1
|
Fowowe M, Yu A, Wang J, Onigbinde S, Nwaiwu J, Bennett AI, Mechref Y. Suppressing the background of LC-ESI-MS analysis of permethylated glycans using the active background ion reduction device. Electrophoresis 2024. [PMID: 38573014 DOI: 10.1002/elps.202300301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Mass spectrometry (MS) has revolutionized analytical chemistry, enabling precise identification and quantification of chemical species, which is pivotal for biomarker discovery and understanding complex biological systems. Despite its versatility, the presence of background ions in MS analysis hinders the sensitive detection of low-abundance analytes. Therefore, studies aimed at lowering background ion levels have become increasingly important. Here, we utilized the commercially available Active Background Ion Reduction Device (ABIRD) to suppress background ions and assess its effect on the liquid chromatography-electrospray ionization (LC-ESI)-MS analyses of N-glycans on the Q Exactive HF mass spectrometer. We also investigated the effect of different solvent vapors in the ESI source on N-glycan analysis by MS. ABIRD generally had no effect on high-mannose and neutral structures but reduced the intensity of some structures that contained sialic acid, fucose, or both when methanol vapor filled the ESI source. Based on our findings on the highest number of identified N-glycans from human serum, methanol vapor in the ion source compartment may enhance N-glycan LC-ESI-MS analyses by improving the desolvation of droplets formed during the ESI process due to its high volatility. This protocol may be further validated and extended to advanced bottom-up proteomic/glycoproteomic studies for the analysis of peptide/glycopeptide ions by MS.
Collapse
Affiliation(s)
- Mojibola Fowowe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Junyao Wang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Sherifdeen Onigbinde
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Judith Nwaiwu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Andrew I Bennett
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, USA
| |
Collapse
|
2
|
Ivanova B. Special Issue with Research Topics on "Recent Analysis and Applications of Mass Spectra on Biochemistry". Int J Mol Sci 2024; 25:1995. [PMID: 38396673 PMCID: PMC10888122 DOI: 10.3390/ijms25041995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
Analytical mass spectrometry applies irreplaceable mass spectrometric (MS) methods to analytical chemistry and chemical analysis, among other areas of analytical science [...].
Collapse
Affiliation(s)
- Bojidarka Ivanova
- Lehrstuhl für Analytische Chemie, Institut für Umweltforschung, Fakultät für Chemie und Chemische Biologie, Universität Dortmund, Otto-Hahn-Straße 6, 44221 Dortmund, Germany
| |
Collapse
|
3
|
Briš A, Baltussen MG, Tripodi GL, Huck WTS, Franceschi P, Roithová J. Direct Analysis of Complex Reaction Mixtures: Formose Reaction. Angew Chem Int Ed Engl 2024; 63:e202316621. [PMID: 38100204 DOI: 10.1002/anie.202316621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Indexed: 12/31/2023]
Abstract
Complex reaction mixtures, like those postulated on early Earth, present an analytical challenge because of the number of components, their similarity, and vastly different concentrations. Interpreting the reaction networks is typically based on simplified or partial data, limiting our insight. We present a new approach based on online monitoring of reaction mixtures formed by the formose reaction by ion-mobility-separation mass-spectrometry. Monitoring the reaction mixtures led to large data sets that we analyzed by non-negative matrix factorization, thereby identifying ion-signal groups capturing the time evolution of the network. The groups comprised ≈300 major ion signals corresponding to sugar-calcium complexes formed during the formose reaction. Multivariate analysis of the kinetic profiles of these complexes provided an overview of the interconnected kinetic processes in the solution, highlighting different pathways for sugar growth and the effects of different initiators on the initial kinetics. Reconstructing the network's topology further, we revealed so far unnoticed fast retro-aldol reaction of ketoses, which significantly affects the initial reaction dynamics. We also detected the onset of sugar-backbone branching for C6 sugars and cyclization reactions starting for C5 sugars. This top-down analytical approach opens a new way to analyze complex dynamic mixtures online with unprecedented coverage and time resolution.
