pot method is a reliable approach that will facilitate advanced characterizations for quality assessments of therapeutic glycoproteins.
Collapse
Affiliation(s)
- Uriel Ortega-Rodriguez
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - John Q Bettinger
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Guozhang Zou
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Vincent M Falkowski
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Mari Lehtimaki
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Alicia M Matthews
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Thomas G Biel
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Jordan D Pritts
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Wells W Wu
- Facility for Biotechnology Resources, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Cyrus Agarabi
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - V Ashutosh Rao
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Hang Xie
- Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Tongzhong Ju
- Office of Biotechnology Products, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA.
| |
Collapse
|
3
|
Willems P, Sterck L, Dard A, Huang J, De Smet I, Gevaert K, Van Breusegem F. The Plant PTM Viewer 2.0: in-depth exploration of plant protein modification landscapes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4611-4624. [PMID: 38872385 DOI: 10.1093/jxb/erae270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/13/2024] [Indexed: 06/15/2024]
Abstract
Post-translational modifications (PTMs) greatly increase protein diversity and functionality. To help the plant research community interpret the ever-increasing number of reported PTMs, the Plant PTM Viewer (https://www.psb.ugent.be/PlantPTMViewer) provides an intuitive overview of plant protein PTMs and the tools to assess it. This update includes 62 novel PTM profiling studies, adding a total of 112 000 modified peptides reporting plant PTMs, including 14 additional PTM types and three species (moss, tomato, and soybean). Furthermore, an open modification re-analysis of a large-scale Arabidopsis thaliana mass spectrometry tissue atlas identified previously uncharted landscapes of lysine acylations predominant in seed and flower tissues and 3-phosphoglycerylation on glycolytic enzymes in plants. An extra 'Protein list analysis' tool was developed for retrieval and assessing the enrichment of PTMs in a protein list of interest. We conducted a protein list analysis on nuclear proteins, revealing a substantial number of redox modifications in the nucleus, confirming previous assumptions regarding the redox regulation of transcription. We encourage the plant research community to use PTM Viewer 2.0 for hypothesis testing and new target discovery, and also to submit new data to expand the coverage of conditions, plant species, and PTM types, thereby enriching our understanding of plant biology.
Collapse
Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Avilien Dard
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jingjing Huang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, 9052 Ghent, Belgium
- VIB Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| |
Collapse
|
4
|
Klein J, Carvalho L, Zaia J. Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity. Nat Commun 2024; 15:6168. [PMID: 39039063 PMCID: PMC11263600 DOI: 10.1038/s41467-024-50338-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/08/2024] [Indexed: 07/24/2024] Open
Abstract
Accurate glycopeptide identification in mass spectrometry-based glycoproteomics is a challenging problem at scale. Recent innovation has been made in increasing the scope and accuracy of glycopeptide identifications, with more precise uncertainty estimates for each part of the structure. We present a dynamically adapting relative retention time model for detecting and correcting ambiguous glycan assignments that are difficult to detect from fragmentation alone, a layered approach to glycopeptide fragmentation modeling that improves N-glycopeptide identification in samples without compromising identification quality, and a site-specific method to increase the depth of the glycoproteome confidently identifiable even further. We demonstrate our techniques on a set of previously published datasets, showing the performance gains at each stage of optimization. These techniques are provided in the open-source glycomics and glycoproteomics platform GlycReSoft available at https://github.com/mobiusklein/glycresoft .
Collapse
Affiliation(s)
- Joshua Klein
- Program for Bioinformatics, Boston University, Boston, MA, US.
| | - Luis Carvalho
- Program for Bioinformatics, Boston University, Boston, MA, US
- Department of Math and Statistics, Boston University, Boston, MA, US
| | - Joseph Zaia
- Program for Bioinformatics, Boston University, Boston, MA, US.
- Department of Biochemistry and Cell Biology, Boston University, Boston, MA, US.
| |
Collapse
|
5
|
Yue S, Wang X, Wang L, Li J, Zhou Y, Chen Y, Zhou Z, Yang X, Shi X, Gao S, Wen Z, Zhu X, Wang Y, Yang S. MOTAI: A Novel Method for the Study of O-GalNAcylation and Complex O-Glycosylation in Cancer. Anal Chem 2024; 96:11137-11145. [PMID: 38953491 PMCID: PMC11257061 DOI: 10.1021/acs.analchem.3c05018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024]
Abstract
The Tn antigen, an immature truncated O-glycosylation, is a promising biomarker for cancer detection and diagnosis. However, reliable methods for analyzing O-GalNAcylation and complex O-glycosylation are lacking. Here, we develop a novel method, MOTAI, for the sequential analysis of O-glycosylation using different O-glycoproteases. MOTAI conjugates glycopeptides on a solid support and releases different types of O-glycosylation through sequential enzymatic digestion by O-glycoproteases, including OpeRATOR and IMPa. Because OpeRATOR has less activity on O-GalNAcylation, MOTAI enriches O-GalNAcylation for subsequent analysis. We demonstrate the effectiveness of MOTAI by analyzing fetuin O-glycosylation and Jurkat cell lines. We then apply MOTAI to analyze colorectal cancer and benign colorectal polyps. We identify 32 Tn/sTn-glycoproteins and 43 T/sT-glycoproteins that are significantly increased in tumor tissues. Gene Ontology analysis reveals that most of these proteins are ECM proteins involved in the adhesion process of the intercellular matrix. Additionally, the protein disulfide isomerase CRELD2 has a significant difference in Tn expression, and the abnormally glycosylated T345 and S349 O-glycosylation sites in cancer group samples may promote the secretion of CRELD2 and ultimately tumorigenesis through ECM reshaping. In summary, MOTAI provides a powerful new tool for the in-depth analysis of O-GalNAcylation and complex O-glycosylation. It also reveals the upregulation of Tn/sTn-glycoproteins in colorectal cancer, which may provide new insights into cancer biology and biomarker discovery.
Collapse
Affiliation(s)
- Shuang Yue
- Center
for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Xiaotong Wang
- Department
of Hepatology and Gastroenterology, The
Affiliated Infectious Hospital of Soochow University, Suzhou 215004, China
| | - Lei Wang
- Protein
Metrics LLC, Room 201-01,
Building A, Novasiot, 58 Xiangke Road, Zhangjiang, Shanghai 201203, China
| | - Jiajia Li
- Center
for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Yufeng Zhou
- Center
for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Yan Chen
- Center
for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
| | - Zeyang Zhou
- Department
of General Surgery, The Second Affiliated
Hospital of Soochow University, Suzhou 215004, China
| | - Xiaodong Yang
- Department
of General Surgery, The Second Affiliated
Hospital of Soochow University, Suzhou 215004, China
| | - Xiaofeng Shi
- New
England Biolabs, Inc., 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Song Gao
- Jiangsu Key
Laboratory of Marine Biological Resources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhongmin Wen
- Health
Management Center, The Second Affiliated
Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Xiaojun Zhu
- Health
Management Center, The Second Affiliated
Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Yan Wang
- Mass
Spectrometry Facility, National Institute of Dental and Craniofacial
Research, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Shuang Yang
- Center
for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Jiangsu, 215123, China
- Health
Management Center, The Second Affiliated
Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| |
Collapse
|
6
|
Chongsaritsinsuk J, Rangel-Angarita V, Mahoney KE, Lucas TM, Enny OM, Katemauswa M, Malaker SA. Quantification and site-specific analysis of co-occupied N- and O-glycopeptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602348. [PMID: 39005468 PMCID: PMC11245114 DOI: 10.1101/2024.07.06.602348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Protein glycosylation is a complex post-translational modification that is generally classified as N- or O-linked. Site-specific analysis of glycopeptides is accomplished with a variety of fragmentation methods, depending on the type of glycosylation being investigated and the instrumentation available. For instance, collisional dissociation methods are frequently used for N-glycoproteomic analysis with the assumption that one N-sequon exists per tryptic peptide. Alternatively, electron-based methods are indispensable for O-glycosite localization. However, the presence of simultaneously N- and O-glycosylated peptides could suggest the necessity of electron-based fragmentation methods for N-glycoproteomics, which is not commonly performed. Thus, we quantified the prevalence of N- and O-glycopeptides in mucins and other glycoproteins. A much higher frequency of co-occupancy within mucins was detected whereas only a negligible occurrence occurred within non-mucin glycoproteins. This was demonstrated from analyses of recombinant and/or purified proteins, as well as more complex samples. Where co-occupancy occurred, O-glycosites were frequently localized to the Ser/Thr within the N-sequon. Additionally, we found that O-glycans in close proximity to the occupied Asn were predominantly unelaborated core 1 structures, while those further away were more extended. Overall, we demonstrate electron-based methods are required for robust site-specific analysis of mucins, wherein co-occupancy is more prevalent. Conversely, collisional methods are generally sufficient for analyses of other types of glycoproteins.
Collapse
|
7
|
Tkalec KI, Hayes AJ, Lim KS, Lewis JM, Davies MR, Scott NE. Glycan-Tailored Glycoproteomic Analysis Reveals Serine is the Sole Residue Subjected to O-Linked Glycosylation in Acinetobacter baumannii. J Proteome Res 2024; 23:2474-2494. [PMID: 38850255 DOI: 10.1021/acs.jproteome.4c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
Protein glycosylation is a ubiquitous process observed across all domains of life. Within the human pathogen Acinetobacter baumannii, O-linked glycosylation is required for virulence; however, the targets and conservation of glycosylation events remain poorly defined. In this work, we expand our understanding of the breadth and site specificity of glycosylation within A. baumannii by demonstrating the value of strain specific glycan electron-transfer/higher-energy collision dissociation (EThcD) triggering for bacterial glycoproteomics. By coupling tailored EThcD-triggering regimes to complementary glycopeptide enrichment approaches, we assessed the observable glycoproteome of three A. baumannii strains (ATCC19606, BAL062, and D1279779). Combining glycopeptide enrichment techniques including ion mobility (FAIMS), metal oxide affinity chromatography (titanium dioxide), and hydrophilic interaction liquid chromatography (ZIC-HILIC), as well as the use of multiple proteases (trypsin, GluC, pepsin, and thermolysis), we expand the known A. baumannii glycoproteome to 33 unique glycoproteins containing 42 glycosylation sites. We demonstrate that serine is the sole residue subjected to glycosylation with the substitution of serine for threonine abolishing glycosylation in model glycoproteins. An A. baumannii pan-genome built from 576 reference genomes identified that serine glycosylation sites are highly conserved. Combined this work expands our knowledge of the conservation and site specificity of A. baumannii O-linked glycosylation.
