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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 DOI: 10.1021/acs.analchem.3c05874] [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: 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.
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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
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2
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Nilsson J, Rimkute I, Sihlbom C, Tenge VR, Lin SC, Atmar RL, Estes MK, Larson G. N-glycoproteomic analyses of human intestinal enteroids, varying in histo-blood group geno- and phenotypes, reveal a wide repertoire of fucosylated glycoproteins. Glycobiology 2024; 34:cwae029. [PMID: 38590172 DOI: 10.1093/glycob/cwae029] [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: 11/03/2023] [Revised: 03/12/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024] Open
Abstract
Human noroviruses, globally the main cause of viral gastroenteritis, show strain specific affinity for histo-blood group antigens (HBGA) and can successfully be propagated ex vivo in human intestinal enteroids (HIEs). HIEs established from jejunal stem cells of individuals with different ABO, Lewis and secretor geno- and phenotypes, show varying susceptibility to such infections. Using bottom-up glycoproteomic approaches we have defined and compared the N-linked glycans of glycoproteins of seven jejunal HIEs. Membrane proteins were extracted, trypsin digested, and glycopeptides enriched by hydrophilic interaction liquid chromatography and analyzed by nanoLC-MS/MS. The Byonic software was used for glycopeptide identification followed by hands-on verifications and interpretations. Glycan structures and attachment sites were identified from MS2 spectra obtained by higher-energy collision dissociation through analysis of diagnostic saccharide oxonium ions (B-ions), stepwise glycosidic fragmentation of the glycans (Y-ions), and peptide sequence ions (b- and y-ions). Altogether 694 unique glycopeptides from 93 glycoproteins were identified. The N-glycans encompassed pauci- and oligomannose, hybrid- and complex-type structures. Notably, polyfucosylated HBGA-containing glycopeptides of the four glycoproteins tetraspanin-8, carcinoembryonic antigen-related cell adhesion molecule 5, sucrose-isomaltase and aminopeptidase N were especially prominent and were characterized in detail and related to donor ABO, Lewis and secretor types of each HIE. Virtually no sialylated N-glycans were identified for these glycoproteins suggesting that terminal sialylation was infrequent compared to fucosylation and HBGA biosynthesis. This approach gives unique site-specific information on the structural complexity of N-linked glycans of glycoproteins of human HIEs and provides a platform for future studies on the role of host glycoproteins in gastrointestinal infectious diseases.
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Affiliation(s)
- Jonas Nilsson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
- Department of Clinical Chemistry, Region Västra Götaland, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
- Proteomics Core Facilities, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9E, SE 413 90, Gothenburg, Sweden
| | - Inga Rimkute
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Medicinaregatan 7A, SE 413 90, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facilities, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 9E, SE 413 90, Gothenburg, Sweden
| | - Victoria R Tenge
- Department of Molecular Virology, Baylor College School of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
| | - Shih-Ching Lin
- Department of Molecular Virology, Baylor College School of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
- Present address: Department of Medicine, Washington University in St. Louis, St. Louis, MO, United States
| | - Robert L Atmar
- Department of Molecular Virology, Baylor College School of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
| | - Mary K Estes
- Department of Molecular Virology, Baylor College School of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 770 30, United States
| | - Göran Larson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
- Department of Clinical Chemistry, Region Västra Götaland, Sahlgrenska University Hospital, Bruna Stråket 16, SE 413 45, Gothenburg, Sweden
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3
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Adams TM, Zhao P, Kong R, Wells L. ppmFixer: a mass error adjustment for pGlyco3.0 to correct near-isobaric mismatches. Glycobiology 2024; 34:cwae006. [PMID: 38263491 PMCID: PMC11005163 DOI: 10.1093/glycob/cwae006] [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: 10/25/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 01/25/2024] Open
Abstract
Modern glycoproteomics experiments require the use of search engines due to the generation of countless spectra. While these tools are valuable, manual validation of search engine results is often required for detailed analysis of glycopeptides as false-discovery rates are often not reliable for glycopeptide data. Near-isobaric mismatches are a common source of misidentifications for the popular glycopeptide-focused search engine pGlyco3.0, and in this technical note we share a strategy and script that improves the accuracy of the search utilizing two manually validated datasets of the glycoproteins CD16a and HIV-1 Env as proof-of-principle.
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Affiliation(s)
- Trevor M Adams
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens 30602, Georgia
| | - Peng Zhao
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens 30602, Georgia
| | - Rui Kong
- Department of Pathology and Laboratory Medicine, Emory Vaccine Center, Emory University, 7 Frist Ave, Atlanta 30317, Georgia
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens 30602, Georgia
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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).
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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
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5
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Geiszler DJ, Polasky DA, Yu F, Nesvizhskii AI. Detecting diagnostic features in MS/MS spectra of post-translationally modified peptides. Nat Commun 2023; 14:4132. [PMID: 37438360 DOI: 10.1038/s41467-023-39828-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 06/23/2023] [Indexed: 07/14/2023] Open
Abstract
Post-translational modifications are an area of great interest in mass spectrometry-based proteomics, with a surge in methods to detect them in recent years. However, post-translational modifications can introduce complexity into proteomics searches by fragmenting in unexpected ways, ultimately hindering the detection of modified peptides. To address these deficiencies, we present a fully automated method to find diagnostic spectral features for any modification. The features can be incorporated into proteomics search engines to improve modified peptide recovery and localization. We show the utility of this approach by interrogating fragmentation patterns for a cysteine-reactive chemoproteomic probe, RNA-crosslinked peptides, sialic acid-containing glycopeptides, and ADP-ribosylated peptides. We also analyze the interactions between a diagnostic ion's intensity and its statistical properties. This method has been incorporated into the open-search annotation tool PTM-Shepherd and the FragPipe computational platform.
