1
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Macauslane KL, Pegg CL, Nouwens AS, Kerr ED, Seitanidou J, Schulz BL. Electron-Activated Dissociation and Collision-Induced Dissociation Glycopeptide Fragmentation for Improved Glycoproteomics. Anal Chem 2024. [PMID: 38935274 DOI: 10.1021/acs.analchem.4c01450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Tandem mass spectrometry coupled with liquid chromatography (LC-MS/MS) has proven a versatile tool for the identification and quantification of proteins and their post-translational modifications (PTMs). Protein glycosylation is a critical PTM for the stability and biological function of many proteins, but full characterization of site-specific glycosylation of proteins remains analytically challenging. Collision-induced dissociation (CID) is the most common fragmentation method used in LC-MS/MS workflows, but the loss of labile modifications renders CID inappropriate for detailed characterization of site-specific glycosylation. Electron-based dissociation methods provide alternatives that retain intact glycopeptide fragments for unambiguous site localization, but these methods often underperform CID due to increased reaction times and reduced efficiency. Electron-activated dissociation (EAD) is another strategy for glycopeptide fragmentation. Here, we use a ZenoTOF 7600 SCIEX instrument to compare the performance of various fragmentation techniques for the analysis of a complex mixture of mammalian O- and N-glycopeptides. We found CID fragmentation identified the most glycopeptides and generally produced higher quality spectra, but EAD provided improved confidence in glycosylation site localization. Supplementing EAD with CID fragmentation (EAciD) further increased the number and quality of glycopeptide identifications, while retaining localization confidence. These methods will be useful for glycoproteomics workflows for either optimal glycopeptide identification or characterization.
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Affiliation(s)
- Kyle L Macauslane
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Amanda S Nouwens
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joy Seitanidou
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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2
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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.
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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
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3
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Liu S, Ryumin P, Albanese J, Zhang Z, Baba T. Analysis of Sialic Acid Linkage in N-Linked Glycopeptides Using Liquid Chromatography-Electron-Activated Dissociation Time-of-Flight Mass Spectrometry. Anal Chem 2023; 95:7458-7467. [PMID: 37146167 DOI: 10.1021/acs.analchem.2c04581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Herein, we report a novel liquid chromatography coupled with tandem mass spectrometry method to characterize N-acetylneuraminic acid (Neu5Ac, Sa) linkage in N-linked glycans in glycopeptides with no sialic acid derivatization. First, we established a separation in reversed-phase high-performance liquid chromatography (HPLC) using a higher formic acid concentration in the mobile phases, which separated the N-glycopeptides depending on the Sa linkage. We also demonstrated a novel characterization method of Sa linkages in N-glycopeptides using electron-activated dissociation. We found that hot electron capture dissociation using an electron beam energy higher than 5 eV cleaved glycosidic bonds in glycopeptides, resulting in each glycosidic bond in the antennas being broken on both sides of the oxygen atom. Such glycosidic bond cleavage at the reducing end (C-type ion) showed the difference in Sa linkages between Sa-Gal, Gal-GlcNAc, and GlcNAc-Man. We proposed a rule to characterize the Sa linkages using the Sa-Gal products. This method was applied to N-glycopeptides in tryptic fetuin digest separated by an optimized reversed-phase HPLC. We successfully identified a number of isomeric glycoforms in the glycopeptides with different Sa links, whose peptide backbones were also simultaneously sequenced by hot ECD.