Collapse
Affiliation(s)
- Kristian I Tkalec
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Andrew J Hayes
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Kataleen S Lim
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jessica M Lewis
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Mark R Davies
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| |
Collapse
|
8
|
DeBono NJ, Moh ESX, Packer NH. Experimentally Determined Diagnostic Ions for Identification of Peptide Glycotopes. J Proteome Res 2024; 23:2661-2673. [PMID: 38888225 DOI: 10.1021/acs.jproteome.3c00858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
The analysis of the structures of glycans present on glycoproteins is an essential component for determining glycoprotein function; however, detailed glycan structural assignment on glycopeptides from proteomics mass spectrometric data remains challenging. Glycoproteomic analysis by mass spectrometry currently can provide significant, yet incomplete, information about the glycans present, including the glycan monosaccharide composition and in some circumstances the site(s) of glycosylation. Advancements in mass spectrometric resolution, using high-mass accuracy instrumentation and tailored MS/MS fragmentation parameters, coupled with a dedicated definition of diagnostic fragmentation ions have enabled the determination of some glycan structural features, or glycotopes, expressed on glycopeptides. Here we present a collation of diagnostic glycan fragments produced by traditional positive-ion-mode reversed-phase LC-ESI MS/MS proteomic workflows and describe the specific fragmentation energy settings required to identify specific glycotopes presented on N- or O-linked glycopeptides in a typical proteomics MS/MS experiment.
Collapse
Affiliation(s)
- Nicholas J DeBono
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Edward S X Moh
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Nicolle H Packer
- ARC Centre of Excellence in Synthetic Biology, School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
9
|
Mahoney KE, Malaker SA. Analysis of Mucin-Domain Glycoproteins Using Mass Spectrometry. Curr Protoc 2024; 4:e1100. [PMID: 38984456 PMCID: PMC11239139 DOI: 10.1002/cpz1.1100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Mucin-domain glycoproteins are characterized by their high density of glycosylated serine and threonine residues, which complicates their analysis by mass spectrometry. The dense glycosylation renders the protein backbone inaccessible to workhorse proteases like trypsin, the vast heterogeneity of glycosylation often results in ion suppression from unmodified peptides, and search algorithms struggle to confidently analyze and site-localize O-glycosites. We have made a number of advances to address these challenges, rendering mucinomics possible for the first time. Here, we summarize these contributions and provide a detailed protocol for mass spectrometric analysis of mucin-domain glycoproteins. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Enrichment of mucin-domain glycoproteins Basic Protocol 2: Enzymatic digestion of mucin-domain glycoprotein(s) Basic Protocol 3: Mass spectrometry data collection for O-glycopeptides Basic Protocol 4: Mass spectrometry data analysis of O-glycopeptides.
Collapse
|
10
|
Polasky DA, Lu L, Yu F, Li K, Shortreed MR, Smith LM, Nesvizhskii AI. Quantitative proteome-wide O-glycoproteomics analysis with FragPipe. Anal Bioanal Chem 2024:10.1007/s00216-024-05382-x. [PMID: 38877149 DOI: 10.1007/s00216-024-05382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/20/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
Abstract
Identification of O-glycopeptides from tandem mass spectrometry data is complicated by the near complete dissociation of O-glycans from the peptide during collisional activation and by the combinatorial explosion of possible glycoforms when glycans are retained intact in electron-based activation. The recent O-Pair search method provides an elegant solution to these problems, using a collisional activation scan to identify the peptide sequence and total glycan mass, and a follow-up electron-based activation scan to localize the glycosite(s) using a graph-based algorithm in a reduced search space. Our previous O-glycoproteomics methods with MSFragger-Glyco allowed for extremely fast and sensitive identification of O-glycopeptides from collisional activation data but had limited support for site localization of glycans and quantification of glycopeptides. Here, we report an improved pipeline for O-glycoproteomics analysis that provides proteome-wide, site-specific, quantitative results by incorporating the O-Pair method as a module within FragPipe. In addition to improved search speed and sensitivity, we add flexible options for oxonium ion-based filtering of glycans and support for a variety of MS acquisition methods and provide a comparison between all software tools currently capable of O-glycosite localization in proteome-wide searches.
Collapse
Affiliation(s)
- Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Lei Lu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Pharmaceutical Chemistry, University of San Francisco, San Francisco, CA, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kai Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | | | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
11
|
Baerenfaenger M, Post MA, Zijlstra F, van Gool AJ, Lefeber DJ, Wessels HJCT. Maximizing Glycoproteomics Results through an Integrated Parallel Accumulation Serial Fragmentation Workflow. Anal Chem 2024; 96:8956-8964. [PMID: 38776126 PMCID: PMC11154686 DOI: 10.1021/acs.analchem.3c05874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 06/05/2024]
Abstract
Glycoproteins play important roles in numerous physiological processes and are often implicated in disease. Analysis of site-specific protein glycobiology through glycoproteomics has evolved rapidly in recent years thanks to hardware and software innovations. Particularly, the introduction of parallel accumulation serial fragmentation (PASEF) on hybrid trapped ion mobility time-of-flight mass spectrometry instruments combined deep proteome sequencing with separation of (near-)isobaric precursor ions or converging isotope envelopes through ion mobility separation. However, the reported use of PASEF in integrated glycoproteomics workflows to comprehensively capture the glycoproteome is still limited. To this end, we developed an integrated methodology using timsTOF Pro 2 to enhance N-glycopeptide identifications in complex mixtures. We systematically optimized the ion optics tuning, collision energies, mobility isolation width, and the use of dopant-enriched nitrogen gas (DEN). Thus, we obtained a marked increase in unique glycopeptide identification rates compared to standard proteomics settings, showcasing our results on a large set of glycopeptides. With short liquid chromatography gradients of 30 min, we increased the number of unique N-glycopeptide identifications in human plasma samples from around 100 identifications under standard proteomics conditions to up to 1500 with our optimized glycoproteomics approach, highlighting the need for tailored optimizations to obtain comprehensive data.
Collapse
Affiliation(s)
- Melissa Baerenfaenger
- Department
of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
- Division
of BioAnalytical Chemistry, AIMMS Amsterdam Institute of Molecular
and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam 1081 HZ, Netherlands
| | - Merel A. Post
- Department
of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Fokje Zijlstra
- Translational
Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Alain J. van Gool
- Translational
Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Dirk J. Lefeber
- Department
of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
- Translational
Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| | - Hans J. C. T. Wessels
- Translational
Metabolic Laboratory, Department of Human Genetics, Radboud University Medical Center, Nijmegen 6525 GA, Netherlands
| |
Collapse
|
12
|
Malaker SA. Glycoproteomics: Charting new territory in mass spectrometry and glycobiology. JOURNAL OF MASS SPECTROMETRY : JMS 2024; 59:e5034. [PMID: 38726698 DOI: 10.1002/jms.5034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 05/24/2024]
Abstract
Glycosylation is an incredibly common and diverse post-translational modification that contributes widely to cellular health and disease. Mass spectrometry is the premier technique to study glycoproteins; however, glycoproteomics has lagged behind traditional proteomics due to the challenges associated with studying glycosylation. For instance, glycans dissociate by collision-based fragmentation, thus necessitating electron-based fragmentation for site-localization. The vast glycan heterogeneity leads to lower overall abundance of each glycopeptide, and often, ion suppression is observed. One of the biggest issues facing glycoproteomics is the lack of reliable software for analysis, which necessitates manual validation and serves as a massive bottleneck in data processing. Here, I will discuss each of these challenges and some ways in which the field is attempting to address them, along with perspectives on how I believe we should move forward.
Collapse
Affiliation(s)
- Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| |
Collapse
|
13
|
Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
14
|
Kang T, Budhraja R, Kim J, Joshi N, Garapati K, Pandey A. Global O-glycoproteome enrichment and analysis enabled by a combinatorial enzymatic workflow. CELL REPORTS METHODS 2024; 4:100744. [PMID: 38582075 PMCID: PMC11046030 DOI: 10.1016/j.crmeth.2024.100744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/25/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024]
Abstract
A comprehensive analysis of site-specific protein O-glycosylation is hindered by the absence of a consensus O-glycosylation motif, the diversity of O-glycan structures, and the lack of a universal enzyme that cleaves attached O-glycans. Here, we report the development of a robust O-glycoproteomic workflow for analyzing complex biological samples by combining four different strategies: removal of N-glycans, complementary digestion using O-glycoprotease (IMPa) with/without another protease, glycopeptide enrichment, and mass spectrometry with fragmentation of glycopeptides using stepped collision energy. Using this workflow, we cataloged 474 O-glycopeptides on 189 O-glycosites derived from 79 O-glycoproteins from human plasma. These data revealed O-glycosylation of several abundant proteins that have not been previously reported. Because many of the proteins that contained unannotated O-glycosylation sites have been extensively studied, we wished to confirm glycosylation at these sites in a targeted fashion. Thus, we analyzed selected purified proteins (kininogen-1, fetuin-A, fibrinogen, apolipoprotein E, and plasminogen) in independent experiments and validated the previously unknown O-glycosites.
Collapse
Affiliation(s)
- Taewook Kang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Rohit Budhraja
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jinyong Kim
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Neha Joshi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Kishore Garapati
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA; Manipal Academy of Higher Education, Manipal, Karnataka 576104, India; Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA.
| |
Collapse
|
15
|
Yang Y, Fang Q. Prediction of glycopeptide fragment mass spectra by deep learning. Nat Commun 2024; 15:2448. [PMID: 38503734 PMCID: PMC10951270 DOI: 10.1038/s41467-024-46771-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/11/2024] [Indexed: 03/21/2024] Open
Abstract
Deep learning has achieved a notable success in mass spectrometry-based proteomics and is now emerging in glycoproteomics. While various deep learning models can predict fragment mass spectra of peptides with good accuracy, they cannot cope with the non-linear glycan structure in an intact glycopeptide. Herein, we present DeepGlyco, a deep learning-based approach for the prediction of fragment spectra of intact glycopeptides. Our model adopts tree-structured long-short term memory networks to process the glycan moiety and a graph neural network architecture to incorporate potential fragmentation pathways of a specific glycan structure. This feature is beneficial to model explainability and differentiation ability of glycan structural isomers. We further demonstrate that predicted spectral libraries can be used for data-independent acquisition glycoproteomics as a supplement for library completeness. We expect that this work will provide a valuable deep learning resource for glycoproteomics.
Collapse
Affiliation(s)
- Yi Yang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
| | - Qun Fang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311200, China.
- Department of Chemistry, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
16
|
Zou Y, Pronker MF, Damen JMA, Heck AJR, Reiding KR. Genotype-dependent N-glycosylation and newly exposed O-glycosylation affect plasmin-induced cleavage of histidine-rich glycoprotein (HRG). J Biol Chem 2024; 300:105683. [PMID: 38272220 PMCID: PMC10882129 DOI: 10.1016/j.jbc.2024.105683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/02/2024] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
Histidine-rich glycoprotein (HRG) is an abundant plasma protein harboring at least three N-glycosylation sites. HRG integrates many biological processes, such as coagulation, antiangiogenic activity, and pathogen clearance. Importantly, HRG is known to exhibit five genetic variants with minor allele frequencies of more than 10%. Among them, Pro204Ser can induce a fourth N-glycosylation site (Asn202). Considerable efforts have been made to reveal the biological function of HRG, whereas data on HRG glycosylation are scarcer. To close this knowledge gap, we used C18-based LC-MS/MS to study the glycosylation characteristics of six HRG samples from different sources. We used endogenous HRG purified from human plasma and compared its glycosylation to that of the recombinant HRG produced in Chinese hamster ovary cells or human embryonic kidney 293 cells, targeting distinct genotypic isoforms. In endogenous plasma HRG, every N-glycosylation site was occupied predominantly with a sialylated diantennary complex-type glycan. In contrast, in the recombinant HRGs, all glycans showed different antennarities, sialylation, and core fucosylation, as well as the presence of oligomannose glycans, LacdiNAcs, and antennary fucosylation. Furthermore, we observed two previously unreported O-glycosylation sites in HRG on residues Thr273 and Thr274. These sites together showed more than 90% glycan occupancy in all HRG samples studied. To investigate the potential relevance of HRG glycosylation, we assessed the plasmin-induced cleavage of HRG under various conditions. These analyses revealed that the sialylation of the N- and O-glycans as well as the genotype-dependent N-glycosylation significantly influenced the kinetics and specificity of plasmin-induced cleavage of HRG.