Collapse
Affiliation(s)
- Anamarija Briš
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
- Laboratory for physical-organic chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Mathieu G Baltussen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Guilherme L Tripodi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Pietro Franceschi
- Research and innovation Centre, Fondazione E. Mach, Via Edmund Mach, 1, 38098, San Michele All'adige TN, Italy
| | - Jana Roithová
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| |
Collapse
|
4
|
Bansal P, Ben Faleh A, Warnke S, Rizzo TR. Multistage Ion Mobility Spectrometry Combined with Infrared Spectroscopy for Glycan Analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:695-700. [PMID: 36881006 PMCID: PMC10080682 DOI: 10.1021/jasms.2c00361] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 05/26/2023]
Abstract
The structural complexity of glycans makes their characterization challenging, not only because of the presence of various isomeric forms of the precursor molecule but also because the fragments can themselves be isomeric. We have recently developed an IMS-CID-IMS approach using structures for lossless ion manipulations (SLIM) combined with cryogenic infrared (IR) spectroscopy for glycan analysis. It allows mobility separation and collision-induced dissociation of a precursor glycan followed by mobility separation and IR spectroscopy of the fragments. While this approach holds great promise for glycan analysis, we often encounter fragments for which we have no standards to identify their spectroscopic fingerprint. In this work, we perform proof-of-principle experiments employing a multistage SLIM-based IMS-CID technique to generate second-generation fragments, followed by their mobility separation and spectroscopic interrogation. This approach provides detailed structural information about the first-generation fragments, including their anomeric form, which in turn can be used to identify the precursor glycan.
Collapse
Affiliation(s)
| | | | | | - Thomas R. Rizzo
- Laboratoire
de Chimie Physique Moléculaire, EPFL SB ISIC LCPM, École Polytechnique Fédérale
de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
| |
Collapse
|
5
|
Marie AL, Ray S, Ivanov AR. Highly-sensitive label-free deep profiling of N-glycans released from biomedically-relevant samples. Nat Commun 2023; 14:1618. [PMID: 36959283 PMCID: PMC10036494 DOI: 10.1038/s41467-023-37365-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 03/13/2023] [Indexed: 03/25/2023] Open
Abstract
Alterations of protein glycosylation can serve as sensitive and specific disease biomarkers. Labeling procedures for improved separation and detectability of oligosaccharides have several drawbacks, including incomplete derivatization, side-products, noticeable desialylation/defucosylation, sample loss, and interference with downstream analyses. Here, we develop a label-free workflow based on high sensitivity capillary zone electrophoresis-mass spectrometry (CZE-MS) for profiling of native underivatized released N-glycans. Our workflow provides a >45-fold increase in signal intensity compared to the conventional CZE-MS approaches used for N-glycan analysis. Qualitative and quantitative N-glycan profiling of purified human serum IgG, bovine serum fetuin, bovine pancreas ribonuclease B, blood-derived extracellular vesicle isolates, and total plasma results in the detection of >250, >400, >150, >310, and >520 N-glycans, respectively, using injected amounts equivalent to <25 ng of model protein and nL-levels of plasma-derived samples. Compared to reported results for biological samples of similar amounts and complexity, the number of identified N-glycans is increased up to ~15-fold, enabling highly sensitive analysis of sample amounts as low as sub-0.2 nL of plasma volume equivalents. Furthermore, highly sialylated N-glycans are identified and structurally characterized, and untreated sialic acid-linkage isomers are resolved in a single CZE-MS analysis.
Collapse
Affiliation(s)
- Anne-Lise Marie
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Somak Ray
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, MA, 02115, USA.
| |
Collapse
|
6
|
Stochastic dynamic quantitative and 3D structural matrix assisted laser desorption/ionization mass spectrometric analyses of mixture of nucleosides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
7
|
Du M, Zhang K, Jiao L, Xu Y, Kong X. Differentiation of disaccharide isomers via a combination of IR and UV photodissociation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9218. [PMID: 34740281 DOI: 10.1002/rcm.9218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
RATIONALE The challenge of glycan identification due to their structural complexity and diversity has profited enormously from recent developments in mass spectrometry (MS)-related methods. For photodissociation MS, infrared (IR) and ultraviolet (UV) lasers can generate complementary fragment ions, so an effective combination of the two methods may provide rich and valuable fragmentation patterns for glycan analysis. METHODS A 7.0 T Fourier transform ion cyclotron resonance (FTICR) mass spectrometer equipped with a double-beam laser system was applied for the experiments. 3,5-Diiodo-L-tyrosine was selected as the assistant molecule to form complex ions with ten isomeric disaccharides through electrospray ionization. The complex ions were further isolated and irradiated by IR and UV lasers separately or continuously in the FTICR cell. RESULTS By combining the two complementary fragment spectra generated from the IR and UV lasers, a clear identification of all the ten isomers was achieved using their binary codes based on their fragmentation patterns. The double-beam method simplifies the experiment by introducing the two lasers sequentially in one experiment, providing richer fragmentation patterns and making the full discrimination easier. CONCLUSIONS This study demonstrates the capabilities of the combination of IR and UV photodissociation MS in the identification of diverse glycan isomers. The double-beam photodissociation method described here distinguished compositional, configurational and connectivity disaccharide isomers successfully. Compared with the data accumulation method based on separate IR and UV experiments, this method is simpler, faster, more flexible and also characterized by richer fragmentation patterns.