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Affiliation(s)
- Suya Liu
- Sciex, 71 Four Valley Dr. Concord, Ontario L4K 4V8, Canada
| | - Pavel Ryumin
- Sciex, 71 Four Valley Dr. Concord, Ontario L4K 4V8, Canada
| | - Jenny Albanese
- Sciex, 1201 Radio Rd, Redwood City, California 94065, United States
| | - Zoe Zhang
- Sciex, 1201 Radio Rd, Redwood City, California 94065, United States
| | - Takashi Baba
- Sciex, 71 Four Valley Dr. Concord, Ontario L4K 4V8, Canada
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4
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Baba T, Zhang Z, Liu S, Burton L, Ryumin P, Le Blanc JCY. Localization of Multiple O-Linked Glycans Exhibited in Isomeric Glycopeptides by Hot Electron Capture Dissociation. J Proteome Res 2022; 21:2462-2471. [PMID: 36074808 DOI: 10.1021/acs.jproteome.2c00378] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a method to obtain a comprehensive profile of multiple glycosylations in glycopeptide isoforms. We detected a wide range of abundances of various O-glycoforms in isomeric glycopeptides using hot electron capture dissociation (hot ECD) in liquid chromatography-tandem mass spectrometry. To capture low abundant glycosylated species, a prototype of a ZenoTOF 7600 system incorporating an efficient electron-activated dissociation device to perform hot ECD was operated in targeted or scheduled high-resolution multiple reaction monitoring workflows. In addition, Zeno trap pulsing was activated to enhance the sensitivity of the time-of-flight mass spectrometer. Sixty-nine O-glycopeptides of the long O-glycopeptides in tryptic bovine fetuin digest were obtained with a relative abundance range from 100 to 0.2%, which included sialylated glycans with Neu5Ac and Neu5Gc.
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Affiliation(s)
- Takashi Baba
- Sciex, 71 Four Valley Dr., Concord, Ontario L4K 4V8, Canada
| | - Zoe Zhang
- Sciex, 1201 Radio Rd., Redwood City, California 94065, United States
| | - Suya Liu
- Sciex, 71 Four Valley Dr., Concord, Ontario L4K 4V8, Canada
| | - Lyle Burton
- Sciex, 71 Four Valley Dr., Concord, Ontario L4K 4V8, Canada
| | - Pavel Ryumin
- Sciex, 71 Four Valley Dr., Concord, Ontario L4K 4V8, Canada
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5
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Baba T, Rajabi K, Liu S, Ryumin P, Zhang Z, Pohl K, Causon J, Le Blanc JCY, Kurogochi M. Electron Impact Excitation of Ions from Organics on Singly Protonated Peptides with and without Post-Translational Modifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1723-1732. [PMID: 35948044 DOI: 10.1021/jasms.2c00146] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We report on the dissociation of singly protonated peptides by electrons using electron-activated dissociation (EAD), which comprises electron impact excitation of ions from organics (EIEIO), electronic-excitation dissociation (EED), and electron ionization dissociation (EIoD). Various singly protonated peptides were dissociated using a recently reported fast EAD device. The dissociation can be induced through two pathways: (i) vibrational dissociation similar to collision-activated dissociation (CAD, or collision-induced dissociation, CID) by relaxation from a molecular electronic excited state to high vibrational states; and (ii) radical-induced dissociation where molecular electronic excitation is followed by homolytic cleavage. EAD is complementary to CAD as additional molecular information can be obtained; e.g., fragile PTM moieties, such as glycosylation and sulfation, can be localized. Simultaneously, the energetic production of radical z• fragments enables Leu and Ile discrimination, like in a hot ECD process. Using the fast EAD device, LC-EIEIO-time-of-flight mass spectrometry was applied to a tryptic monoclonal antibody digest containing short singly protonated peptides.