Collapse
Affiliation(s)
- Yang Zou
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Matti F Pronker
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - J Mirjam A Damen
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Karli R Reiding
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
| |
Collapse
|
17
|
Park CS, Moon C, Kim M, Kim J, Yang S, Jang L, Jang JY, Jeong CM, Lee HS, Kim DK, Kim HH. Comparison of sialylated and fucosylated N-glycans attached to Asn 6 and Asn 41 with different roles in hyaluronan and proteoglycan link protein 1 (HAPLN1). Int J Biol Macromol 2024; 260:129575. [PMID: 38246450 DOI: 10.1016/j.ijbiomac.2024.129575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
Hyaluronan and proteoglycan link protein 1 (HAPLN1) is an extracellular matrix protein stabilizing interactions between hyaluronan and proteoglycan. Although HAPLN1 is being investigated for various biological roles, its N-glycosylation is poorly understood. In this study, the structure of N-glycopeptides of trypsin-treated recombinant human HAPLN1 (rhHAPLN1) expressed from CHO cells were identified by nano-liquid chromatography-tandem mass spectrometry. A total of 66 N-glycopeptides were obtained, including 16 and 12 N-glycans at sites Asn 6 (located in the N-terminal region) and Asn 41 (located in the Ig-like domain, which interacts with proteoglycan), respectively. The quantities (%) of each N-glycan relative to the totals (100 %) at each site were calculated. Tri- and tetra-sialylation (to resist proteolysis and extend half-life) were more abundant at Asn 6, and di- (core- and terminal-) fucosylation (to increase binding affinity and stability) and sialyl-Lewis X/a epitope (a major ligand for E-selectin) were more abundant at Asn 41. These results indicate that N-glycans attached to Asn 6 (protecting HAPLN1) and Asn 41 (supporting molecular interactions) play different roles in HAPLN1. This is the first study of site-specific N-glycosylation in rhHAPLN1, which will be useful for understanding its molecular interactions in the extracellular matrix.
Collapse
Affiliation(s)
- Chi Soo Park
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chulmin Moon
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Mirae Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Jieun Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Subin Yang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Leeseul Jang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ji Yeon Jang
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Chang Myeong Jeong
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Han Seul Lee
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Dae Kyong Kim
- Department of Environmental & Health Chemistry, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Ha Hyung Kim
- Biotherapeutics and Glycomics Laboratory, College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea.
| |
Collapse
|
18
|
Helms A, Brodbelt JS. Mass Spectrometry Strategies for O-Glycoproteomics. Cells 2024; 13:394. [PMID: 38474358 PMCID: PMC10930906 DOI: 10.3390/cells13050394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Glycoproteomics has accelerated in recent decades owing to numerous innovations in the analytical workflow. In particular, new mass spectrometry strategies have contributed to inroads in O-glycoproteomics, a field that lags behind N-glycoproteomics due to several unique challenges associated with the complexity of O-glycosylation. This review will focus on progress in sample preparation, enrichment strategies, and MS/MS techniques for the identification and characterization of O-glycoproteins.
Collapse
Affiliation(s)
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA;
| |
Collapse
|
19
|
Hevér H, Xue A, Nagy K, Komka K, Vékey K, Drahos L, Révész Á. Can We Boost N-Glycopeptide Identification Confidence? Smart Collision Energy Choice Taking into Account Structure and Search Engine. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:333-343. [PMID: 38286027 PMCID: PMC10853973 DOI: 10.1021/jasms.3c00375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
Abstract
High confidence and reproducibility are still challenges in bottom-up mass spectrometric N-glycopeptide identification. The collision energy used in the MS/MS measurements and the database search engine used to identify the species are perhaps the two most decisive factors. We investigated how the structural features of N-glycopeptides and the choice of the search engine influence the optimal collision energy, delivering the highest identification confidence. We carried out LC-MS/MS measurements using a series of collision energies on a large set of N-glycopeptides with both the glycan and peptide part varied and studied the behavior of Byonic, pGlyco, and GlycoQuest scores. We found that search engines show a range of behavior between peptide-centric and glycan-centric, which manifests itself already in the dependence of optimal collision energy on m/z. Using classical statistical and machine learning methods, we revealed that peptide hydrophobicity, glycan and peptide masses, and the number of mobile protons also have significant and search-engine-dependent influence, as opposed to a series of other parameters we probed. We envisioned an MS/MS workflow making a smart collision energy choice based on online available features such as the hydrophobicity (described by retention time) and glycan mass (potentially available from a scout MS/MS). Our assessment suggests that this workflow can lead to a significant gain (up to 100%) in the identification confidence, particularly for low-scoring hits close to the filtering limit, which has the potential to enhance reproducibility of N-glycopeptide analyses. Data are available via MassIVE (MSV000093110).
Collapse
Affiliation(s)
- Helga Hevér
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
| | - Andrea Xue
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
| | - Kinga Nagy
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
- Faculty
of Science, Institute of Chemistry, Hevesy György PhD School
of Chemistry, Eötvös Loránd
University, Pázmány
Péter sétány 1/A, Budapest H-1117, Hungary
| | - Kinga Komka
- Department
of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Budapest H-1111, Hungary
| | - Károly Vékey
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
| | - László Drahos
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
| | - Ágnes Révész
- MS
Proteomics Research Group, HUN-REN Research
Centre for Natural Sciences, Magyar Tudósok körútja 2., Budapest H-1117, Hungary
| |
Collapse
|
20
|
Houlahan CB, Kong Y, Johnston B, Cielesh M, Chau TH, Fenwick J, Coleman PR, Hao H, Haltiwanger RS, Thaysen-Andersen M, Passam FH, Larance M. Analysis of the Healthy Platelet Proteome Identifies a New Form of Domain-Specific O-Fucosylation. Mol Cell Proteomics 2024; 23:100717. [PMID: 38237698 PMCID: PMC10879016 DOI: 10.1016/j.mcpro.2024.100717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 01/04/2024] [Accepted: 01/11/2024] [Indexed: 02/17/2024] Open
Abstract
Platelet activation induces the secretion of proteins that promote platelet aggregation and inflammation. However, detailed analysis of the released platelet proteome is hampered by platelets' tendency to preactivate during their isolation and a lack of sensitive protocols for low abundance releasate analysis. Here, we detail the most sensitive analysis to date of the platelet releasate proteome with the detection of >1300 proteins. Unbiased scanning for posttranslational modifications within releasate proteins highlighted O-glycosylation as being a major component. For the first time, we detected O-fucosylation on previously uncharacterized sites including multimerin-1 (MMRN1), a major alpha granule protein that supports platelet adhesion to collagen and is a carrier for platelet factor V. The N-terminal elastin microfibril interface (EMI) domain of MMRN1, a key site for protein-protein interaction, was O-fucosylated at a conserved threonine within a new domain context. Our data suggest that either protein O-fucosyltransferase 1, or a novel protein O-fucosyltransferase, may be responsible for this modification. Mutating this O-fucose site on the EMI domain led to a >50% reduction of MMRN1 secretion, supporting a key role of EMI O-fucosylation in MMRN1 secretion. By comparing releasates from resting and thrombin-treated platelets, 202 proteins were found to be significantly released after high-dose thrombin stimulation. Complementary quantification of the platelet lysates identified >3800 proteins, which confirmed the platelet origin of releasate proteins by anticorrelation analysis. Low-dose thrombin treatment yielded a smaller subset of significantly regulated proteins with fewer secretory pathway enzymes. The extensive platelet proteome resource provided here (larancelab.com/platelet-proteome) allows identification of novel regulatory mechanisms for drug targeting to address platelet dysfunction and thrombosis.
Collapse
Affiliation(s)
- Callum B Houlahan
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Yvonne Kong
- Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Bede Johnston
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Michelle Cielesh
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - The Huong Chau
- School of Natural Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - Jemma Fenwick
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia; Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Paul R Coleman
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Huilin Hao
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Robert S Haltiwanger
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Macquarie Park, New South Wales, Australia; Institute for Glyco-Core Research, Nagoya University, Nagoya, Aichi, Japan
| | - Freda H Passam
- The Heart Research Institute, Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia; Central Clinical School, The University of Sydney, Sydney, New South Wales, Australia.
| | - Mark Larance
- Charles Perkins Centre, School of Medical Sciences, The University of Sydney, Sydney, New South Wales, Australia.
| |
Collapse
|
21
|
Hackett WE, Chang D, Carvalho L, Zaia J. RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein composition that occur during biological processes. BIOINFORMATICS ADVANCES 2024; 4:vbae012. [PMID: 38384861 PMCID: PMC10879752 DOI: 10.1093/bioadv/vbae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/15/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
Motivation Glycosylation elaborates the structures and functions of glycoproteins; glycoproteins are common post-translationally modified proteins and are heterogeneous and non-deterministically synthesized as an evolutionarily driven mechanism that elaborates the functions of glycosylated gene products. Glycoproteins, accounting for approximately half of all proteins, require specialized proteomics data analysis methods due to micro- and macro-heterogeneities as a given glycosite can be divided into several glycosylated forms, each of which must be quantified. Sampling of heterogeneous glycopeptides is limited by mass spectrometer speed and sensitivity, resulting in missing values. In conjunction with the low sample size inherent to glycoproteomics, a specialized toolset is needed to determine if observed changes in glycopeptide abundances are biologically significant or due to data quality limitations. Results We developed an R package, Relative Assessment of m/z Identifications by Similarity (RAMZIS), that uses similarity metrics to guide researchers to a more rigorous interpretation of glycoproteomics data. RAMZIS uses a permutation test to generate contextual similarity, which assesses the quality of mass spectral data and outputs a graphical demonstration of the likelihood of finding biologically significant differences in glycosylation abundance datasets. Investigators can assess dataset quality, holistically differentiate glycosites, and identify which glycopeptides are responsible for glycosylation pattern change. RAMZIS is validated by theoretical cases and a proof-of-concept application. RAMZIS enables comparison between datasets too stochastic, small, or sparse for interpolation while acknowledging these issues in its assessment. Using this tool, researchers will be able to rigorously define the role of glycosylation and the changes that occur during biological processes. Availability and implementation https://github.com/WillHackett22/RAMZIS.