Collapse
Affiliation(s)
- Mengying Du
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Kailin Zhang
- Life and Health Intelligent Research Institute, Tianjin University of Technology, Tianjin, China
| | - Luyang Jiao
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Yicheng Xu
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
| | - Xianglei Kong
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, China
| |
Collapse
|
8
|
Grabarics M, Lettow M, Kirschbaum C, Greis K, Manz C, Pagel K. Mass Spectrometry-Based Techniques to Elucidate the Sugar Code. Chem Rev 2022; 122:7840-7908. [PMID: 34491038 PMCID: PMC9052437 DOI: 10.1021/acs.chemrev.1c00380] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Indexed: 12/22/2022]
Abstract
Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.
Collapse
Affiliation(s)
- Márkó Grabarics
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Maike Lettow
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Carla Kirschbaum
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kim Greis
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Christian Manz
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| | - Kevin Pagel
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
- Department
of Molecular Physics, Fritz Haber Institute
of the Max Planck Society, Faradayweg 4−6, 14195 Berlin, Germany
| |
Collapse
|
9
|
Abikhodr AH, Yatsyna V, Ben Faleh A, Warnke S, Rizzo TR. Identifying Mixtures of Isomeric Human Milk Oligosaccharides by the Decomposition of IR Spectral Fingerprints. Anal Chem 2021; 93:14730-14736. [PMID: 34704745 PMCID: PMC8581968 DOI: 10.1021/acs.analchem.1c03190] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/19/2021] [Indexed: 12/17/2022]
Abstract
The analysis of glycans presents a significant challenge that arises from their isomeric heterogeneity. While high-resolution ion mobility spectrometry (IMS) has shown the ability to resolve subtly different glycan isomers, their unambiguous assignment remains difficult. Here, we demonstrate an infrared (IR) spectroscopic approach for identifying isomers in a glycan mixture. To display the feasibility of this approach, we have constructed a small database of cryogenic spectra of five lacto-N-fucopentaose (LNFP) and six disaccharide isomers and demonstrated that in the cases where they cannot be separated by IMS, we can use a cryogenic IR spectrum to identify the isomeric components of a mixture.
Collapse
Affiliation(s)
- Ali H. Abikhodr
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Vasyl Yatsyna
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
- Department
of Physics, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Ahmed Ben Faleh
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Stephan Warnke
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire
de Chimie Physique Moléculaire, École Polytechnique
Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| |
Collapse
|
10
|
Schrader RL, Marsh BM, Cooks RG. Atmospheric Pressure Drift Tube Ion Mobility Spectrometry Coupled with Two-Dimensional Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2105-2109. [PMID: 34232037 DOI: 10.1021/jasms.1c00180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Atmospheric pressure drift tube ion mobility was coupled with two-dimensional tandem mass spectrometry (2D MS/MS) in a linear ion trap to simultaneously collect ion mobility and the entire MS/MS data domain. Utilizing ion intensities from precursor ion and neutral loss scan lines, ion mobility spectra of multiple compounds with particular functional groups were acquired in a single experiment. Functional group-specific ion mobility spectra were demonstrated for a standard mixture of lipids. Additionally, ion mobility was used to separate isobaric ions prior to 2D MS/MS. The combination of these two methods offers improvements for the analysis of complex mixtures.