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Affiliation(s)
- Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I Nesvizhskii
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
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6
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Shipman J, Sommers C, Keire DA, Chen K, Zhu H. Comprehensive N-Glycan Mapping using Parallel Reaction Monitoring LC-MS/MS. Pharm Res 2023; 40:1399-1410. [PMID: 36513905 DOI: 10.1007/s11095-022-03453-1] [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: 07/05/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE Glycan composition can impact a biotherapeutic's safety and efficacy. For example, changes in the relative abundance of different glycan attributes like afucosylation, galactosylation or high-mannose content can change the properties or functions of a monoclonal antibody (mAb). While established methods can effectively characterize major glycan species in biotherapeutic drug products, there is still a need for more sensitive and specific methods that can effectively monitor low abundance species which may impact mAb function. METHODS Glycans released from two mAbs, adalimumab and trastuzumab, were derivatized with Rapifluor-MS™. Glycans were separated using HILIC and detected using either fluorescence (FLD) or mass spectrometry (MS). A parallel reaction monitoring (PRM) workflow was used for the MS analysis. RESULTS AND CONCLUSION FLD analysis identified 18 and 19 glycan peaks in adalimumab and trastuzumab, respectively. Glycan identities were determined using MS-analysis and a high number of FLD peaks containing co-eluting glycan species were observed. PRM analysis quantified 38 and 39 glycan species in adalimumab and trastuzumab, respectively, and the increase in glycans that could be identified was due to superior sensitivity and selectivity compared to FLD. Notably, many low abundance glycans identified by PRM included species that were not reported in other studies. PRM also offered several additional advantages; unique structural features could be identified using the collected MS/MS spectra and de-coupling MS acquisition and data processing simplified the transfer of methods between instruments. The results established PRM as a precise, informative tool for glycan analysis and quantitation.
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Affiliation(s)
- Joshua Shipman
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA
| | - Cynthia Sommers
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA
| | - David A Keire
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA
| | - Kang Chen
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA.
| | - Hongbin Zhu
- Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, MO, 63110, USA.
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7
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Cerrato A, Cavaliere C, Montone CM, Piovesana S. New hydrophilic material based on hydrogel polymer for the selective enrichment of intact glycopeptides from serum protein digests. Anal Chim Acta 2023; 1245:340862. [PMID: 36737137 DOI: 10.1016/j.aca.2023.340862] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/21/2023]
Abstract
The paper describes the preparation and characterization of a new HILIC material for the enrichment of N-linked glycopeptides. The material was prepared using 2-acrylamido-2-methyl-1-propanesulfonic acid as the monomer and ethylene glycol dimethacrylate as the cross-linker. The material was developed by a Box-Behnken experimental design, taking into consideration the amount of monomer-to-crosslinker ratio, the composition, and the amount of porogen mixture. By this approach, the property of the resulting polymer could be fine-tuned to modulate the hydrophilicity and porosity. As HILIC enrichment is mostly dependent on hydrophilic interactions, including H-bonding, the amount of swelling was expected to have an important function, therefore the optimization considered a monomer percent in the range of 20-80%, which implied very different water swelling capacities. After assessing the potential of this new polymer family on fetuin digests, the 17 materials resulting from the Box-Behnken experimental design were used for the enrichment of glycopeptides from serum protein digests. The materials displayed a superior performance over cotton HILIC enrichment, both in terms of the number of enriched N-linked glycopeptides and selectivity, providing up to 762 N-linked glycopeptides with 77% selectivity. The optimization indicated that a high amount of monomer significantly affected the number of enriched glycopeptides, which is also closely connected with the hydrogel nature of the resulting polymers. The results not only provide one additional HILIC material for the enrichment of glycopeptides but also pave the way for the use and development of hydrogel materials for the enrichment of N-linked glycopeptides.
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Affiliation(s)
- Andrea Cerrato
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Susy Piovesana
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
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8
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Piovesana S, Cavaliere C, Cerrato A, Laganà A, Montone CM, Capriotti AL. Recent trends in glycoproteomics by characterization of intact glycopeptides. Anal Bioanal Chem 2023:10.1007/s00216-023-04592-z. [PMID: 36811677 PMCID: PMC10328862 DOI: 10.1007/s00216-023-04592-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/31/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023]
Abstract
This trends article provides an overview of the state of the art in the analysis of intact glycopeptides by proteomics technologies based on LC-MS analysis. A brief description of the main techniques used at the different steps of the analytical workflow is provided, giving special attention to the most recent developments. The topics discussed include the need for dedicated sample preparation for intact glycopeptide purification from complex biological matrices. This section covers the common approaches with a special description of new materials and innovative reversible chemical derivatization strategies, specifically devised for intact glycopeptide analysis or dual enrichment of glycosylation and other post-translational modifications. The approaches are described for the characterization of intact glycopeptide structures by LC-MS and data analysis by bioinformatics for spectra annotation. The last section covers the open challenges in the field of intact glycopeptide analysis. These challenges include the need of a detailed description of the glycopeptide isomerism, the issues with quantitative analysis, and the lack of analytical methods for the large-scale characterization of glycosylation types that remain poorly characterized, such as C-mannosylation and tyrosine O-glycosylation. This bird's-eye view article provides both a state of the art in the field of intact glycopeptide analysis and open challenges to prompt future research on the topic.
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Affiliation(s)
- Susy Piovesana
- Department of Chemistry, Sapienza Università Di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Chiara Cavaliere
- Department of Chemistry, Sapienza Università Di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Andrea Cerrato
- Department of Chemistry, Sapienza Università Di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Aldo Laganà
- Department of Chemistry, Sapienza Università Di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Carmela Maria Montone
- Department of Chemistry, Sapienza Università Di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Anna Laura Capriotti
- Department of Chemistry, Sapienza Università Di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
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9
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Baralić M, Pažitná L, Brković V, Laušević M, Gligorijević N, Katrlík J, Nedić O, Robajac D. Prediction of Mortality in Patients on Peritoneal Dialysis Based on the Fibrinogen Mannosylation. Cells 2023; 12:cells12030351. [PMID: 36766693 PMCID: PMC9913213 DOI: 10.3390/cells12030351] [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: 11/17/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
As we already reported, fibrinogen fucosylation emerged as a prognostic marker of peritoneal membrane function in end-stage renal disease (ESRD) patients on peritoneal dialysis. After a follow-up period of 18 months, we estimated the ability of employed lectins, as well as other biochemical parameters, to serve as mortality predictors in these patients. Following a univariate Cox regression analysis, ferritin, urea clearance, residual diuresis, hyperglycemia, and an increase in the signal intensity obtained with Galanthus nivalis lectin (GNL) emerged as potential mortality predictors, but additional multivariate Cox regression analysis pointed only to glucose concentration and GNL as mortality predictors. Higher signal intensity obtained with GNL in patients that died suggested the importance of paucimannosidic/highly mannosidic N-glycan structures on fibrinogen as factors that are related to unwanted cardiovascular events and all-cause mortality and can possibly be seen as a prediction tool. Altered glycan structures composed of mannose residues are expected to affect the reactivity of mannosylated glycoproteins with mannose-binding lectin and possibly the entire cascade of events linked to this lectin. Since patients with ESRD are prone to cardiovascular complications and the formation of atherosclerotic plaques, one can hypothesize that fibrinogen with increasingly exposed mannose residues may contribute to the unwanted events.