Collapse
Affiliation(s)
| | - Deborah Chang
- Department of Biochemistry, Boston University, Boston, MA 02215, United States
| | - Luis Carvalho
- Bioinformatics Program, Boston University, Boston, MA 02215, United States
- Department of Mathematics, Boston University, Boston, MA 02215, United States
| | - Joseph Zaia
- Bioinformatics Program, Boston University, Boston, MA 02215, United States
- Department of Biochemistry, Boston University, Boston, MA 02215, United States
| |
Collapse
|
22
|
Li R, Xia C, Wu S, Downs MJ, Tong H, Tursumamat N, Zaia J, Costello CE, Lin C, Wei J. Direct and Detailed Site-Specific Glycopeptide Characterization by Higher-Energy Electron-Activated Dissociation Tandem Mass Spectrometry. Anal Chem 2024; 96:1251-1258. [PMID: 38206681 PMCID: PMC10885852 DOI: 10.1021/acs.analchem.3c04484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Glycosylation is widely recognized as the most complex post-translational modification due to the widespread presence of macro- and microheterogeneities, wherein its biological consequence is closely related to both the glycosylation sites and the glycan fine structures. Yet, efficient site-specific detailed glycan characterization remains a significant analytical challenge. Here, utilizing an Orbitrap-Omnitrap platform, higher-energy electron-activated dissociation (heExD) tandem mass spectrometry (MS/MS) revealed extraordinary efficacy for the structural characterization of intact glycopeptides. HeExD produced extensive fragmentation within both the glycan and the peptide, including A-/B-/C-/Y-/Z-/X-ions from the glycan motif and a-/b-/c-/x-/y-/z-type peptide fragments (with or without the glycan). The intensity of cross-ring cleavage and backbone fragments retaining the intact glycan was highly dependent on the electron energy. Among the four electron energy levels investigated, electronic excitation dissociation (EED) provided the most comprehensive structural information, yielding a complete series of glycosidic fragments for accurate glycan topology determination, a wealth of cross-ring fragments for linkage definition, and the most extensive peptide backbone fragments for accurate peptide sequencing and glycosylation site localization. The glycan fragments observed in the EED spectrum correlated well with the fragmentation patterns observed in EED MS/MS of the released glycans. The advantages of EED over higher-energy collisional dissociation (HCD), stepped collision energy HCD (sceHCD), and electron-transfer/higher-energy collisional dissociation (EThcD) were demonstrated for the characterization of a glycopeptide bearing a biantennary disialylated glycan. EED can produce a complete peptide backbone and glycan sequence coverage even for doubly protonated precursors. The exceptional performance of heExD MS/MS, particularly EED MS/MS, in site-specific detailed glycan characterization on an Orbitrap-Omnitrap hybrid instrument presents a novel option for in-depth glycosylation analysis.
Collapse
Affiliation(s)
- Ruiqing Li
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmaceutical Sciences, National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Chaoshuang Xia
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, 670 Albany Street, Boston, Massachusetts 02118, United States
| | - Shuye Wu
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmaceutical Sciences, National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Margaret J Downs
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, 670 Albany Street, Boston, Massachusetts 02118, United States
| | - Haowei Tong
- School of Life Science, Shanghai Jiao Tong University, Shanghai, 800 Dongchuan Road, Shanghai 200240, China
| | - Nafisa Tursumamat
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmaceutical Sciences, National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, 670 Albany Street, Boston, Massachusetts 02118, United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, 670 Albany Street, Boston, Massachusetts 02118, United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University Chobanian & Avedisian School of Medicine, 670 Albany Street, Boston, Massachusetts 02118, United States
| | - Juan Wei
- Engineering Research Center of Cell & Therapeutic Antibody, Ministry of Education, School of Pharmaceutical Sciences, National Key Laboratory of Innovative Immunotherapy, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| |
Collapse
|
23
|
Mut J, Altmann S, Reising S, Meißner-Weigl J, Driessen MD, Ebert R, Seibel J. SiaNAl can be efficiently incorporated in glycoproteins of human mesenchymal stromal cells by metabolic glycoengineering. ACS Biomater Sci Eng 2024; 10:139-148. [PMID: 36946521 DOI: 10.1021/acsbiomaterials.2c01534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Metabolic glycoengineering involves the stimulation of cells with functionalized monosaccharides. Glucosamine, galactosamine, and mannosamine derivatives are commercially available, but their application may lead to undirected (i.e., chemical) incorporation into proteins. However, sialic acids are attached to the ends of complex sugar chains of glycoproteins, which might be beneficial for cell surface modification via click chemistry. Thus, we studied the incorporation of chemically synthesized unnatural alkyne modified sialic acid (SiaNAl) into glycoproteins of human telomerase-immortalized mesenchymal stromal cells (hMSC-TERT) and we show that SiaNAl can be efficiently incorporated in glycoproteins involved in signal transduction and cell junction.
Collapse
Affiliation(s)
- Jürgen Mut
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Stephan Altmann
- Department of Musculoskeletal Tissue Regeneration, University of Würzburg, Friedrich-Bergius-Ring 15, Würzburg 97076, Germany
| | - Sabine Reising
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Jutta Meißner-Weigl
- Department of Musculoskeletal Tissue Regeneration, University of Würzburg, Friedrich-Bergius-Ring 15, Würzburg 97076, Germany
| | - Marc D Driessen
- Institute for Molecular Medicine, Proteome Research, University Hospital and Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf 40225, Germany
| | - Regina Ebert
- Department of Musculoskeletal Tissue Regeneration, University of Würzburg, Friedrich-Bergius-Ring 15, Würzburg 97076, Germany
| | - Jürgen Seibel
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| |
Collapse
|
24
|
Wang J, Onigbinde S, Purba W, Nwaiwu J, Mechref Y. O-Glycoproteomics Sample Preparation and Analysis Using NanoHPLC and Tandem MS. Methods Mol Biol 2024; 2762:281-290. [PMID: 38315372 DOI: 10.1007/978-1-0716-3666-4_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Glycosylation refers to the biological processes that covalently attach carbohydrates to the peptide backbone after the synthesis of proteins. As one of the most common post-translational modifications (PTMs), glycosylation can greatly affect proteins' features and functions. Moreover, aberrant glycosylation has been linked to various diseases. There are two major types of glycosylation, known as N-linked and O-linked glycosylation. Here, we focus on O-linked glycosylation and thoroughly describe a bottom-up strategy to perform O-linked glycoproteomics studies. The experimental section involves enzymatic digestions using trypsin and O-glycoprotease at 37 °C. The prepared samples containing O-glycopeptides are analyzed using nanoHPLC coupled with tandem mass spectrometry (MS) for accurate identification and quantification.
Collapse
Affiliation(s)
- Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Waziha Purba
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Judith Nwaiwu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.
| |
Collapse
|
25
|
Luo M, Su T, Cheng Q, Zhang X, Cai F, Yin Z, Li F, Yang H, Liu F, Zhang Y. GlycoTCFM: Glycoproteomics Based on Two Complementary Fragmentation Methods Reveals Distinctive O-Glycosylation in Human Sperm and Seminal Plasma. J Proteome Res 2023; 22:3833-3842. [PMID: 37943980 DOI: 10.1021/acs.jproteome.3c00489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Human semen, consisting of spermatozoa (sperm) and seminal plasma, represents a special clinical sample type in human body fluid. Protein glycosylation in sperm and seminal plasma plays key roles in spermatogenesis, maturation, capacitation, sperm-egg recognition, motility of sperm, and fertilization. In this study, we profiled the most comprehensive O-glycoproteome map of human sperm and seminal plasma using our recently presented Glycoproteomics based on Two Complementary Fragmentation Methods (GlycoTCFM). We showed that sperm and seminal plasma contain many novel and distinctive O-glycoproteins, which are mostly located in the extracellular region (seminal plasma) and sperm membrane, enriched in the biological processes of cell adhesion and angiogenesis, and mainly involved in multiple biological functions including extracellular matrix structural constituents and binding. Based on GlycoTCFM, we created a comprehensive human sperm and seminal plasma O-glycoprotein database that contains 371 intact O-glycopeptides and 202 O-glycosites from 68 O-glycoproteins. Interestingly, 105 manually confirmed O-glycosites from 25 O-glycoproteins were reported for the first time, and they were mainly modified by core 1 O-glycans. We also found that three highly abundant, highly complex, and highly O-glycosylated proteins (semenogelin-1, semenogelin-2, and equatorin) may play important roles in sperm or seminal plasma composition and function. These data deepen our knowledge about O-glycosylation in sperm and seminal plasma and lay the foundation for the functional study of O-glycoproteins in male infertility.
Collapse
Affiliation(s)
- Mengqi Luo
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Su
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qingyuan Cheng
- Human Sperm Bank, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu 610041, China
| | - Xue Zhang
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fei Cai
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zaiwen Yin
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fuping Li
- Human Sperm Bank, Key Laboratory of Birth Defects and Related Diseases of Women and Children of Ministry of Education, West China Second University Hospital of Sichuan University, Chengdu 610041, China
| | - Hao Yang
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fang Liu
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Zhang
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
26
|
Gass DT, Cordes MS, Alberti SN, Kim HJ, Gallagher ES. Evidence of H/D Exchange within Metal-Adducted Carbohydrates after Ion/Ion-Dissociation Reactions. J Am Chem Soc 2023; 145:23972-23985. [PMID: 37874934 DOI: 10.1021/jacs.3c05793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Tandem mass spectrometry (MS/MS) using fragmentation has become one of the most effective methods for gaining sequence and structural information on biomolecules. Ion/ion reactions are competitive reactions, where either proton transfer (PT) or electron transfer (ET) can occur from interactions between multiply charged cations and singly charged anions. Utilizing ion/ion reactions with fluoranthene has offered a unique method of fragment formation for the structural elucidation of biomolecules. Fluoranthene is considered an ideal anion reagent because it selectively causes electron-transfer dissociation (ETD) and minimizes PT when interacting with peptides. However, limited investigations have sought to understand how fluoranthene─the primary, commercially available anion reagent─interacts with other biomolecules. Here, we apply deuterium labeling to investigate ion/ion reaction mechanisms between fluoranthene and divalent, metal-adducted carbohydrates (Ca2+, Mg2+, Co2+, and Ni2+). Deuterium labeling of carbohydrates allowed us to observe evidence of hydrogen/deuterium exchange (HDX) occurring after ion/ion dissociation reactions. The extent of deuterium loss is dependent on several factors, including the physical properties of the metal ion and the fragment structure. Based on the deuterium labeling data, we have proposed ETD, PTD, and intermolecular PT─also described as HDX─mechanisms. This research provides a fundamental perspective of ion/ion and ion/molecule reaction mechanisms and illustrates properties that impact ion/ion and ion/molecule reactions for carbohydrates. Together, this could improve the capability to distinguish complex and heterogeneous biomolecules, such as carbohydrates.