Collapse
Affiliation(s)
- Robert L Schrader
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brett M Marsh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
11
|
Dumontier R, Loutelier-Bourhis C, Walet-Balieu ML, Burel C, Mareck A, Afonso C, Lerouge P, Bardor M. Identification of N-glycan oligomannoside isomers in the diatom Phaeodactylum tricornutum. Carbohydr Polym 2021; 259:117660. [PMID: 33673983 DOI: 10.1016/j.carbpol.2021.117660] [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: 11/04/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 01/09/2023]
Abstract
Microalgae are emerging production systems for recombinant proteins like monoclonal antibodies. In this context, the characterization of the host cell N-glycosylation machinery and of the microalgae-made biopharmaceuticals, which are mainly glycoprotein-based products, requires efficient analytical methodologies dedicated to the profiling of the N-glycans. Herein, in order to gain knowledge regarding its N-glycosylation pathway, we profile the protein N-linked oligosaccharides isolated from the diatom Phaeodactylum tricornutum that has been used successfully to produce functional monoclonal antibodies. The combination of ion mobility spectrometry-mass Spectrometry and electrospray ionization-multistage tandem mass spectrometry allows us to decipher the detailed structure of the oligomannoside isomers and to demonstrate that the processing of the oligomannosides N-linked to proteins occurs in this diatom as reported in mammals. Therefore, P. tricornutum synthesizes human-like oligomannosides in contrast to other microalgae species. This represent an advantage as an alternative ecofriendly expression system to produce biopharmaceuticals used for human therapy.
Collapse
Affiliation(s)
- Rodolphe Dumontier
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, 76000 Rouen, France; Normandie University, UNIROUEN, SFR NORVEGE, 76000 Rouen, France
| | | | - Marie-Laure Walet-Balieu
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, 76000 Rouen, France; Normandie University, UNIROUEN, SFR NORVEGE, 76000 Rouen, France
| | - Carole Burel
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, 76000 Rouen, France; Normandie University, UNIROUEN, SFR NORVEGE, 76000 Rouen, France
| | - Alain Mareck
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, 76000 Rouen, France; Normandie University, UNIROUEN, SFR NORVEGE, 76000 Rouen, France
| | - Carlos Afonso
- Normandie University, UNIROUEN, INSA Rouen, CNRS, UMR6014 - COBRA, 76000 Rouen, France
| | - Patrice Lerouge
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, 76000 Rouen, France; Normandie University, UNIROUEN, SFR NORVEGE, 76000 Rouen, France
| | - Muriel Bardor
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale (Glyco-MEV) EA4358, 76000 Rouen, France; Normandie University, UNIROUEN, SFR NORVEGE, 76000 Rouen, France; Univ Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F- 59000 Lille, France.
| |
Collapse
|
12
|
Wu X, Zhang Y, Qin R, Li P, Wen Y, Yin Z, Zhang Z, Xu H. Discrimination of isomeric monosaccharide derivatives using collision-induced fingerprinting coupled to ion mobility mass spectrometry. Talanta 2021; 224:121901. [PMID: 33379106 DOI: 10.1016/j.talanta.2020.121901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/04/2020] [Accepted: 11/12/2020] [Indexed: 10/23/2022]
Abstract
Because of the isomeric heterogeneity that is ubiquitous in analytical science, a formidable analytical challenge is to fully discriminate multiple isomers, especially those candidate isomers with various biological functions. Ion mobility mass spectrometry (IM-MS) has gained impressive advances for gaining molecular conformations, whereas coexisting structurally similar isomers often make unambiguous discrimination impossible due to the limited IM resolution of commercially available instruments. Herein, we demonstrate an energy-resolved collision-induced fingerprint (CIF) method to fully discriminate isomeric monosaccharide derivatives that differ in terms of composition, connectivity and configuration without complex instrument modifications. By simply increasing the collisional energy in the trap cell, the full width at half maximum (FWHM) of IM peaks can be markedly narrowed by at least 2-fold. Given the excellent reproducibility of CIF measurements, the full discrimination of isomers can benefit from their unique feature values and root-mean square deviation (RMSD) in CIF spectra. Moreover, rapid discrimination of each monosaccharide derivate isomer from binary mixtures is demonstrated. This strategy will expand the horizons of IM-MS platform in the rapid differentiation of a wider range of isomers more than monosaccharide derivatives in complex systems, which facilitates the identification and evaluation of innovative isomer candidates with unexplored functions.