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Affiliation(s)
- Marko Baralić
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Clinic of Nephrology, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Lucia Pažitná
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
| | - Voin Brković
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Clinic of Nephrology, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Mirjana Laušević
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
- Clinic of Nephrology, University Clinical Centre of Serbia, 11000 Belgrade, Serbia
| | - Nikola Gligorijević
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia
| | - Olgica Nedić
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia
| | - Dragana Robajac
- Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia
- Correspondence:
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10
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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11
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Pabst M, Grouzdev DS, Lawson CE, Kleikamp HBC, de Ram C, Louwen R, Lin YM, Lücker S, van Loosdrecht MCM, Laureni M. A general approach to explore prokaryotic protein glycosylation reveals the unique surface layer modulation of an anammox bacterium. THE ISME JOURNAL 2022; 16:346-357. [PMID: 34341504 PMCID: PMC8776859 DOI: 10.1038/s41396-021-01073-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023]
Abstract
The enormous chemical diversity and strain variability of prokaryotic protein glycosylation makes their large-scale exploration exceptionally challenging. Therefore, despite the universal relevance of protein glycosylation across all domains of life, the understanding of their biological significance and the evolutionary forces shaping oligosaccharide structures remains highly limited. Here, we report on a newly established mass binning glycoproteomics approach that establishes the chemical identity of the carbohydrate components and performs untargeted exploration of prokaryotic oligosaccharides from large-scale proteomics data directly. We demonstrate our approach by exploring an enrichment culture of the globally relevant anaerobic ammonium-oxidizing bacterium Ca. Kuenenia stuttgartiensis. By doing so we resolve a remarkable array of oligosaccharides, which are produced by two seemingly unrelated biosynthetic routes, and which modify the same surface-layer protein simultaneously. More intriguingly, the investigated strain also accomplished modulation of highly specialized sugars, supposedly in response to its energy metabolism-the anaerobic oxidation of ammonium-which depends on the acquisition of substrates of opposite charges. Ultimately, we provide a systematic approach for the compositional exploration of prokaryotic protein glycosylation, and reveal a remarkable example for the evolution of complex oligosaccharides in bacteria.
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Affiliation(s)
- Martin Pabst
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | | | - Christopher E. Lawson
- grid.184769.50000 0001 2231 4551DOE Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA USA
| | - Hugo B. C. Kleikamp
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Carol de Ram
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Rogier Louwen
- grid.5645.2000000040459992XDepartment of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Yue Mei Lin
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Sebastian Lücker
- grid.5590.90000000122931605Department of Microbiology, IWWR, Radboud University, Nijmegen, the Netherlands
| | - Mark C. M. van Loosdrecht
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
| | - Michele Laureni
- grid.5292.c0000 0001 2097 4740Delft University of Technology, Department of Biotechnology, Delft, The Netherlands
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12
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Polasky DA, Geiszler DJ, Yu F, Nesvizhskii AI. Multi-attribute Glycan Identification and FDR Control for Glycoproteomics. Mol Cell Proteomics 2022; 21:100205. [PMID: 35091091 PMCID: PMC8933705 DOI: 10.1016/j.mcpro.2022.100205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 11/18/2022] Open
Abstract
Rapidly improving methods for glycoproteomics have enabled increasingly large-scale analyses of complex glycopeptide samples, but annotating the resulting mass spectrometry data with high confidence remains a major bottleneck. We recently introduced a fast and sensitive glycoproteomics search method in our MSFragger search engine, which reports glycopeptides as a combination of a peptide sequence and the mass of the attached glycan. In samples with complex glycosylation patterns, converting this mass to a specific glycan composition is not straightforward; however, as many glycans have similar or identical masses. Here, we have developed a new method for determining the glycan composition of N-linked glycopeptides fragmented by collisional or hybrid activation that uses multiple sources of information from the spectrum, including observed glycan B-type (oxonium) and Y-type ions and mass and precursor monoisotopic selection errors to discriminate between possible glycan candidates. Combined with false discovery rate estimation for the glycan assignment, we show that this method is capable of specifically and sensitively identifying glycans in complex glycopeptide analyses and effectively controls the rate of false glycan assignments. The new method has been incorporated into the PTM-Shepherd modification analysis tool to work directly with the MSFragger glyco search in the FragPipe graphical user interface, providing a complete computational pipeline for annotation of N-glycopeptide spectra with false discovery rate control of both peptide and glycan components that is both sensitive and robust against false identifications. Identifying the glycan on intact glycopeptides remains difficult in glycoproteomics. We developed a method to assign glycan compositions in N-glycoproteomics searches. We demonstrate well-controlled glycan FDR in multiple sample types. The method annotates more glycopeptide spectra than competing tools. The method is included PTM-Shepherd for a full glycoproteomics workflow in FragPipe.
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Affiliation(s)
- Daniel A Polasky
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Daniel J Geiszler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
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13
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Oliveira T, Thaysen-Andersen M, Packer NH, Kolarich D. The Hitchhiker's guide to glycoproteomics. Biochem Soc Trans 2021; 49:1643-1662. [PMID: 34282822 PMCID: PMC8421054 DOI: 10.1042/bst20200879] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023]
Abstract
Protein glycosylation is one of the most common post-translational modifications that are essential for cell function across all domains of life. Changes in glycosylation are considered a hallmark of many diseases, thus making glycoproteins important diagnostic and prognostic biomarker candidates and therapeutic targets. Glycoproteomics, the study of glycans and their carrier proteins in a system-wide context, is becoming a powerful tool in glycobiology that enables the functional analysis of protein glycosylation. This 'Hitchhiker's guide to glycoproteomics' is intended as a starting point for anyone who wants to explore the emerging world of glycoproteomics. The review moves from the techniques that have been developed for the characterisation of single glycoproteins to technologies that may be used for a successful complex glycoproteome characterisation. Examples of the variety of approaches, methodologies, and technologies currently used in the field are given. This review introduces the common strategies to capture glycoprotein-specific and system-wide glycoproteome data from tissues, body fluids, or cells, and a perspective on how integration into a multi-omics workflow enables a deep identification and characterisation of glycoproteins - a class of biomolecules essential in regulating cell function.