Collapse
Affiliation(s)
- Darren T Gass
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Michael S Cordes
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sebastian N Alberti
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - H Jamie Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| |
Collapse
|
27
|
Downs M, Curran J, Zaia J, Sethi MK. Analysis of complex proteoglycans using serial proteolysis and EThcD provides deep N- and O-glycoproteomic coverage. Anal Bioanal Chem 2023; 415:6995-7009. [PMID: 37728749 PMCID: PMC10865727 DOI: 10.1007/s00216-023-04934-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/24/2023] [Accepted: 08/28/2023] [Indexed: 09/21/2023]
Abstract
Proteoglycans are a small but diverse family of proteins that play a wide variety of roles at the cell surface and in the extracellular matrix. In addition to their glycosaminoglycan (GAG) chains, they are N- and O-glycosylated. All of these types of glycosylation are crucial to their function but present a considerable analytical challenge. We describe the combination of serial proteolysis followed by the application of higher-energy collisional dissociation (HCD) and electron transfer/higher-energy collisional dissociation (EThcD) to optimize protein sequence coverage and glycopeptide identification from proteoglycans. In many cases, the use of HCD alone allows the identification of more glycopeptides. However, the localization of glycoforms on multiply glycosylated peptides has remained elusive. We demonstrate the use of EThcD for the confident assignment of glycan compositions on multiply glycosylated peptides. Dense glycosylation on proteoglycans is key to their biological function; thus, developing tools to identify and quantify doubly glycosylated peptides is of interest. Additionally, glycoproteomics searches identify glycopeptides in otherwise poorly covered regions of proteoglycans. The development of these and other analytical tools may permit glycoproteomic similarity comparisons in biological samples.
Collapse
Affiliation(s)
- Margaret Downs
- Department of Biochemistry and Cell Biology, Center for Biomedical Mass Spectrometry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Jillian Curran
- Department of Biochemistry and Cell Biology, Center for Biomedical Mass Spectrometry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Joseph Zaia
- Department of Biochemistry and Cell Biology, Center for Biomedical Mass Spectrometry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Manveen K Sethi
- Department of Biochemistry and Cell Biology, Center for Biomedical Mass Spectrometry, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA.
| |
Collapse
|
28
|
Lin T, Chen Z, Luo M, Zhao Y, Zeng W, Zheng S, Su T, Zhong Y, Wang S, Jin Y, Hu L, Zhao W, Li J, Wang X, Wu C, Li D, Liu F, Li G, Yang H, Zhang Y. Characterization of site-specific N-glycosylation signatures of isolated uromodulin from human urine. Analyst 2023; 148:5041-5049. [PMID: 37667671 DOI: 10.1039/d3an01018j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Uromodulin (Umod, Tamm-Horsfall protein) is the most abundant urinary N-glycoprotein produced exclusively by the kidney. It can form filaments to antagonize the adhesion of uropathogens. However, the site-specific N-glycosylation signatures of Umod in healthy individuals and patients with IgA nephropathy (IgAN) remain poorly understood due to the lack of suitable isolation and analytical methods. In this study, we first presented a simple and fast method based on diatomaceous earth adsorption to isolate Umod. These isolated glycoproteins were digested by trypsin and/or Glu-C. Intact N-glycopeptides with or without HILIC enrichment were analyzed using our developed EThcD-sceHCD-MS/MS. Based on the optimized workflow, we identified a total of 780 unique intact N-glycopeptides (7 N-glycosites and 152 N-glycan compositions) from healthy individuals. As anticipated, these glycosites exhibited glycoform heterogeneity. Almost all N-glycosites were modified completely by the complex type, except for one N-glycosite (N275), which was nearly entirely occupied by the high-mannose type for mediating Umod's antiadhesive activity. Then, we compared the N-glycosylation of Umod between healthy controls (n = 9) and IgAN patients (n = 9). The N-glycosylation of Umod in IgAN patients will drastically decrease and be lost. Finally, we profiled the most comprehensive site-specific N-glycosylation map of Umod and revealed its alterations in IgAN patients. Our method provides a high-throughput workflow for characterizing the N-glycosylation of Umod, which can aid in understanding its roles in physiology and pathology, as well as serving as a potential diagnostic tool for evolution of renal tubular function.
Collapse
Affiliation(s)
- Tianhai Lin
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhuo Chen
- Transplant Center and NHC Key Lab of Transplant Engineering and Immunology, Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mengqi Luo
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Yang Zhao
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Wenjuan Zeng
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Shanshan Zheng
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Tao Su
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Yi Zhong
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Shisheng Wang
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Youmei Jin
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Liqiang Hu
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Wanjun Zhao
- Division of Thyroid Surgery, Department of General Surgery of Nursing, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiaxu Li
- School of Nursing, Chengde Medical University, Chengde, Hebei 067000, China
| | - Xuanyi Wang
- Mingde College, Zhangjiakou University, Zhangjiakou, Hebei 075000, China
| | - Changwei Wu
- Renal Department and Institute of Nephrology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 611731, China.
| | - Dapeng Li
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Fang Liu
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Guisen Li
- Renal Department and Institute of Nephrology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Sichuan Clinical Research Center for Kidney Diseases, Chengdu 611731, China.
| | - Hao Yang
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
- Transplant Center and NHC Key Lab of Transplant Engineering and Immunology, Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Zhang
- Department of Nephrology and Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
- Transplant Center and NHC Key Lab of Transplant Engineering and Immunology, Regenerative Medical Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
29
|
Söhngen C, Thomas DJ, Skowron MA, Bremmer F, Eckstein M, Stefanski A, Driessen MD, Wakileh GA, Stühler K, Altevogt P, Theodorescu D, Klapdor R, Schambach A, Nettersheim D. CD24 targeting with NK-CAR immunotherapy in testis, prostate, renal and (luminal-type) bladder cancer and identification of direct CD24 interaction partners. FEBS J 2023; 290:4864-4876. [PMID: 37254618 PMCID: PMC11129509 DOI: 10.1111/febs.16880] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/26/2023] [Accepted: 05/26/2023] [Indexed: 06/01/2023]
Abstract
Alternative therapeutic options targeting urologic malignancies, such as germ cell tumours, as well as urothelial, renal and prostate carcinomas, are still urgently needed. The membrane protein CD24 represents a promising immunotherapeutical approach. The present study aimed to decipher the molecular function of CD24 in vitro and evaluate the cytotoxic capacity of a third-generation natural killer (NK) cell chimeric antigen receptor (CAR) against CD24 in urologic tumour cell lines. Up to 20 urologic tumour cell lines and several non-malignant control cells were included. XTT viability assays and annexin V/propidium iodide flow cytometry analyses were performed to measure cell viability and apoptosis rates, respectively. Co-immunoprecipitation followed by mass spectrometry analyses identified direct interaction partners of CD24. Luciferase reporter assays were used to functionally validate transactivation of CD24 expression by SOX2. N- and O-glycosylation of CD24 were evaluated by enzymatic digestion and mass spectrometry. The study demonstrates that SOX2 transactivates CD24 expression in embryonal carcinoma cells. In cells of different urological origins, CD24 interacted with proteins involved in cell adhesion, ATP binding, phosphoprotein binding and post-translational modifications, such as histone acetylation and ubiquitination. Treatment of urological tumour cells with NK-CD24-CAR cells resulted in a decreased cell viability and apoptosis induction specifically in CD24+ tumour cells. Limitations of the study include the in vitro setting, which still has to be confirmed in vivo. In conclusion, we show that CD24 is a promising novel target for immune therapeutic approaches targeting urologic malignancies.
Collapse
Affiliation(s)
- Christian Söhngen
- Department of Urology, Urological Research Laboratory, Translational UroOncology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
| | - David J. Thomas
- Department of Urology, Urological Research Laboratory, Translational UroOncology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
| | - Margaretha A. Skowron
- Department of Urology, Urological Research Laboratory, Translational UroOncology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
| | - Felix Bremmer
- Institute of Pathology, University Medical Center Goettingen, Goettingen, Germany
| | - Markus Eckstein
- Institute of Pathology, Friedrich Alexander University Erlangen-Nürnberg, University Hospital, Erlangen, Germany
| | - Anja Stefanski
- Molecular Proteomics Laboratory, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Marc D. Driessen
- Molecular Proteomics Laboratory, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Gamal A. Wakileh
- Department of Urology, Urological Research Laboratory, Translational UroOncology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
- Department of Urology, University Hospital Ulm, Ulm, Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Peter Altevogt
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University Heidelberg, Germany
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rüdiger Klapdor
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Department of Gynecology and Obstetrics, Hannover Medical School, Hannover, Germany
- Institute for Experimental Hematology, Hannover Medical School, Hannover, Germany
| | - Daniel Nettersheim
- Department of Urology, Urological Research Laboratory, Translational UroOncology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Germany
| |
Collapse
|
30
|
Suttapitugsakul S, Matsumoto Y, Aryal RP, Cummings RD. Large-Scale and Site-Specific Mapping of the Murine Brain O-Glycoproteome with IMPa. Anal Chem 2023; 95:13423-13430. [PMID: 37624755 PMCID: PMC10501376 DOI: 10.1021/acs.analchem.3c00408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/16/2023] [Indexed: 08/27/2023]
Abstract
Altered protein glycosylation is typically associated with cognitive defects and other phenotypes, but there is a lack of knowledge about the brain glycoproteome. Here, we used the newly available O-glycoprotease IMPa from Pseudomonas aeruginosa for comprehensive O-glycoproteomic analyses of the mouse brain. In this approach, total tryptic glycopeptides were prepared, extracted, purified, and conjugated to a solid support before an enzymatic cleavage by IMPa. O-glycopeptides were analyzed by electron-transfer/higher-energy collision dissociation (EThcD), which permits site-specific and global analysis of all types of O-glycans. We developed two complementary approaches for the analysis of the total O-glycoproteome using HEK293 cells and derivatives. The results demonstrated that IMPa and EThcD facilitate the confident localization of O-glycans on glycopeptides. We then applied these approaches to characterize the O-glycoproteome of the mouse brain, which revealed the high frequency of various sialylated O-glycans along with the unusual presence of the Tn antigen. Unexpectedly, the results demonstrated that glycoproteins in the brain O-glycoproteome only partly overlap with those reported for the brain N-glycoproteome. These approaches will aid in identifying the novel O-glycoproteomes of different cells and tissues and foster clinical and translational insights into the functions of protein O-glycosylation in the brain and other organs.
Collapse
Affiliation(s)
- Suttipong Suttapitugsakul
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts 02215, United States
| | | | - Rajindra P. Aryal
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts 02215, United States
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts 02215, United States
| |
Collapse
|
31
|
DeYong AE, Trinidad JC, Pohl NLB. An identification method to distinguish monomeric sugar isomers on glycopeptides. Analyst 2023; 148:4438-4446. [PMID: 37555458 DOI: 10.1039/d3an01036h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
A one-step protocol for the automated flow synthesis of protected glycosylated amino acids is described using pumps with open-source controls in overall yields of 21-50%. The resulting glycosylated amino acids could be used directly in solid-phase peptide synthesis (SPPS) protocols to quickly produce glycopeptide standards. Access to a variety of stereoisomers of the sugar enabled the development of an LC-MS/MS protocol that can distinguish between peptides modified with carbohydrates having the same exact mass. This method could definitively identify fucose in an O-glycosylation site on the transmembrane protein, Notch1.