Collapse
Affiliation(s)
- Xinzhou Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Yue Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Run Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Ping Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Yingjie Wen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, 510642, China
| | - Zhibin Yin
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China; School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Zhixiang Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, 510642, China.
| | - Hanhong Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources and Key Laboratory of Natural Pesticide and Chemical Biology of the Ministry of Education, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
13
|
Sastre Toraño J, Aizpurua‐Olaizola O, Wei N, Li T, Unione L, Jiménez‐Osés G, Corzana F, Somovilla VJ, Falcon‐Perez JM, Boons G. Identification of Isomeric N-Glycans by Conformer Distribution Fingerprinting using Ion Mobility Mass Spectrometry. Chemistry 2021; 27:2149-2154. [PMID: 33047840 PMCID: PMC7898647 DOI: 10.1002/chem.202004522] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Indexed: 12/14/2022]
Abstract
Glycans possess unparalleled structural complexity arising from chemically similar monosaccharide building blocks, configurations of anomeric linkages and different branching patterns, potentially giving rise to many isomers. This level of complexity is one of the main reasons that identification of exact glycan structures in biological samples still lags behind that of other biomolecules. Here, we introduce a methodology to identify isomeric N-glycans by determining gas phase conformer distributions (CDs) by measuring arrival time distributions (ATDs) using drift-tube ion mobility spectrometry-mass spectrometry. Key to the approach is the use of a range of well-defined synthetic glycans that made it possible to investigate conformer distributions in the gas phase of isomeric glycans in a systematic manner. In addition, we have computed CD fingerprints by molecular dynamics (MD) simulation, which compared well with experimentally determined CDs. It supports that ATDs resemble conformational populations in the gas phase and offer the prospect that such an approach can contribute to generating a library of CCS distributions (CCSDs) for structure identification.
Collapse
Affiliation(s)
- Javier Sastre Toraño
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Oier Aizpurua‐Olaizola
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- Exosomes LabCIC bioGUNE, CIBERehdDerioSpain
| | - Na Wei
- The University of GeorgiaComplex Carbohydrate Research CenterAthensGAUSA
| | - Tiehai Li
- The University of GeorgiaComplex Carbohydrate Research CenterAthensGAUSA
| | - Luca Unione
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | - Gonzalo Jiménez‐Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNEBasque Research and Technology Alliance (BRTA)Bizkaia Technology Park, Building 801A48160DerioSpain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis QuímicaUniversidad de La Rioja26006LogroñoSpain
| | - Victor J. Somovilla
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
| | | | - Geert‐Jan Boons
- Department of Chemical Biology and Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUtrecht UniversityUtrechtThe Netherlands
- The University of GeorgiaComplex Carbohydrate Research CenterAthensGAUSA
| |
Collapse
|
14
|
She YM, Tam RY, Li X, Rosu-Myles M, Sauvé S. Resolving Isomeric Structures of Native Glycans by Nanoflow Porous Graphitized Carbon Chromatography-Mass Spectrometry. Anal Chem 2020; 92:14038-14046. [PMID: 32960038 DOI: 10.1021/acs.analchem.0c02951] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Characterization of the structural diversity of glycans by liquid chromatography-tandem mass spectrometry (LC-MS/MS) remains an analytical challenge in large-scale glycomics applications because of the presence of heterogeneous composition, ubiquitous isomers, lability of post-translational glycan modifications, and complexity of data interpretation. High-resolution separation of glycan isomers differentiating from positional, linkage, branching, and anomeric structures is often a prerequisite to ensure the comprehensive glycan identification. Here, we developed a straightforward method using self-packed capillary porous graphitic carbon (PGC) columns for nanoflow LC-MS/MS analyses of native glycans released from glycoproteins. The technique enables highly resolved chromatographic separation of over 20 high-mannose glycan isomers in ribonuclease B and a diverse range of hybrid and complex-type sialoglycoforms of fetuin. The distinct structures of anomeric glycans and linkage sialoglycan isomers, α2,3 and α2,6, were identified by the characteristic MS/MS fragment ions. A glycan sequencing strategy utilizing diagnostic ions and complementary fragments specific to branching residues was established to simplify the MS/MS data interpretation of closely related isomeric structures. To promote the PGC-LC-MS/MS-based method for glycome-wide applications, we extended analyses to native sulfoglycans from the egg-propagated and cell culture-derived influenza vaccines and demonstrate the high-resolution separation and structural characterization of underivatized neutral and anionic glycoforms including oligomannosidic glycan anomers, sialoglycan linkage isomers, and regioisomers of afucosylated and fucosylated sulfoglycans containing sulfated-6-GlcNAc and sulfated-4-GalNAc residues.