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Affiliation(s)
- Tiago Oliveira
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
| | | | - Nicolle H. Packer
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast Campus, Gold Coast, Queensland, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD and Macquarie University, NSW, Australia
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14
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Gaunitz S, Tjernberg LO, Schedin-Weiss S. What Can N-glycomics and N-glycoproteomics of Cerebrospinal Fluid Tell Us about Alzheimer Disease? Biomolecules 2021; 11:858. [PMID: 34207636 PMCID: PMC8226827 DOI: 10.3390/biom11060858] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 12/18/2022] Open
Abstract
Proteomics-large-scale studies of proteins-has over the last decade gained an enormous interest for studies aimed at revealing proteins and pathways involved in disease. To fully understand biological and pathological processes it is crucial to also include post-translational modifications in the "omics". To this end, glycomics (identification and quantification of glycans enzymatically or chemically released from proteins) and glycoproteomics (identification and quantification of peptides/proteins with the glycans still attached) is gaining interest. The study of protein glycosylation requires a workflow that involves an array of sample preparation and analysis steps that needs to be carefully considered. Herein, we briefly touch upon important steps such as sample preparation and preconcentration, glycan release, glycan derivatization and quantification and advances in mass spectrometry that today are the work-horse for glycomics and glycoproteomics studies. Several proteins related to Alzheimer disease pathogenesis have altered protein glycosylation, and recent glycomics studies have shown differences in cerebrospinal fluid as well as in brain tissue in Alzheimer disease as compared to controls. In this review, we discuss these techniques and how they have been used to shed light on Alzheimer disease and to find glycan biomarkers in cerebrospinal fluid.
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Affiliation(s)
- Stefan Gaunitz
- Department of Clinical Chemistry, Karolinska University Hospital, 14186 Stockholm, Sweden;
| | - Lars O. Tjernberg
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 17164 Solna, Sweden;
| | - Sophia Schedin-Weiss
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, 17164 Solna, Sweden;
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15
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Pralow A, Nikolay A, Leon A, Genzel Y, Rapp E, Reichl U. Site-specific N-glycosylation analysis of animal cell culture-derived Zika virus proteins. Sci Rep 2021; 11:5147. [PMID: 33664361 PMCID: PMC7933209 DOI: 10.1038/s41598-021-84682-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 02/18/2021] [Indexed: 01/09/2023] Open
Abstract
Here, we present for the first time, a site-specific N-glycosylation analysis of proteins from a Brazilian Zika virus (ZIKV) strain. The virus was propagated with high yield in an embryo-derived stem cell line (EB66, Valneva SE), and concentrated by g-force step-gradient centrifugation. Subsequently, the sample was proteolytically digested with different enzymes, measured via a LC–MS/MS-based workflow, and analyzed in a semi-automated way using the in-house developed glyXtoolMS software. The viral non-structural protein 1 (NS1) was glycosylated exclusively with high-mannose structures on both potential N-glycosylation sites. In case of the viral envelope (E) protein, no specific N-glycans could be identified with this method. Nevertheless, N-glycosylation could be proved by enzymatic de-N-glycosylation with PNGase F, resulting in a strong MS-signal of the former glycopeptide with deamidated asparagine at the potential N-glycosylation site N444. This confirmed that this site of the ZIKV E protein is highly N-glycosylated but with very high micro-heterogeneity. Our study clearly demonstrates the progress made towards site-specific N-glycosylation analysis of viral proteins, i.e. for Brazilian ZIKV. It allows to better characterize viral isolates, and to monitor glycosylation of major antigens. The method established can be applied for detailed studies regarding the impact of protein glycosylation on antigenicity and human pathogenicity of many viruses including influenza virus, HIV and corona virus.
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Affiliation(s)
- Alexander Pralow
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Alexander Nikolay
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | | | - Yvonne Genzel
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany. .,glyXera GmbH, Magdeburg, Germany.
| | - Udo Reichl
- Bioprocess Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
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16
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Pralow A, Hoffmann M, Nguyen-Khuong T, Pioch M, Hennig R, Genzel Y, Rapp E, Reichl U. Comprehensive N-glycosylation analysis of the influenza A virus proteins HA and NA from adherent and suspension MDCK cells. FEBS J 2021; 288:4869-4891. [PMID: 33629527 DOI: 10.1111/febs.15787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/25/2022]
Abstract
Glycosylation is considered as a critical quality attribute for the production of recombinant biopharmaceuticals such as hormones, blood clotting factors, or monoclonal antibodies. In contrast, glycan patterns of immunogenic viral proteins, which differ significantly between the various expression systems, are hardly analyzed yet. The influenza A virus (IAV) proteins hemagglutinin (HA) and neuraminidase (NA) have multiple N-glycosylation sites, and alteration of N-glycan micro- and macroheterogeneity can have strong effects on virulence and immunogenicity. Here, we present a versatile and powerful glycoanalytical workflow that enables a comprehensive N-glycosylation analysis of IAV glycoproteins. We challenged our workflow with IAV (A/PR/8/34 H1N1) propagated in two closely related Madin-Darby canine kidney (MDCK) cell lines, namely an adherent MDCK cell line and its corresponding suspension cell line. As expected, N-glycan patterns of HA and NA from virus particles produced in both MDCK cell lines were similar. Detailed analysis of the HA N-glycan microheterogeneity showed an increasing variability and a higher complexity for N-glycosylation sites located closer to the head region of the molecule. In contrast, NA was found to be exclusively N-glycosylated at site N73. Almost all N-glycan structures were fucosylated. Furthermore, HA and NA N-glycan structures were exclusively hybrid- and complex-type structures, to some extent terminated with alpha-linked galactose(s) but also with blood group H type 2 and blood group A epitopes. In contrast to the similarity of the overall glycan pattern, differences in the relative abundance of individual structures were identified. This concerned, in particular, oligomannose-type, alpha-linked galactose, and multiantennary complex-type N-glycans.