Collapse
Affiliation(s)
- Ashley E DeYong
- Chemistry, Indiana University, 212 S Hawthorne Dr., Bloomington, IN 47405, USA.
| | - Jonathan C Trinidad
- Chemistry, Indiana University, 212 S Hawthorne Dr., Bloomington, IN 47405, USA.
| | - Nicola L B Pohl
- Chemistry, Indiana University, 212 S Hawthorne Dr., Bloomington, IN 47405, USA.
| |
Collapse
|
32
|
Liu J, Cheng B, Fan X, Zhou X, Wang J, Zhou W, Li H, Zeng W, Yang P, Chen X. Click-iG: Simultaneous Enrichment and Profiling of Intact N-linked, O-GalNAc, and O-GlcNAcylated Glycopeptides. Angew Chem Int Ed Engl 2023; 62:e202303410. [PMID: 37431278 DOI: 10.1002/anie.202303410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/12/2023]
Abstract
Proteins are ubiquitously modified with glycans of varied chemical structures through distinct glycosidic linkages, making the landscape of protein glycosylation challenging to map. Profiling of intact glycopeptides with mass spectrometry (MS) has recently emerged as a powerful tool for revealing matched information of the glycosylation sites and attached glycans (i.e., intact glycosites), but is largely limited to individual glycosylation types. Herein, we describe Click-iG, which integrates metabolic labeling of glycans with clickable unnatural sugars, an optimized MS method, and a tailored version of pGlyco3 software to enable simultaneous enrichment and profiling of three types of intact glycopeptides: N-linked, mucin-type O-linked, and O-GlcNAcylated glycopeptides. We demonstrate the utility of Click-iG by the identification of thousands of intact glycosites in cell lines and living mice. From the mouse lung, heart, and spleen, a total of 2053 intact N-glycosites, 262 intact O-GalNAc glycosites, and 1947 O-GlcNAcylation sites were identified. Click-iG-enabled comprehensive coverage of the protein glycosylation landscape lays the foundation for interrogating crosstalk between different glycosylation pathways.
Collapse
Affiliation(s)
- Jialin Liu
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
- Institute of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xinqi Fan
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Xinyue Zhou
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Jiankun Wang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Wen Zhou
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Hengyu Li
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| | - Wenfeng Zeng
- Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS) and Institute of Computing Technology, CAS, Beijing, 100190, China
| | - Pengyuan Yang
- Institute of Biomedical Sciences and Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, and Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
| |
Collapse
|
33
|
Nagy K, Gellén G, Papp D, Schlosser G, Révész Á. Optimum collision energies for proteomics: The impact of ion mobility separation. JOURNAL OF MASS SPECTROMETRY : JMS 2023; 58:e4957. [PMID: 37415399 DOI: 10.1002/jms.4957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/28/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Ion mobility spectrometry (IMS) is a widespread separation technique used in various research fields. It can be coupled to liquid chromatography-mass spectrometry (LC-MS/MS) methods providing an additional separation dimension. During IMS, ions are subjected to multiple collisions with buffer gas, which may cause significant ion heating. The present project addresses this phenomenon from the bottom-up proteomics point of view. We performed LC-MS/MS measurements on a cyclic ion mobility mass spectrometer with varied collision energy (CE) settings both with and without IMS. We investigated the CE dependence of identification score, using Byonic search engine, for more than 1000 tryptic peptides from HeLa digest standard. We determined the optimal CE values-giving the highest identification score-for both setups (i.e., with and without IMS). Results show that lower CE is advantageous when IMS separation is applied, by 6.3 V on average. This value belongs to the one-cycle separation configuration, and multiple cycles may supposedly have even larger impact. The effect of IMS is also reflected in the trends of optimal CE values versus m/z functions. The parameters suggested by the manufacturer were found to be almost optimal for the setup without IMS; on the other hand, they are obviously too high with IMS. Practical consideration on setting up a mass spectrometric platform hyphenated to IMS is also presented. Furthermore, the two CID (collision induced dissociation) fragmentation cells of the instrument-located before and after the IMS cell-were also compared, and we found that CE adjustment is needed when the trap cell is used for activation instead of the transfer cell. Data have been deposited in the MassIVE repository (MSV000090944).
Collapse
Affiliation(s)
- Kinga Nagy
- MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Gabriella Gellén
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Dávid Papp
- Hevesy György PhD School of Chemistry, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Faculty of Science, Institute of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Ágnes Révész
- MS Proteomics Research Group, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| |
Collapse
|
34
|
Downs M, Zaia J, Sethi MK. Mass spectrometry methods for analysis of extracellular matrix components in neurological diseases. MASS SPECTROMETRY REVIEWS 2023; 42:1848-1875. [PMID: 35719114 PMCID: PMC9763553 DOI: 10.1002/mas.21792] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/12/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
The brain extracellular matrix (ECM) is a highly glycosylated environment and plays important roles in many processes including cell communication, growth factor binding, and scaffolding. The formation of structures such as perineuronal nets (PNNs) is critical in neuroprotection and neural plasticity, and the formation of molecular networks is dependent in part on glycans. The ECM is also implicated in the neuropathophysiology of disorders such as Alzheimer's disease (AD), Parkinson's disease (PD), and Schizophrenia (SZ). As such, it is of interest to understand both the proteomic and glycomic makeup of healthy and diseased brain ECM. Further, there is a growing need for site-specific glycoproteomic information. Over the past decade, sample preparation, mass spectrometry, and bioinformatic methods have been developed and refined to provide comprehensive information about the glycoproteome. Core ECM molecules including versican, hyaluronan and proteoglycan link proteins, and tenascin are dysregulated in AD, PD, and SZ. Glycomic changes such as differential sialylation, sulfation, and branching are also associated with neurodegeneration. A more thorough understanding of the ECM and its proteomic, glycomic, and glycoproteomic changes in brain diseases may provide pathways to new therapeutic options.
Collapse
Affiliation(s)
- Margaret Downs
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
- Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
35
|
Xu S, Wu R. Glycobiology and proteomics: has mass spectrometry moved the field forward? Expert Rev Proteomics 2023; 20:303-307. [PMID: 37667879 PMCID: PMC10841282 DOI: 10.1080/14789450.2023.2255748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/26/2023] [Indexed: 09/06/2023]
Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| |
Collapse
|
36
|
Révész Á, Hevér H, Steckel A, Schlosser G, Szabó D, Vékey K, Drahos L. Collision energies: Optimization strategies for bottom-up proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1261-1299. [PMID: 34859467 DOI: 10.1002/mas.21763] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 06/07/2023]
Abstract
Mass-spectrometry coupled to liquid chromatography is an indispensable tool in the field of proteomics. In the last decades, more and more complex and diverse biochemical and biomedical questions have arisen. Problems to be solved involve protein identification, quantitative analysis, screening of low abundance modifications, handling matrix effect, and concentrations differing by orders of magnitude. This led the development of more tailored protocols and problem centered proteomics workflows, including advanced choice of experimental parameters. In the most widespread bottom-up approach, the choice of collision energy in tandem mass spectrometric experiments has outstanding role. This review presents the collision energy optimization strategies in the field of proteomics which can help fully exploit the potential of MS based proteomics techniques. A systematic collection of use case studies is then presented to serve as a starting point for related further scientific work. Finally, this article discusses the issue of comparing results from different studies or obtained on different instruments, and it gives some hints on methodology transfer between laboratories based on measurement of reference species.
Collapse
Affiliation(s)
- Ágnes Révész
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Helga Hevér
- Chemical Works of Gedeon Richter Plc, Budapest, Hungary
| | - Arnold Steckel
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Dániel Szabó
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - Károly Vékey
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| | - László Drahos
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Budapest, Hungary
| |
Collapse
|
37
|
Helms A, Escobar EE, Vainauskas S, Taron CH, Brodbelt JS. Ultraviolet Photodissociation Permits Comprehensive Characterization of O-Glycopeptides Cleaved with O-Glycoprotease IMPa. Anal Chem 2023; 95:9280-9287. [PMID: 37290223 PMCID: PMC10587910 DOI: 10.1021/acs.analchem.3c01111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Complete O-glycosite characterization, including identification of the peptides, localization of the glycosites, and mapping of the glycans, has been a persistent challenge in O-glycoproteomics owing to the technical challenges surrounding O-glycan analysis. Multi-glycosylated peptides pose an even greater challenge owing to their potential heterogeneity. Ultraviolet photodissociation (UVPD) can localize multiple post-translational modifications and is well-suited for the characterization of glycans. Three glycoproteins were assessed based on a strategy combining the use of O-glycoprotease IMPa and HCD-triggered UVPD for the complete characterization of O-glycopeptides. This approach localized multiple adjacent or proximal O-glycosites on individual glycopeptides and identified a previously unknown glycosite on etanercept at S218. Nine different glycoforms were characterized as a multi-glycosylated peptide from etanercept. The performance of UVPD was compared to that of HCD and EThcD for the localization of O-glycosites and the characterization of the constituent peptides and glycans.
Collapse
Affiliation(s)
- Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Edwin E Escobar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
- New England Biolabs, Ipswich, Massachusetts 01938, United States
| | | | | | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
38
|
Hollander MJ, Malaker SA, Riley NM, Perez I, Abney NM, Gray MA, Maxson JE, Cochran JR, Bertozzi CR. Mutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity. J Biol Chem 2023; 299:104755. [PMID: 37116708 PMCID: PMC10245049 DOI: 10.1016/j.jbc.2023.104755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 04/30/2023] Open
Abstract
The colony-stimulating factor 3 receptor (CSF3R) controls the growth of neutrophils, the most abundant type of white blood cell. In healthy neutrophils, signaling is dependent on CSF3R binding to its ligand, CSF3. A single amino acid mutation in CSF3R, T618I, instead allows for constitutive, ligand-independent cell growth and leads to a rare type of cancer called chronic neutrophilic leukemia. However, the disease mechanism is not well understood. Here, we investigated why this threonine to isoleucine substitution is the predominant mutation in chronic neutrophilic leukemia and how it leads to uncontrolled neutrophil growth. Using protein domain mapping, we demonstrated that the single CSF3R domain containing residue 618 is sufficient for ligand-independent activity. We then applied an unbiased mutational screening strategy focused on this domain and found that activating mutations are enriched at sites normally occupied by asparagine, threonine, and serine residues-the three amino acids which are commonly glycosylated. We confirmed glycosylation at multiple CSF3R residues by mass spectrometry, including the presence of GalNAc and Gal-GalNAc glycans at WT threonine 618. Using the same approach applied to other cell surface receptors, we identified an activating mutation, S489F, in the interleukin-31 receptor alpha chain. Combined, these results suggest a role for glycosylated hotspot residues in regulating receptor signaling, mutation of which can lead to ligand-independent, uncontrolled activity and human disease.