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Affiliation(s)
- Takashi Baba
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | - Khadijeh Rajabi
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | - Suya Liu
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | - Pavel Ryumin
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | - Zoe Zhang
- SCIEX, 1201 Radio Rd, Redwood City, California 94065, United States
| | - Kerstin Pohl
- SCIEX, 500 Old Connecticut Path, Framingham, Massachusetts 01701, United States
| | - Jason Causon
- SCIEX, 71 Four Valley Dr., Concord, Ontario L4K 4 V8, Canada
| | | | - Masaki Kurogochi
- The Noguchi Institute, 1-9-7, Kaga, Itabashi-ku, Tokyo 173-0003, Japan
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6
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Baba T, Ryumin P, Duchoslav E, Chen K, Chelur A, Loyd B, Chernushevich I. Dissociation of Biomolecules by an Intense Low-Energy Electron Beam in a High Sensitivity Time-of-Flight Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1964-1975. [PMID: 34080873 DOI: 10.1021/jasms.0c00425] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We report the progress on an electron-activated dissociation (EAD) device coupled to a quadrupole TOF mass spectrometer (QqTOF MS) developed in our group. This device features a new electron beam optics design allowing up to 100 times stronger electron currents in the reaction cell. The electron beam current reached the space-charge limit of 0.5 μA at near-zero electron kinetic energies. These advances enable fast and efficient dissociation of various analytes ranging from singly charged small molecules to multiply protonated proteins. Tunable electron energy provides access to different fragmentation regimes: ECD, hot ECD, and electron-impact excitation of ions from organics (EIEIO). The efficiency of the device was tested on a wide range of precursor charge states. The EAD device was installed in a QqTOF MS employing a novel trap-and-release strategy facilitating spatial mass focusing of ions at the center of the TOF accelerator. This technique increased the sensitivity 6-10 times and allows for the first time comprehensive structural lipidomics on an LC time scale. The system was evaluated for other compound classes such as intact proteins and glycopeptides. Application of hot ECD for the analysis of glycopeptides resulted in rich fragmentation with predominantly peptide backbone fragments; however, glycan fragments attributed to the ECD process were also observed. A standard small protein ubiquitin (8.6 kDa) was sequenced with 90% cleavage coverage at spectrum accumulation times of 100 ms and 98% at 800 ms. Comparable cleavage coverage for a medium-size protein (carbonic anhydrase: 29 kDa) could be achieved, albeit with longer accumulation times.
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Affiliation(s)
- Takashi Baba
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Pavel Ryumin
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Eva Duchoslav
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Keqin Chen
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Anjali Chelur
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
| | - Bill Loyd
- Sciex, 71 Four Valley Drive Concord, Ontario L4K 4V8, Canada
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7
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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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8
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Aboufazeli F, Dodds ED. Precursor ion survival energies of protonated N-glycopeptides and their weak dependencies on high mannose N-glycan composition in collision-induced dissociation. Analyst 2018; 143:4459-4468. [PMID: 30151520 PMCID: PMC6131044 DOI: 10.1039/c8an00830b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fully realizing the capabilities of tandem mass spectrometry (MS/MS) for analysis of glycosylated peptides will require further understanding of the unimolecular dissociation chemistry that dictates their fragmentation pathways. In this context, the overall composition of a given glycopeptide ion is a key characteristic; however, the extent to which the carbohydrate moiety influences the preferred dissociation channels has received relatively little study. Here, the effect of glycan composition on energy-resolved collision-induced dissociation (CID) behavior was studied for a select menu of 30 protonated high mannose type N-linked glycopeptide ions. Groups of analytes which shared a common charge state, polypeptide sequence, and glycosylation site exhibited 50% precursor ion survival energies that varied only slightly as the size and composition of the oligosaccharide was varied. This was found to be true regardless of whether the precursor ion survival energies were normalized for the number of available vibrational degrees of freedom. The practical consequence of this was that a given collision energy brought about highly similar levels of precursor ion depletion and structural information despite systematic variation of the glycan identity. This lack of sensitivity to oligosaccharide composition stands in contrast to other physicochemical properties of glycopeptide ions (e.g., polypeptide composition, charge state, charge carrier) which sharply influence their energy-resolved CID characteristics. On the whole, these findings imply that the deliberate selection of CID energies to bring about a desired range of fragmentation pathways does not necessarily hinge on the nature of the glycan.