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Affiliation(s)
- Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Terry Nguyen-Khuong
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Markus Pioch
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - René Hennig
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,glyXera GmbH, Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.,Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
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17
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Towards structure-focused glycoproteomics. Biochem Soc Trans 2021; 49:161-186. [PMID: 33439247 PMCID: PMC7925015 DOI: 10.1042/bst20200222] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While diverse quantitative glycoproteomics strategies capable of mapping monosaccharide compositions of N- and O-linked glycans to discrete sites of proteins within complex biological mixtures with considerable sensitivity, quantitative accuracy and coverage have become available, developments supporting the advancement of structure-focused glycoproteomics, a recognised frontier in the field, have emerged. Technologies capable of providing site-specific information of the glycan fine structures in a glycoproteome-wide context are indeed necessary to address many pending questions in glycobiology. In this review, we firstly survey the latest glycoproteomics studies published in 2018–2020, their approaches and their findings, and then summarise important technological innovations in structure-focused glycoproteomics. Our review illustrates that while the O-glycoproteome remains comparably under-explored despite the emergence of new O-glycan-selective mucinases and other innovative tools aiding O-glycoproteome profiling, quantitative glycoproteomics is increasingly used to profile the N-glycoproteome to tackle diverse biological questions. Excitingly, new strategies compatible with structure-focused glycoproteomics including novel chemoenzymatic labelling, enrichment, separation, and mass spectrometry-based detection methods are rapidly emerging revealing glycan fine structural details including bisecting GlcNAcylation, core and antenna fucosylation, and sialyl-linkage information with protein site resolution. Glycoproteomics has clearly become a mainstay within the glycosciences that continues to reach a broader community. It transpires that structure-focused glycoproteomics holds a considerable potential to aid our understanding of systems glycobiology and unlock secrets of the glycoproteome in the immediate future.
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18
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Noor SI, Hoffmann M, Rinis N, Bartels MF, Winterhalter PR, Hoelscher C, Hennig R, Himmelreich N, Thiel C, Ruppert T, Rapp E, Strahl S. Glycosyltransferase POMGNT1 deficiency strengthens N-cadherin-mediated cell-cell adhesion. J Biol Chem 2021; 296:100433. [PMID: 33610554 PMCID: PMC7994789 DOI: 10.1016/j.jbc.2021.100433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/08/2021] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Defects in protein O-mannosylation lead to severe congenital muscular dystrophies collectively known as α-dystroglycanopathy. A hallmark of these diseases is the loss of the O-mannose-bound matriglycan on α-dystroglycan, which reduces cell adhesion to the extracellular matrix. Mutations in protein O-mannose β1,2-N-acetylglucosaminyltransferase 1 (POMGNT1), which is crucial for the elongation of O-mannosyl glycans, have mainly been associated with muscle-eye-brain (MEB) disease. In addition to defects in cell-extracellular matrix adhesion, aberrant cell-cell adhesion has occasionally been observed in response to defects in POMGNT1. However, specific molecular consequences of POMGNT1 deficiency on cell-cell adhesion are largely unknown. We used POMGNT1 knockout HEK293T cells and fibroblasts from an MEB patient to gain deeper insight into the molecular changes in POMGNT1 deficiency. Biochemical and molecular biological techniques combined with proteomics, glycoproteomics, and glycomics revealed that a lack of POMGNT1 activity strengthens cell-cell adhesion. We demonstrate that the altered intrinsic adhesion properties are due to an increased abundance of N-cadherin (N-Cdh). In addition, site-specific changes in the N-glycan structures in the extracellular domain of N-Cdh were detected, which positively impact on homotypic interactions. Moreover, in POMGNT1-deficient cells, ERK1/2 and p38 signaling pathways are activated and transcriptional changes that are comparable with the epithelial-mesenchymal transition (EMT) are triggered, defining a possible molecular mechanism underlying the observed phenotype. Our study indicates that changes in cadherin-mediated cell-cell adhesion and other EMT-related processes may contribute to the complex clinical symptoms of MEB or α-dystroglycanopathy in general and suggests that the impact of changes in O-mannosylation on N-glycosylation has been underestimated.
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Affiliation(s)
- Sina Ibne Noor
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Heidelberg, Germany
| | - Marcus Hoffmann
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany
| | - Natalie Rinis
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Heidelberg, Germany
| | - Markus F Bartels
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Heidelberg, Germany
| | - Patrick R Winterhalter
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Heidelberg, Germany
| | - Christina Hoelscher
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Heidelberg, Germany
| | - René Hennig
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany; glyXera GmbH, Magdeburg, Germany
| | - Nastassja Himmelreich
- Center for Child and Adolescent Medicine, Department Pediatrics I, University of Heidelberg, Heidelberg, Germany
| | - Christian Thiel
- Center for Child and Adolescent Medicine, Department Pediatrics I, University of Heidelberg, Heidelberg, Germany
| | - Thomas Ruppert
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Magdeburg, Germany; glyXera GmbH, Magdeburg, Germany
| | - Sabine Strahl
- Centre for Organismal Studies (COS), Glycobiology, Heidelberg University, Heidelberg, Germany.
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19
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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20
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Glycoproteomics Technologies in Glycobiotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2020; 175:413-434. [PMID: 33205259 DOI: 10.1007/10_2020_144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Glycosylation is a key factor determining the pharmacological properties of biotherapeutics, including their stability, solubility, bioavailability, pharmacokinetics, and immunogenicity. As such, comprehensive information about glycosylation of biotherapeutics is critical to demonstrate similarity. Regulatory agencies also require extensive documentation of the comprehensive analyses of glycosylation-related critical quality attributes (CQAs) during the development, manufacturing, and release of biosimilars. Mass spectrometry has catalysed tremendous advancements in the characterisation of glycosylation CQAs of biotherapeutics. Here we provide a perspective overview on the MS-based technologies relevant for biotherapeutic product characterisation with an emphasis on the recent developments that allow determination of glycosylation features such as site of glycosylation, sialic acid linkage, glycan structure, and content.