Collapse
Affiliation(s)
- Michael J Hollander
- Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA
| | - Stacy A Malaker
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA
| | - Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA
| | - Idalia Perez
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Nayla M Abney
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Melissa A Gray
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA
| | - Julia E Maxson
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Chemical Engineering, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA.
| |
Collapse
|
39
|
Hackett WE, Chang D, Carvalho L, Zaia J. RAMZIS: a bioinformatic toolkit for rigorous assessment of the alterations to glycoprotein structure that occur during biological processes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542895. [PMID: 37398011 PMCID: PMC10312533 DOI: 10.1101/2023.05.30.542895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Motivation Glycosylation elaborates the structures and functions of glycoproteins; glycoproteins are common post-translationally modified proteins and are heterogeneous and non-deterministically syn-thesized as an evolutionarily driven mechanism that elaborates the functions of glycosylated gene products. While glycoproteins account for approximately half of all proteins, their macro- and micro-heterogeneity requires specialized proteomics data analysis methods as a given glycosite can be divided into several glycosylated forms, each of which must be quantified. Sampling of heterogeneous glycopeptides is limited by mass spectrometer speed and sensitivity, resulting in missing values. In conjunction with the low sample size inherent to glycoproteomics, this necessitated specialized statistical metrics to identify if observed changes in glycopeptide abundances are biologically significant or due to data quality limitations. Results We developed an R package, Relative Assessment of m/z Identifications by Similarity (RAMZIS), that uses similarity metrics to guide biomedical researchers to a more rigorous interpretation of glycoproteomics data. RAMZIS uses contextual similarity to assess the quality of mass spectral data and generates graphical output that demonstrates the likelihood of finding biologically significant differences in glycosylation abundance dataset. Investigators can assess dataset quality, holistically differentiate glycosites, and identify which glycopeptides are responsible for glycosylation pattern expression change. Herein RAMZIS approach is validated by theoretical cases and by a proof-of-concept application. RAMZIS enables comparison between datasets too stochastic, small, or sparse for interpolation while acknowledging these issues in its assessment. Using our tool, researchers will be able to rigor-ously define the role of glycosylation and the changes that occur during biological processes.
Collapse
Affiliation(s)
| | - Deborah Chang
- Department of Biochemistry, Boston University, One Silber Way, Boston 02215
| | - Luis Carvalho
- Boston University, Bioinformatics Program, One Silber Way, Boston 02215, MA, USA
- Department of Mathematics, Boston University, One Silber Way, Boston 02215
| | - Joseph Zaia
- Boston University, Bioinformatics Program, One Silber Way, Boston 02215, MA, USA
- Department of Biochemistry, Boston University, One Silber Way, Boston 02215
| |
Collapse
|
40
|
Toul M, Slonkova V, Mican J, Urminsky A, Tomkova M, Sedlak E, Bednar D, Damborsky J, Hernychova L, Prokop Z. Identification, characterization, and engineering of glycosylation in thrombolyticsa. Biotechnol Adv 2023; 66:108174. [PMID: 37182613 DOI: 10.1016/j.biotechadv.2023.108174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/09/2023] [Accepted: 05/09/2023] [Indexed: 05/16/2023]
Abstract
Cardiovascular diseases, such as myocardial infarction, ischemic stroke, and pulmonary embolism, are the most common causes of disability and death worldwide. Blood clot hydrolysis by thrombolytic enzymes and thrombectomy are key clinical interventions. The most widely used thrombolytic enzyme is alteplase, which has been used in clinical practice since 1986. Another clinically used thrombolytic protein is tenecteplase, which has modified epitopes and engineered glycosylation sites, suggesting that carbohydrate modification in thrombolytic enzymes is a viable strategy for their improvement. This comprehensive review summarizes current knowledge on computational and experimental identification of glycosylation sites and glycan identity, together with methods used for their reengineering. Practical examples from previous studies focus on modification of glycosylations in thrombolytics, e.g., alteplase, tenecteplase, reteplase, urokinase, saruplase, and desmoteplase. Collected clinical data on these glycoproteins demonstrate the great potential of this engineering strategy. Outstanding combinatorics originating from multiple glycosylation sites and the vast variety of covalently attached glycan species can be addressed by directed evolution or rational design. Directed evolution pipelines would benefit from more efficient cell-free expression and high-throughput screening assays, while rational design must employ structure prediction by machine learning and in silico characterization by supercomputing. Perspectives on challenges and opportunities for improvement of thrombolytic enzymes by engineering and evolution of protein glycosylation are provided.
Collapse
Affiliation(s)
- Martin Toul
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Veronika Slonkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jan Mican
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Adam Urminsky
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic
| | - Maria Tomkova
- Center for Interdisciplinary Biosciences, P. J. Safarik University in Kosice, Jesenna 5, 04154 Kosice, Slovakia
| | - Erik Sedlak
- Center for Interdisciplinary Biosciences, P. J. Safarik University in Kosice, Jesenna 5, 04154 Kosice, Slovakia
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Lenka Hernychova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Zluty kopec 7, 656 53 Brno, Czech Republic.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
| |
Collapse
|
41
|
Wang Z, Fang Z, Liu L, Zhu H, Wang Y, Zhao C, Guo Z, Qin H, Nie Y, Liang X, Dong M, Ye M. Development of an Integrated Platform for the Simultaneous Enrichment and Characterization of N- and O-Linked Intact Glycopeptides. Anal Chem 2023; 95:7448-7457. [PMID: 37146305 DOI: 10.1021/acs.analchem.2c04305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Both N-linked glycosylation and O-linked glycosylation play essential roles in the onset and progression of various diseases including cancer, and N-/O-linked site-specific glycans have been proven to be promising biomarkers for the discrimination of cancer. However, the micro-heterogeneity and low abundance nature of N-/O-linked glycosylation, as well as the time-consuming and tedious procedures for the enrichment of O-linked intact glycopeptides, pose great challenges for their efficient and accurate characterization. In this study, we developed an integrated platform for the simultaneous enrichment and characterization of N- and O-linked intact glycopeptides from the same serum sample. By fine-tuning the experimental conditions, we demonstrated that this platform allowed the selective separation of N- and O-linked intact glycopeptides into two fractions, with 85.1% O-linked intact glycopeptides presented in the first fraction and 93.4% N-linked intact glycopeptides presented in the second fraction. Determined with high reproducibility, this platform was further applied to the differential analysis of serum samples of gastric cancer and health control, which revealed 17 and 181 significantly changed O-linked and N-linked intact glycopeptides. Interestingly, five glycoproteins containing both significant regulation of N- and O-glycosylation were observed, hinting potential co-regulation of different types of glycosylation during tumor progress. In summary, this integrated platform opened a potentially useful avenue for the global analysis of protein glycosylation and can serve as a useful tool for the characterization of N-/O-linked intact glycopeptides at the proteomics scale.
Collapse
Affiliation(s)
- Zhongyu Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luyao Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - He Zhu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| | - Changrui Zhao
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning 116023, China
| | - Zhimou Guo
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, China
| | - Xinmiao Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| | - Mingming Dong
- Liaoning Key Laboratory of Molecular Recognition and Imaging, School of Bioengineering, Dalian University of Technology, Dalian, Liaoning 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, Liaoning 116023, China
| |
Collapse
|
42
|
Bradberry MM, Peters-Clarke TM, Shishkova E, Chapman ER, Coon JJ. N-glycoproteomics of brain synapses and synaptic vesicles. Cell Rep 2023; 42:112368. [PMID: 37036808 PMCID: PMC10560701 DOI: 10.1016/j.celrep.2023.112368] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 01/13/2023] [Accepted: 03/23/2023] [Indexed: 04/11/2023] Open
Abstract
At mammalian neuronal synapses, synaptic vesicle (SV) glycoproteins are essential for robust neurotransmission. Asparagine (N)-linked glycosylation is required for delivery of the major SV glycoproteins synaptophysin and SV2A to SVs. Despite this key role for N-glycosylation, the molecular compositions of SV N-glycans are largely unknown. In this study, we combined organelle isolation techniques and high-resolution mass spectrometry to characterize N-glycosylation at synapses and SVs from mouse brain. Detecting over 2,500 unique glycopeptides, we found that SVs harbor a distinct population of oligomannose and highly fucosylated N-glycans. Using complementary fluorescence methods, we identify at least one highly fucosylated N-glycan enriched in SVs compared with synaptosomes. High fucosylation was characteristic of SV proteins, plasma membrane proteins, and cell adhesion molecules with key roles in synaptic function and development. Our results define the N-glycoproteome of a specialized neuronal organelle and inform timely questions in the glycobiology of synaptic pruning and neuroinflammation.
Collapse
Affiliation(s)
- Mazdak M Bradberry
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA; Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA; Department of Psychiatry, Columbia University, New York, NY 10032, USA.
| | - Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - Evgenia Shishkova
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
| | - Edwin R Chapman
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| |
Collapse
|
43
|
Čaval T, Alisson-Silva F, Schwarz F. Roles of glycosylation at the cancer cell surface: opportunities for large scale glycoproteomics. Theranostics 2023; 13:2605-2615. [PMID: 37215580 PMCID: PMC10196828 DOI: 10.7150/thno.81760] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Cell surface glycosylation has a variety of functions, and its dysregulation in cancer contributes to impaired signaling, metastasis and the evasion of the immune responses. Recently, a number of glycosyltransferases that lead to altered glycosylation have been linked to reduced anti-tumor immune responses: B3GNT3, which is implicated in PD-L1 glycosylation in triple negative breast cancer, FUT8, through fucosylation of B7H3, and B3GNT2, which confers cancer resistance to T cell cytotoxicity. Given the increased appreciation of the relevance of protein glycosylation, there is a critical need for the development of methods that allow for an unbiased interrogation of cell surface glycosylation status. Here we provide an overview of the broad changes in glycosylation at the surface of cancer cell and describe selected examples of receptors with aberrant glycosylation leading to functional changes, with emphasis on immune checkpoint inhibitors, growth-promoting and growth-arresting receptors. Finally, we posit that the field of glycoproteomics has matured to an extent where large-scale profiling of intact glycopeptides from the cell surface is feasible and is poised for discovery of new actionable targets against cancer.
Collapse
|
44
|
Conjugation site characterization of antibody-drug conjugates using electron-transfer/higher-energy collision dissociation (EThcD). Anal Chim Acta 2023; 1251:340978. [PMID: 36925279 DOI: 10.1016/j.aca.2023.340978] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Antibody-drug conjugates (ADCs) are formed by binding of cytotoxic drugs to monoclonal antibodies (mAbs) through chemical linkers. A comprehensive evaluation of the critical quality attributes (CQAs) of ADCs is vital for drug development but remains challenging owing to ADC structural heterogeneity than mAbs. Drug conjugation sites can considerably affect ADC properties, such as stability and pharmacokinetics, however, few studies have focused on method development in this area owing to technical challenges. Hybrid electron-transfer/higher-energy collision dissociation (EThcD) produces more fragment ions than conventional higher-energy collision dissociation (HCD) fragmentation, which aids in identifying and localizing post-translational modifications. Herein, we systematically employ EThcD to assess the fragmentation mode impact on conjugation site characterization for randomly conjugated and site-specific ADCs. EThcD generates more fragment ions in tandem mass spectrometry (MS/MS) spectra compared with HCD. Additional ions aid in pinpointing the correct conjugation sites that bear complex linker payload structures. Our study may contribute to the quality control of various preclinical and clinical ADCs.