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Affiliation(s)
- Forouzan Aboufazeli
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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9
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Zhang Q, Li Z, Wang Y, Zheng Q, Li J. Mass spectrometry for protein sialoglycosylation. MASS SPECTROMETRY REVIEWS 2018; 37:652-680. [PMID: 29228471 DOI: 10.1002/mas.21555] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/17/2017] [Indexed: 06/07/2023]
Abstract
Sialic acids are a family of structurally unique and negatively charged nine-carbon sugars, normally found at the terminal positions of glycan chains on glycoproteins and glycolipids. The glycosylation of proteins is a universal post-translational modification in eukaryotic species and regulates essential biological functions, in which the most common sialic acid is N-acetyl-neuraminic acid (2-keto-5-acetamido-3,5-dideoxy-D-glycero-D-galactononulopyranos-1-onic acid) (Neu5NAc). Because of the properties of sialic acids under general mass spectrometry (MS) conditions, such as instability, ionization discrimination, and mixed adducts, the use of MS in the analysis of protein sialoglycosylation is still challenging. The present review is focused on the application of MS related methodologies to the study of both N- and O-linked sialoglycans. We reviewed MS-based strategies for characterizing sialylation by analyzing intact glycoproteins, proteolytic digested glycopeptides, and released glycans. The review concludes with future perspectives in the field.
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Affiliation(s)
- Qiwei Zhang
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Zack Li
- School of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Haidian District, Beijing, China
| | - Qi Zheng
- Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Institute for Interdisciplinary Research, Institute of Environment and Health, School of Chemical and Environmental Engineering, Jianghan University, Wuhan, China
| | - Jianjun Li
- National Research Council Canada, Ottawa, Ontario, Canada
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10
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Khatri K, Pu Y, Klein JA, Wei J, Costello CE, Lin C, Zaia J. Comparison of Collisional and Electron-Based Dissociation Modes for Middle-Down Analysis of Multiply Glycosylated Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1075-1085. [PMID: 29663256 PMCID: PMC6004259 DOI: 10.1007/s13361-018-1909-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/09/2018] [Accepted: 01/29/2018] [Indexed: 05/12/2023]
Abstract
Analysis of singly glycosylated peptides has evolved to a point where large-scale LC-MS analyses can be performed at almost the same scale as proteomics experiments. While collisionally activated dissociation (CAD) remains the mainstay of bottom-up analyses, it performs poorly for the middle-down analysis of multiply glycosylated peptides. With improvements in instrumentation, electron-activated dissociation (ExD) modes are becoming increasingly prevalent for proteomics experiments and for the analysis of fragile modifications such as glycosylation. While these methods have been applied for glycopeptide analysis in isolated studies, an organized effort to compare their efficiencies, particularly for analysis of multiply glycosylated peptides (termed here middle-down glycoproteomics), has not been made. We therefore compared the performance of different ExD modes for middle-down glycopeptide analyses. We identified key features among the different dissociation modes and show that increased electron energy and supplemental activation provide the most useful data for middle-down glycopeptide analysis. Graphical Abstract.
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Affiliation(s)
- Kshitij Khatri
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Yi Pu
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Joshua A Klein
- Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Juan Wei
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Catherine E Costello
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
- Department of Chemistry, Boston University, Boston, MA, USA
| | - Cheng Lin
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA.
- Boston University Medical Campus, 670 Albany St., Suite 504, Boston, MA, 02118, USA.
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA.
- Program in Bioinformatics, Boston University, Boston, MA, USA.
- Boston University Medical Campus, 670 Albany St., Suite 504, Boston, MA, 02118, USA.
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11
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine , Leiden University Medical Center , 2333 ZA Leiden , The Netherlands
| | - Gege Xu
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Qiongyu Li
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Elisha Goonatilleke
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States
| | - Carlito B Lebrilla
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , California 95616 , United States.,Department of Biochemistry and Molecular Medicine , University of California, Davis , Davis , California 95616 , United States.,Foods for Health Institute , University of California, Davis , Davis , California 95616 , United States
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12
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Wong YLE, Chen X, Wu R, Hung YLW, Chan TWD. Structural Characterization of Intact Glycoconjugates by Tandem Mass Spectrometry Using Electron-Induced Dissociation. Anal Chem 2017; 89:10111-10117. [PMID: 28838234 DOI: 10.1021/acs.analchem.7b03128] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Characterizing the structures of glycoconjungates is important because of glycan heterogeneity and structural complexity of aglycon. The presence of relatively weak glycosidic linkages leads to preferential cleavages that limit the acquisition of structural information under typical mass spectrometry dissociation conditions, such as collision-induced dissociation (CID) and infrared multiphoton dissociation. In this paper, we explored the dissociation behaviors of different members of glycoconjugates, including glycopeptides, glycoalkaloids, and glycolipids, under electron-induced dissociation (EID) conditions. Using CID spectra as references, we found that EID is not only a complementary method to CID, but also a method that can generate extensive fragment ions for the structural characterization of all intact glycoconjugates studied. Furthermore, isomeric ganglioside species can be differentiated, and the double bond location in the ceramide moiety of the gangliosides can be identified through the MS3 approach involving sequential CID and EID processes.