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21
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Wu M, Zhang Q, Zhou X, Kong S, Zhao H, Liu M, Yang P, Cao W. An ultrafast and highly efficient enrichment method for both N-Glycopeptides and N-Glycans by bacterial cellulose. Anal Chim Acta 2020; 1140:60-68. [PMID: 33218490 DOI: 10.1016/j.aca.2020.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 09/30/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022]
Abstract
A powerful and fast glycopeptide/glycan enrichment method is critical for the efficiency and throughput of mass spectrometry (MS)-based glycoproteomic and glycomic analyses, especially for large-scale sample analysis. Here, we report an ultrafast and effective method for both intact N-glycopeptide and N-glycan enrichment and apply it to human serum samples. In this method, a natural hydrophilic material, bacterial cellulose (BC), was adopted and fully optimized for enrichment. This method offers the following advantages: (i) The enrichment material has natural hydrophilicity and is low-cost, biocompatible, biodegradable and easily accessible; (ii) the whole enrichment procedure is remarkably simple and fast. It takes only 10 min for intact glycopeptides/glycans to be easily purified from mixtures; (iii) the specificity of this method is over 94% for both glycan and glycopeptide enrichment; and (iv) the outstanding specificity of this technique enables high isolation efficiency for the enrichment of both intact glycopeptides and glycans. A total of 36 N-glycans and 31 N-glycopeptides were identified from human immunoglobulin G (IgG). The glycan and glycopeptide absorption capacity of BC was as high as 333 μg/mg and 250 μg/mg (IgG/BC) respectively. The selectivity for glycan and glycopeptide enrichment reached 1:100 (IgG/bovine serum albumin (BSA), molar ratio) and 1:200 (maltoheptaose (DP7)/BSA, molar ratio), respectively. Furthermore, a total of 159 N-glycans and 523 N-glycopeptides were identified in human serum by using this method. Overall, the BC-based enrichment method we present here provides an ultrafast and highly efficient method for the enrichment of both N-glycopeptides and N-glycans in complex samples and shows great potential in large-scale glycoproteomic and glycomic analyses.
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Affiliation(s)
- Mengxi Wu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, 200032, China
| | - Quanqing Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinwen Zhou
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Siyuan Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Huanhuan Zhao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Mingqi Liu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, 200032, China; NHC Key Laboratory of Glycoconjugates Research (Fudan University), Shanghai, 200032, China.
| | - Weiqian Cao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; The Fifth People's Hospital, Fudan University, and the Shanghai Key Laboratory of Medical Epigenetics, the International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Fudan University, Shanghai, 200032, China; NHC Key Laboratory of Glycoconjugates Research (Fudan University), Shanghai, 200032, China.
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22
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Baralić M, Gligorijević N, Brković V, Katrlík J, Pažitná L, Šunderić M, Miljuš G, Penezić A, Dobrijević Z, Laušević M, Nedić O, Robajac D. Fibrinogen Fucosylation as a Prognostic Marker of End-Stage Renal Disease in Patients on Peritoneal Dialysis. Biomolecules 2020; 10:E1165. [PMID: 32784866 PMCID: PMC7466146 DOI: 10.3390/biom10081165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/01/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022] Open
Abstract
Glycosylation may strongly affect protein structure and functions. A high risk of cardiovascular complications seen in patients with end-stage renal disease (ESRD) is, at least partly associated with delayed clot formation, increased clot strength, and delayed cloth lysis. Taking into consideration that fibrinogen mediates these processes, we isolated fibrinogen from the plasma from patients with ESRD on peritoneal dialysis (ESRD-PD), and examined glycosylation of native fibrinogen and its subunits by lectin-based microarray and lectin blotting. Compared to healthy controls, fibrinogen from patients had increased levels of A2BG2 and decreased levels of FA2 glycan. The distribution of glycans on individual chains was also affected, with the γ chain, responsible for physiological functions of fibrinogen (such as coagulation and platelet aggregation), being most prone to these alterations. Increased levels of multi-antennary N-glycans in ESRD-PD patients were also associated with the type of dialysis solutions, whereas an increase in the fucosylation levels was strongly related to the peritoneal membrane damage. Consequently, investigation of fibrinogen glycans can offer better insight into fibrinogen-related complications observed in ESRD-PD patients and, additionally, contribute to prognosis, choice of personalised therapy, determination of peritoneal membrane damage, and the length of utilization of peritoneum for dialysis.
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Affiliation(s)
- Marko Baralić
- Department of Nephrology, Clinical Centre of Serbia, 11000 Belgrade, Serbia; (M.B.); (V.B.); (M.L.)
| | - Nikola Gligorijević
- Department of Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia; (N.G.); (M.Š.); (G.M.); (A.P.); (Z.D.); (O.N.)
| | - Voin Brković
- Department of Nephrology, Clinical Centre of Serbia, 11000 Belgrade, Serbia; (M.B.); (V.B.); (M.L.)
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Jaroslav Katrlík
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia; (J.K.); (L.P.)
| | - Lucia Pažitná
- Institute of Chemistry, Slovak Academy of Sciences, 84538 Bratislava, Slovakia; (J.K.); (L.P.)
| | - Miloš Šunderić
- Department of Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia; (N.G.); (M.Š.); (G.M.); (A.P.); (Z.D.); (O.N.)
| | - Goran Miljuš
- Department of Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia; (N.G.); (M.Š.); (G.M.); (A.P.); (Z.D.); (O.N.)
| | - Ana Penezić
- Department of Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia; (N.G.); (M.Š.); (G.M.); (A.P.); (Z.D.); (O.N.)
| | - Zorana Dobrijević
- Department of Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia; (N.G.); (M.Š.); (G.M.); (A.P.); (Z.D.); (O.N.)
| | - Mirjana Laušević
- Department of Nephrology, Clinical Centre of Serbia, 11000 Belgrade, Serbia; (M.B.); (V.B.); (M.L.)
- School of Medicine, University of Belgrade, 11000 Belgrade, Serbia
| | - Olgica Nedić
- Department of Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia; (N.G.); (M.Š.); (G.M.); (A.P.); (Z.D.); (O.N.)
| | - Dragana Robajac
- Department of Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, 11080 Belgrade, Serbia; (N.G.); (M.Š.); (G.M.); (A.P.); (Z.D.); (O.N.)