Collapse
|
45
|
Chau TH, Chernykh A, Kawahara R, Thaysen-Andersen M. Critical considerations in N-glycoproteomics. Curr Opin Chem Biol 2023; 73:102272. [PMID: 36758418 DOI: 10.1016/j.cbpa.2023.102272] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 02/10/2023]
Abstract
N-Glycoproteomics, the system-wide study of glycans asparagine-linked to protein carriers, holds a unique and still largely untapped potential to provide deep insights into the complexity and dynamics of the heterogeneous N-glycoproteome. Despite the advent of innovative analytical and informatics tools aiding the analysis, N-glycoproteomics remains challenging and consequently largely restricted to specialised laboratories. Aiming to stimulate discussions of method harmonisation, data standardisation and reporting guidelines to make N-glycoproteomics more reproducible and accessible to the community, we here discuss critical considerations related to the design and execution of N-glycoproteomics experiments and highlight good practices in N-glycopeptide data collection, analysis, interpretation and sharing. Giving the rapid maturation and, expectedly, a wide-spread implementation of N-glycoproteomics capabilities across the community in future years, this piece aims to point out common pitfalls, to encourage good data sharing and documentation practices, and to highlight practical solutions and strategies to enhance the insight into the N-glycoproteome.
Collapse
Affiliation(s)
- The Huong Chau
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Anastasia Chernykh
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Rebeca Kawahara
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Biomolecular Discovery Research Centre, Macquarie University, Sydney, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan.
| |
Collapse
|
46
|
Hellinger R, Sigurdsson A, Wu W, Romanova EV, Li L, Sweedler JV, Süssmuth RD, Gruber CW. Peptidomics. NATURE REVIEWS. METHODS PRIMERS 2023; 3:25. [PMID: 37250919 PMCID: PMC7614574 DOI: 10.1038/s43586-023-00205-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 05/31/2023]
Abstract
Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.
Collapse
Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Arnar Sigurdsson
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Wenxin Wu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| |
Collapse
|
47
|
Gonzalez-Rodriguez E, Zol-Hanlon M, Bineva-Todd G, Marchesi A, Skehel M, Mahoney KE, Roustan C, Borg A, Di Vagno L, Kjær S, Wrobel AG, Benton DJ, Nawrath P, Flitsch SL, Joshi D, González-Ramírez A, Wilkinson KA, Wilkinson RJ, Wall EC, Hurtado-Guerrero R, Malaker SA, Schumann B. O-Linked Sialoglycans Modulate the Proteolysis of SARS-CoV-2 Spike and Likely Contribute to the Mutational Trajectory in Variants of Concern. ACS CENTRAL SCIENCE 2023; 9:393-404. [PMID: 36968546 PMCID: PMC10037455 DOI: 10.1021/acscentsci.2c01349] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 06/18/2023]
Abstract
The emergence of a polybasic cleavage motif for the protease furin in SARS-CoV-2 spike has been established as a major factor for human viral transmission. The region N-terminal to that motif is extensively mutated in variants of concern (VOCs). Besides furin, spikes from these variants appear to rely on other proteases for maturation, including TMPRSS2. Glycans near the cleavage site have raised questions about proteolytic processing and the consequences of variant-borne mutations. Here, we identify that sialic acid-containing O-linked glycans on Thr678 of SARS-CoV-2 spike influence furin and TMPRSS2 cleavage and posit O-linked glycosylation as a likely driving force for the emergence of VOC mutations. We provide direct evidence that the glycosyltransferase GalNAc-T1 primes glycosylation at Thr678 in the living cell, an event that is suppressed by mutations in the VOCs Alpha, Delta, and Omicron. We found that the sole incorporation of N-acetylgalactosamine did not impact furin activity in synthetic O-glycopeptides, but the presence of sialic acid reduced the furin rate by up to 65%. Similarly, O-glycosylation with a sialylated trisaccharide had a negative impact on TMPRSS2 cleavage. With a chemistry-centered approach, we substantiate O-glycosylation as a major determinant of spike maturation and propose disruption of O-glycosylation as a substantial driving force for VOC evolution.
Collapse
Affiliation(s)
- Edgar Gonzalez-Rodriguez
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mia Zol-Hanlon
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Signalling
and Structural Biology Lab, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Ganka Bineva-Todd
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
| | - Andrea Marchesi
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Mark Skehel
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Keira E. Mahoney
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Chloë Roustan
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Annabel Borg
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Lucia Di Vagno
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Proteomics
Science Technology Platform, The Francis
Crick Institute, NW1 1AT London, United Kingdom
| | - Svend Kjær
- Structural
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Antoni G. Wrobel
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Donald J. Benton
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Philipp Nawrath
- Structural
Biology of Disease Processes Laboratory, Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Sabine L. Flitsch
- Manchester
Institute of Biotechnology, University of
Manchester, 131 Princess Street, M1 7DN Manchester, United Kingdom
| | - Dhira Joshi
- Chemical
Biology Science Technology Platform, The
Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Katalin A. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Robert J. Wilkinson
- Tuberculosis
Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Wellcome
Centre for Infectious Diseases Research in Africa, University of Cape Town, 7925 Observatory, Cape Town, South Africa
- Department
of Infectious Diseases, Imperial College
London, W12 0NN London, United Kingdom
- Institute
of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, 7925 Observatory, Cape Town, South Africa
| | - Emma C. Wall
- The Francis
Crick Institute, NW1 1AT London, United Kingdom
- University
College London Hospitals (UCLH) Biomedical Research Centre, W1T 7DN London, United Kingdom
| | - Ramón Hurtado-Guerrero
- Institute
of Biocomputation and Physics of Complex Systems, University of Zaragoza, 50018 Zaragoza, Spain
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
- Fundación
ARAID, 50018 Zaragoza, Spain
| | - Stacy A. Malaker
- Department
of Chemistry, Yale University, 275 Prospect Street, 06511 New Haven, Connecticut, United States
| | - Benjamin Schumann
- Chemical
Glycobiology Laboratory, The Francis Crick
Institute, NW1 1AT London, United Kingdom
- Department
of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| |
Collapse
|
48
|
Xu M, Yang A, Xia J, Jiang J, Liu CF, Ye Z, Ma J, Yang S. Protein glycosylation in urine as a biomarker of diseases. Transl Res 2023; 253:95-107. [PMID: 35952983 DOI: 10.1016/j.trsl.2022.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023]
Abstract
Human body fluids have become an indispensable resource for clinical research, diagnosis and prognosis. Urine is widely used to discover disease-specific glycoprotein biomarkers because of its recurrently non-invasive collection and disease-indicating properties. While urine is an unstable fluid in that its composition changes with ingested nutrients and further as it is excreted through micturition, urinary proteins are more stable and their abnormal glycosylation is associated with diseases. It is known that aberrant glycosylation can define tumor malignancy and indicate disease initiation and progression. However, a thorough and translational survey of urinary glycosylation in diseases has not been performed. In this article, we evaluate the clinical applications of urine, introduce methods for urine glycosylation analysis, and discuss urine glycoprotein biomarkers. We emphasize the importance of mining urinary glycoproteins and searching for disease-specific glycosylation in various diseases (including cancer, neurodegenerative diseases, diabetes, and viral infections). With advances in mass spectrometry-based glycomics/glycoproteomics/glycopeptidomics, characterization of disease-specific glycosylation will optimistically lead to the discovery of disease-related urinary biomarkers with better sensitivity and specificity in the near future.
Collapse
Affiliation(s)
- Mingming Xu
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Arthur Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Jun Xia
- Clinical Laboratory Center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Junhong Jiang
- Department of Pulmonary and Critical Care Medicine, Dushu Lake Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chun-Feng Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhenyu Ye
- Department of General Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, District of Columbia.
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China.
| |
Collapse
|
49
|
Phetsanthad A, Vu NQ, Yu Q, Buchberger AR, Chen Z, Keller C, Li L. Recent advances in mass spectrometry analysis of neuropeptides. MASS SPECTROMETRY REVIEWS 2023; 42:706-750. [PMID: 34558119 PMCID: PMC9067165 DOI: 10.1002/mas.21734] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 08/22/2021] [Accepted: 08/28/2021] [Indexed: 05/08/2023]
Abstract
Due to their involvement in numerous biochemical pathways, neuropeptides have been the focus of many recent research studies. Unfortunately, classic analytical methods, such as western blots and enzyme-linked immunosorbent assays, are extremely limited in terms of global investigations, leading researchers to search for more advanced techniques capable of probing the entire neuropeptidome of an organism. With recent technological advances, mass spectrometry (MS) has provided methodology to gain global knowledge of a neuropeptidome on a spatial, temporal, and quantitative level. This review will cover key considerations for the analysis of neuropeptides by MS, including sample preparation strategies, instrumental advances for identification, structural characterization, and imaging; insightful functional studies; and newly developed absolute and relative quantitation strategies. While many discoveries have been made with MS, the methodology is still in its infancy. Many of the current challenges and areas that need development will also be highlighted in this review.
Collapse
Affiliation(s)
- Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Nhu Q. Vu
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qing Yu
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Amanda R. Buchberger
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Zhengwei Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| |
Collapse
|
50
|
Yin H, Zhu J. Methods for quantification of glycopeptides by liquid separation and mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:887-917. [PMID: 35099083 PMCID: PMC9339036 DOI: 10.1002/mas.21771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/14/2021] [Accepted: 01/13/2022] [Indexed: 05/05/2023]
Abstract
Recent advances in analytical techniques provide the opportunity to quantify even low-abundance glycopeptides derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Herein, we discuss the sample preparation procedures and the mass spectrometry (MS) strategies that have facilitated glycopeptide quantification, as well as the standards used for glycopeptide quantification. For sample preparation, various glycopeptide enrichment methods are summarized including the columns used for glycopeptide separation in liquid chromatography separation. For MS analysis strategies, MS1 level-based quantification and MS2 level-based quantification are described, either with or without labeling, where we have covered isotope labeling, TMT/iTRAQ labeling, data dependent acquisition, data independent acquisition, multiple reaction monitoring, and parallel reaction monitoring. The strengths and weaknesses of these methods are compared, particularly those associated with the figures of merit that are important for clinical biomarker studies and the pathological and functional studies of glycoproteins in various diseases. Possible future developments for glycopeptide quantification are discussed.
Collapse
Affiliation(s)
- Haidi Yin
- Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518132, China
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| | - Jianhui Zhu
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
- Correspondence to: Haidi Yin, Shenzhen Bay Laboratory, A1201, Shenzhen, Guangdong, 518132, China. Phone: 0755-26849276. , Jianhui Zhu, Department of Surgery, University of Michigan, 1150 West Medical Center Drive, Building MSRB1, Rm A500, Ann Arbor, MI 48109-0656, USA. Tel: 734-615-2567. Fax: 734-615-2088.
| |
Collapse
|