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Affiliation(s)
- Y L Elaine Wong
- Department of Chemistry, The Chinese University of Hong Kong , Hong Kong SAR, People's Republic of China
| | - Xiangfeng Chen
- Department of Chemistry, The Chinese University of Hong Kong , Hong Kong SAR, People's Republic of China.,Shandong Analysis and Test Centre, Shandong Academy of Sciences, Qilu University of Technology , Jinan, Shandong, People's Republic of China
| | - Ri Wu
- Department of Chemistry, The Chinese University of Hong Kong , Hong Kong SAR, People's Republic of China
| | - Y L Winnie Hung
- Department of Chemistry, The Chinese University of Hong Kong , Hong Kong SAR, People's Republic of China
| | - T-W Dominic Chan
- Department of Chemistry, The Chinese University of Hong Kong , Hong Kong SAR, People's Republic of China
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13
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Campbell JL, Baba T, Liu C, Lane CS, Le Blanc JCY, Hager JW. Analyzing Glycopeptide Isomers by Combining Differential Mobility Spectrometry with Electron- and Collision-Based Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1374-1381. [PMID: 28432653 DOI: 10.1007/s13361-017-1663-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 05/16/2023]
Abstract
Differential mobility spectrometry (DMS) has been employed to separate isomeric species in several studies. Under the right conditions, factors such as separation voltage, temperature, the presence of chemical modifiers, and residence time can combine to provide unique signal channels for isomeric species. In this study, we examined a set of glycopeptide isomers, MUC5AC-3 and MUC5AC-13, which bear an N-acetyl-galactosamine (GalNAc) group on either threonine-3 or threonine-13. When analyzed as a mixture, the resulting MS and MS/MS spectra yield fragmentation patterns that cannot discern these convolved species. However, when DMS is implemented during the analysis of this mixture, two features emerge in the DMS ionogram representing the two glycopeptide isomers. In addition, by locking in DMS parameters at each feature, we could observe several low intensity CID fragments that contain the GalNAc functionality-specific amino acid residues - identifying the DMS separation of each isomer without standards. Besides conventional CID MS/MS, we also implemented electron-capture dissociation (ECD) after DMS separation, and clearly resolved both isomers with this fragmentation method, as well. The electron energy used in these ECD experiments could be tuned to obtain maximum sequence coverage for these glycopeptides; this was critical as these ions were present as doubly protonated species, which are much more difficult to fragment efficiently via electron-transfer dissociation (ETD). Overall, the combination of DMS with electron- or collision-based MS/MS methods provided enhanced separation and sequence coverage for these glycopeptide isomers. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Takashi Baba
- SCIEX, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada
| | - Chang Liu
- SCIEX, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada
| | | | | | - James W Hager
- SCIEX, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada
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Baba T, Campbell JL, Le Blanc JCY, Baker PRS, Hager JW, Thomson BA. Development of a Branched Radio-Frequency Ion Trap for Electron Based Dissociation and Related Applications. Mass Spectrom (Tokyo) 2017; 6:A0058. [PMID: 28630811 PMCID: PMC5469727 DOI: 10.5702/massspectrometry.a0058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/02/2017] [Indexed: 11/23/2022] Open
Abstract
Collision-induced dissociation (CID) is the most common tool for molecular analysis in mass spectrometry to date. However, there are difficulties associated with many applications because CID does not provide sufficient information to permit details of the molecular structures to be elucidated, including post-translational-modifications in proteomics, as well as isomer differentiation in metabolomics and lipidomics. To face these challenges, we are developing fast electron-based dissociation devices using a novel radio-frequency ion trap (i.e., a branched ion trap). These devices have the ability to perform electron capture dissociation (ECD) on multiply protonated peptide/proteins; in addition, the electron impact excitation of ions from organics (EIEIO) can be also performed on singly charged molecules using such a device. In this article, we review the development of this technology, in particular on how reaction speed for EIEIO analyses on singly charged ions can be improved. We also overview some unique, recently reported applications in both lipidomics and glycoproteomics.