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23
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Synthesis of lipid-linked oligosaccharides by a compartmentalized multi-enzyme cascade for the in vitro N-glycosylation of peptides. J Biotechnol 2020; 322:54-65. [PMID: 32653637 DOI: 10.1016/j.jbiotec.2020.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 06/18/2020] [Accepted: 07/08/2020] [Indexed: 01/21/2023]
Abstract
A wide range of glycoproteins can be recombinantly expressed in aglycosylated forms in bacterial and cell-free production systems. To investigate the effect of glycosylation of these proteins on receptor binding, stability, efficacy as drugs, pharmacodynamics and pharmacokinetics, an efficient glycosylation platform is required. Here, we present a cell-free synthetic platform for the in vitro N-glycosylation of peptides mimicking the endoplasmic reticulum (ER) glycosylation machinery of eukaryotes. The one-pot, two compartment multi-enzyme cascade consisting of eight recombinant enzymes including the three Leloir glycosyltransferases, Alg1, Alg2 and Alg11, expressed in E. coli and S. cerevisiae, respectively, has been engineered to produce the core lipid-linked (LL) oligosaccharide mannopentaose-di-(N-acetylglucosamine) (LL-Man5). Pythanol (C20H42O), a readily available alcohol consisting of regular isoprenoid units, was utilized as the lipid anchor. As part of the cascade, GDP-mannose was de novo produced from the inexpensive substrates ADP, polyphosphate and mannose. To prevent enzyme inhibition, the nucleotide sugar cascade and the glycosyltransferase were segregated into two compartments by a cellulose ester membrane with 3.5 kDa cut-off allowing for the effective diffusion of GDP-mannose across compartments. Finally, as a proof-of-principle, pythanyl-linked Man5 and the single-subunit oligosaccharyltransferase Trypanosoma brucei STT3A expressed in Sf9 insect cells were used to in vitro N-glycosylate a synthetic peptide of ten amino acids bearing the eukaryotic consensus motif N-X-S/T.
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24
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Riley NM, Malaker SA, Driessen MD, Bertozzi CR. Optimal Dissociation Methods Differ for N- and O-Glycopeptides. J Proteome Res 2020; 19:3286-3301. [PMID: 32500713 PMCID: PMC7425838 DOI: 10.1021/acs.jproteome.0c00218] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
![]()
Site-specific
characterization of glycosylation requires intact
glycopeptide analysis, and recent efforts have focused on how to best
interrogate glycopeptides using tandem mass spectrometry (MS/MS).
Beam-type collisional activation, i.e., higher-energy collisional
dissociation (HCD), has been a valuable approach, but stepped collision
energy HCD (sceHCD) and electron transfer dissociation with HCD supplemental
activation (EThcD) have emerged as potentially more suitable alternatives.
Both sceHCD and EThcD have been used with success in large-scale glycoproteomic
experiments, but they each incur some degree of compromise. Most progress
has occurred in the area of N-glycoproteomics. There
is growing interest in extending this progress to O-glycoproteomics, which necessitates comparisons of method performance
for the two classes of glycopeptides. Here, we systematically explore
the advantages and disadvantages of conventional HCD, sceHCD, ETD,
and EThcD for intact glycopeptide analysis and determine their suitability
for both N- and O-glycoproteomic
applications. For N-glycopeptides, HCD and sceHCD
generate similar numbers of identifications, although sceHCD generally
provides higher quality spectra. Both significantly outperform EThcD
methods in terms of identifications, indicating that ETD-based methods
are not required for routine N-glycoproteomics even
if they can generate higher quality spectra. Conversely, ETD-based
methods, especially EThcD, are indispensable for site-specific analyses
of O-glycopeptides. Our data show that O-glycopeptides cannot be robustly characterized with HCD-centric
methods that are sufficient for N-glycopeptides,
and glycoproteomic methods aiming to characterize O-glycopeptides must be constructed accordingly.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Marc D Driessen
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305-6104, United States.,Howard Hughes Medical Institute, Stanford, California 94305-6104, United States
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25
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Sanda M, Benicky J, Goldman R. Low Collision Energy Fragmentation in Structure-Specific Glycoproteomics Analysis. Anal Chem 2020; 92:8262-8267. [PMID: 32441515 DOI: 10.1021/acs.analchem.0c00519] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Glycosylation is a major post-translational modification of proteins that regulates many biological processes including protein folding, structure stability, receptor activation, and immune responses. The glycans attached to proteins represent an important determinant of the protein interaction-specificity and maintain the 3D structure of proteins. Mass spectrometry (MS) is one of the most efficient tools used in the current studies of glycoproteins and structure of their glycoforms. Collision energy (CE) is a crucial instrument parameter that can be exploited to improve structural resolution because different linkages of glycan units show different stabilities under CID/HCD fragmentation. Here we report the utility of CE modulation for qualitative and quantitative analysis of site- and structure-specific glycoforms of proteins. Using CE modulation, we were able to break selectively specific glycan linkages on intact glycopeptides and get, to some degree, structure-specific mass spectrometric signals. Structure- and CE-specific oxonium ions provide sufficient information for the resolution of outer arm structure motifs with recognized biological functions. The complementary Y-ions, generated under optimized low CE (soft) conditions, provide additional structural information including features specific to the chitobiose core. This methodology of multiple CE fragmentation without merging spectral information can significantly improve confidence of glycopeptide identification and structural resolution by providing additional information to the established glycopeptide-search algorithms and tools.