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Thaysen-Andersen M, Packer NH, Schulz BL. Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease. Mol Cell Proteomics 2016; 15:1773-90. [PMID: 26929216 PMCID: PMC5083109 DOI: 10.1074/mcp.o115.057638] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/09/2016] [Indexed: 12/21/2022] Open
Abstract
The glycoproteome remains severely understudied because of significant analytical challenges associated with glycoproteomics, the system-wide analysis of intact glycopeptides. This review introduces important structural aspects of protein N-glycosylation and summarizes the latest technological developments and applications in LC-MS/MS-based qualitative and quantitative N-glycoproteomics. These maturing technologies provide unique structural insights into the N-glycoproteome and its synthesis and regulation by complementing existing methods in glycoscience. Modern glycoproteomics is now sufficiently mature to initiate efforts to capture the molecular complexity displayed by the N-glycoproteome, opening exciting opportunities to increase our understanding of the functional roles of protein N-glycosylation in human health and disease.
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Affiliation(s)
- Morten Thaysen-Andersen
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia;
| | - Nicolle H Packer
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Benjamin L Schulz
- §School of Chemistry & Molecular Biosciences, St Lucia, The University of Queensland, Brisbane, QLD, Australia
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16
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Baba T, Campbell JL. Capturing Polyradical Protein Cations after an Electron Capture Event: Evidence for their Stable Distonic Structures in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1695-1701. [PMID: 26231348 DOI: 10.1007/s13361-015-1207-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 06/04/2023]
Abstract
We report on the formation and "capture" of polyradical protein cations after an electron capture event. Performed in a unique electron-capture dissociation (ECD) instrument, these experiments can generate reduced forms of multiply protonated proteins by sequential charge reduction using electrons with ~1 eV. The true structures of these possible polyradicals is considered: Do the introduced unpaired electrons recombine quickly to form a new two-electron bond, or do these unpaired electrons exist as radical sites with appropriate chemical reactivity? Using an established chemical probe--radical quenching with molecular oxygen--we demonstrate that these charge-reduced protein cations are indeed polyradicals that form adducts with up to three molecules of oxygen (i.e., tri-radical protein cations) that are stable for at least 100 ms.
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Affiliation(s)
- Takashi Baba
- Sciex, 71 Four Valley Drive, Concord, ON, L4K 4V8, Canada.
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17
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Zhu Z, Desaire H. Carbohydrates on Proteins: Site-Specific Glycosylation Analysis by Mass Spectrometry. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2015; 8:463-483. [PMID: 26070719 DOI: 10.1146/annurev-anchem-071114-040240] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Glycosylation on proteins adds complexity and versatility to these biologically vital macromolecules. To unveil the structure-function relationship of glycoproteins, glycopeptide-centric analysis using mass spectrometry (MS) has become a method of choice because the glycan is preserved on the glycosylation site and site-specific glycosylation profiles of proteins can be readily determined. However, glycopeptide analysis is still challenging given that glycopeptides are usually low in abundance and relatively difficult to detect and the resulting data require expertise to analyze. Viewing the urgent need to address these challenges, emerging methods and techniques are being developed with the goal of analyzing glycopeptides in a sensitive, comprehensive, and high-throughput manner. In this review, we discuss recent advances in glycoprotein and glycopeptide analysis, with topics covering sample preparation, analytical separation, MS and tandem MS techniques, as well as data interpretation and automation.
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Affiliation(s)
- Zhikai Zhu
- Ralph N. Adams Institute for Bioanalytical Chemistry, Department of Chemistry, University of Kansas, Lawrence, Kansas 66047;
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18
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Aboufazeli F, Kolli V, Dodds ED. A comparison of energy-resolved vibrational activation/dissociation characteristics of protonated and sodiated high mannose N-glycopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:587-595. [PMID: 25582509 DOI: 10.1007/s13361-014-1070-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/11/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Fragmentation of glycopeptides in tandem mass spectrometry (MS/MS) plays a pivotal role in site-specific protein glycosylation profiling by allowing specific oligosaccharide compositions and connectivities to be associated with specific loci on the corresponding protein. Although MS/MS analysis of glycopeptides has been successfully performed using a number of distinct ion dissociation methods, relatively little is known regarding the fragmentation characteristics of glycopeptide ions with various charge carriers. In this study, energy-resolved vibrational activation/dissociation was examined via collision-induced dissociation for a group of related high mannose tryptic glycopeptides as their doubly protonated, doubly sodiated, and hybrid protonated sodium adduct ions. The doubly protonated glycopeptide ions with various compositions were found to undergo fragmentation over a relatively low but wide range of collision energies compared with the doubly sodiated and hybrid charged ions, and were found to yield both glycan and peptide fragmentation depending on the applied collision energy. By contrast, the various doubly sodiated glycopeptides were found to dissociate over a significantly higher but narrow range of collision energies, and exhibited only glycan cleavages. Interestingly, the hybrid protonated sodium adduct ions were consistently the most stable of the precursor ions studied, and provided fragmentation information spanning both the glycan and the peptide moieties. Taken together, these findings illustrate the influence of charge carrier over the energy-resolved vibrational activation/dissociation characteristics of glycopeptides, and serve to suggest potential strategies that exploit the analytically useful features uniquely afforded by specific charge carriers or combinations thereof.
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Affiliation(s)
- Forouzan Aboufazeli
- Department of Chemistry, University of Nebraska-Lincoln, 711 Hamilton Hall, Lincoln, NE, 68588-0304, USA
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Baba T, Campbell JL, Le Blanc JCY, Hager JW, Thomson BA. Electron Capture Dissociation in a Branched Radio-Frequency Ion Trap. Anal Chem 2014; 87:785-92. [DOI: 10.1021/ac503773y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Takashi Baba
- AB Sciex, 71 Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
| | | | | | - James W. Hager
- AB Sciex, 71 Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
| | - Bruce A. Thomson
- AB Sciex, 71 Four Valley Drive, Concord, Ontario, L4K 4V8, Canada
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20
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Recent developments and applications of electron transfer dissociation mass spectrometry in proteomics. Amino Acids 2014; 46:1625-34. [PMID: 24687149 DOI: 10.1007/s00726-014-1726-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 03/07/2014] [Indexed: 12/30/2022]
Abstract
Electron transfer dissociation (ETD) has been developed recently as an efficient ion fragmentation technique in mass spectrometry (MS), being presently considered a step forward in proteomics with real perspectives for improvement, upgrade and application. Available also on affordable ion trap mass spectrometers, ETD induces specific N-Cα bond cleavages of the peptide backbone with the preservation of the post-translational modifications and generation of product ions that are diagnostic for the modification site(s). In addition, in the last few years ETD contributed significantly to the development of top-down approaches which enable tandem MS of intact protein ions. The present review, covering the last 5 years highlights concisely the major achievements and the current applications of ETD fragmentation technique in proteomics. An ample part of the review is dedicated to ETD contribution in the elucidation of the most common posttranslational modifications, such as phosphorylation and glycosylation. Further, a brief section is devoted to top-down by ETD method applied to intact proteins. As the last few years have witnessed a major expansion of the microfluidics systems, a few considerations on ETD in combination with chip-based nanoelectrospray (nanoESI) as a platform for high throughput top-down proteomics are also presented.
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Kolli V, Dodds ED. Energy-resolved collision-induced dissociation pathways of model N-linked glycopeptides: implications for capturing glycan connectivity and peptide sequence in a single experiment. Analyst 2014; 139:2144-53. [DOI: 10.1039/c3an02342g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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