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Affiliation(s)
- Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, DC 20057, United States
| | - Julius Benicky
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, DC 20057, United States
| | - Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, United States.,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, United States.,Clinical and Translational Glycoscience Research Center, Georgetown University, Washington, DC 20057, United States
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26
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Qing G, Yan J, He X, Li X, Liang X. Recent advances in hydrophilic interaction liquid interaction chromatography materials for glycopeptide enrichment and glycan separation. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.06.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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The Cannabis Proteome Draft Map Project. Int J Mol Sci 2020; 21:ijms21030965. [PMID: 32024021 PMCID: PMC7037972 DOI: 10.3390/ijms21030965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
Recently we have seen a relaxation of the historic restrictions on the use and subsequent research on the Cannabis plants, generally classified as Cannabis sativa and Cannabis indica. What research has been performed to date has centered on chemical analysis of plant flower products, namely cannabinoids and various terpenes that directly contribute to phenotypic characteristics of the female flowers. In addition, we have seen many groups recently completing genetic profiles of various plants of commercial value. To date, no comprehensive attempt has been made to profile the proteomes of these plants. We report herein our progress on constructing a comprehensive draft map of the Cannabis proteome. To date we have identified over 17,000 potential protein sequences. Unfortunately, no annotated genome of Cannabis plants currently exists. We present a method by which “next generation” DNA sequencing output and shotgun proteomics data can be combined to produce annotated FASTA files, bypassing the need for annotated genetic information altogether in traditional proteomics workflows. The resulting material represents the first comprehensive annotated protein FASTA for any Cannabis plant. Using this annotated database as reference we can refine our protein identifications, resulting in the confident identification of 13,000 proteins with putative function. Furthermore, we demonstrate that post-translational modifications play an important role in the proteomes of Cannabis flower, particularly lysine acetylation and protein glycosylation. To facilitate the evolution of analytical investigations into these plant materials, we have created a portal to host resources developed from our proteomic and metabolomic analysis of Cannabis plant material as well as our results integrating these resources.
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28
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Čaval T, Zhu J, Heck AJR. Simply Extending the Mass Range in Electron Transfer Higher Energy Collisional Dissociation Increases Confidence in N-Glycopeptide Identification. Anal Chem 2019; 91:10401-10406. [PMID: 31287300 PMCID: PMC6706795 DOI: 10.1021/acs.analchem.9b02125] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Glycopeptide-centric
mass spectrometry has become a popular approach
for studying protein glycosylation. However, current approaches still
utilize fragmentation schemes and ranges originally optimized and
intended for the analysis of typically much smaller unmodified tryptic
peptides. Here, we show that by merely increasing the tandem mass
spectrometry m/z range from 2000
to 4000 during electron transfer higher energy collisional dissociation
(EThcD) fragmentation, a wealth of highly informative c and z ion
fragment ions are additionally detected, facilitating improved identification
of glycopeptides. We demonstrate the benefit of this extended mass
range on various classes of glycopeptides containing phosphorylated,
fucosylated, and/or sialylated N-glycans. We conclude that the current
software solutions for glycopeptide identification also require further
improvements to realize the full potential of extended mass range
glycoproteomics. To stimulate further developments, we provide data
sets containing all classes of glycopeptides (high mannose, hybrid,
and complex) measured with standard (2000) and extended (4000) m/z range that can be used as test cases
for future development of software solutions enhancing automated glycopeptide
analysis.
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Affiliation(s)
- Tomislav Čaval
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Center , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Jing Zhu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Center , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht , Padualaan 8 , 3584 CH Utrecht , The Netherlands.,Netherlands Proteomics Center , Padualaan 8 , 3584 CH Utrecht , The Netherlands
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29
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Identification of bioactive short peptides in cow milk by high-performance liquid chromatography on C18 and porous graphitic carbon coupled to high-resolution mass spectrometry. Anal Bioanal Chem 2019; 411:3395-3404. [DOI: 10.1007/s00216-019-01815-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 12/24/2022]
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30
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Gränicher G, Coronel J, Pralow A, Marichal-Gallardo P, Wolff M, Rapp E, Karlas A, Sandig V, Genzel Y, Reichl U. Efficient influenza A virus production in high cell density using the novel porcine suspension cell line PBG.PK2.1. Vaccine 2019; 37:7019-7028. [PMID: 31005427 DOI: 10.1016/j.vaccine.2019.04.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/29/2019] [Accepted: 04/08/2019] [Indexed: 12/22/2022]
Abstract
Seasonal and pandemic influenza respiratory infections are still a major public health issue. Vaccination is the most efficient way to prevent influenza infection. One option to produce influenza vaccines is cell-culture based virus propagation. Different host cell lines, such as MDCK, Vero, AGE1.CR or PER.C6 cells have been shown to be a good substrate for influenza virus production. With respect to the ease of scale-up, suspension cells should be preferred over adherent cells. Ideally, they should replicate different influenza virus strains with high cell-specific yields. Evaluation of new cell lines and further development of processes is of considerable interest, as this increases the number of options regarding the design of manufacturing processes, flexibility of vaccine production and efficiency. Here, PBG.PK2.1, a new mammalian cell line that was developed by ProBioGen AG (Germany) for virus production is presented. The cells derived from immortal porcine kidney cells were previously adapted to growth in suspension in a chemically-defined medium. Influenza virus production was improved after virus adaptation to PBG.PK2.1 cells and optimization of infection conditions, namely multiplicity of infection and trypsin concentration. Hemagglutinin titers up to 3.24 log10(HA units/100 µL) were obtained in fed-batch mode in bioreactors (700 mL working volume). Evaluation of virus propagation in high cell density culture using a hollow-fiber based system (ATF2) demonstrated promising performance: Cell concentrations of up to 50 × 106 cells/mL with viabilities exceeding 95%, and a maximum HA titer of 3.93 log10(HA units/100 µL). Analysis of glycosylation of the viral HA antigen expressed showed clear differences compared to HA produced in MDCK or Vero cell lines. With an average cell-specific productivity of 5000 virions/cell, we believe that PBG.PK2.1 cells are a very promising candidate to be considered for next-generation influenza virus vaccine production.
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Affiliation(s)
- Gwendal Gränicher
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106 Magdeburg, Germany.
| | - Juliana Coronel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106 Magdeburg, Germany
| | - Alexander Pralow
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106 Magdeburg, Germany
| | - Pavel Marichal-Gallardo
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106 Magdeburg, Germany
| | - Michael Wolff
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106 Magdeburg, Germany; Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Gießen, Germany
| | - Erdmann Rapp
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106 Magdeburg, Germany
| | | | | | - Yvonne Genzel
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106 Magdeburg, Germany
| | - Udo Reichl
- Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, Sandtorstr. 1, 39106 Magdeburg, Germany; Chair for Bioprocess Engineering, Otto-von-Guericke-University Magdeburg, Universitätsplatz 2, 39106 Magdeburg, Germany
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