Collapse
Affiliation(s)
- Yi-Min She
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Roger Y Tam
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Michael Rosu-Myles
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| | - Simon Sauvé
- Centre for Biologics Evaluation, Biologic and Radiopharmaceutical Drugs Directorate, Health Canada, Ottawa, Ontario K1A 0K9, Canada
| |
Collapse
|
15
|
Wei J, Tang Y, Ridgeway ME, Park MA, Costello CE, Lin C. Accurate Identification of Isomeric Glycans by Trapped Ion Mobility Spectrometry-Electronic Excitation Dissociation Tandem Mass Spectrometry. Anal Chem 2020; 92:13211-13220. [PMID: 32865981 DOI: 10.1021/acs.analchem.0c02374] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ion mobility-mass spectrometry (IM-MS) has become a powerful tool for glycan structural characterization due to its ability to separate isomers and provide collision cross section (CCS) values that facilitate structural assignment. However, IM-based isomer analysis may be complicated by the presence of multiple gas-phase conformations of a single structure that not only increases difficulty in isomer separation but can also introduce the possibility for misinterpretation of conformers as isomers. Here, the ion mobility behavior of several sets of isomeric glycans, analyzed as their permethylated derivatives, in both nonreduced and reduced forms, was investigated by gated-trapped ion mobility spectrometry (G-TIMS). Notably, reducing-end reduction, commonly performed to remove anomerism-induced chromatographic peak splitting, did not eliminate the conformational heterogeneity of permethylated glycans in the gas phase. At a mobility resolving power of ∼100, 14 out of 22 structures showed more than one conformation. These results highlight the need to use IMS devices with high mobility resolving power for better separation of isomers and to acquire additional structural information that can differentiate isomers from conformers. Online electronic excitation dissociation (EED) MS/MS analysis of isomeric glycan mixtures following G-TIMS separation showed that EED can generate isomer-specific fragments while producing nearly identical tandem mass spectra for conformers, thus allowing confident identification of isomers with minimal evidence of any ambiguity resulting from the presence of conformers. G-TIMS EED MS/MS analysis of N-linked glycans released from ovalbumin revealed that several mobility features previously thought to arise from isomeric structures were conformers of a single structure. Finally, analysis of ovalbumin N-glycans from different sources showed that the G-TIMS EED MS/MS approach can accurately determine the batch-to-batch variations in glycosylation profiles at the isomer level, with confident assignment of each isomeric structure.
Collapse
Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Mark E Ridgeway
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, 670 Albany Street, Room 508, Boston, Massachusetts 02118, United States
| |
Collapse
|
16
|
Guo J, Tu H, Rao B M, Chillara AK, Chang E, Atouf F. More comprehensive standards for monitoring glycosylation. Anal Biochem 2020; 612:113896. [PMID: 32818506 DOI: 10.1016/j.ab.2020.113896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/06/2020] [Accepted: 07/28/2020] [Indexed: 11/25/2022]
Abstract
Biologics manufacturers must continually monitor the attachment of carbohydrates, called glycans, to their products, because any variability can impact safety and efficacy. To help the industry meet this challenge, the United States Pharmacopeial Convention (USP) offers glycan reference standards and validated methods for glycoprofiling using high-performance liquid chromatography (HPLC). The industry has recently adopted more advanced technologies for glycan analysis, including ultra-high performance liquid chromatography (UHPLC) and mass spectrometry. In this study, we confirm that USP's glycan reference standards are compatible with UHPLC by demonstrating comparable peak separation and glycan identification to HPLC methods. The improved resolving power and shorter run-times of UHPLC also allowed us to identify many of the minor glycan components present in USP's glycan reference standards. These more comprehensively characterized glycan reference standards will enable manufacturers to assess the micro-heterogeneity that can negatively impact the safety and efficacy of biological products.
Collapse
Affiliation(s)
- Jingzhong Guo
- United States Pharmacopeial Convention, 12601 Twinbrook Pkwy, Rockville, MD, 20852, USA
| | - Huiping Tu
- United States Pharmacopeial Convention, 12601 Twinbrook Pkwy, Rockville, MD, 20852, USA
| | - Maheswara Rao B
- United States Pharmacopeial Convention, 12601 Twinbrook Pkwy, Rockville, MD, 20852, USA
| | | | - Edith Chang
- United States Pharmacopeial Convention, 12601 Twinbrook Pkwy, Rockville, MD, 20852, USA
| | - Fouad Atouf
- United States Pharmacopeial Convention, 12601 Twinbrook Pkwy, Rockville, MD, 20852, USA.
| |
Collapse
|
17
|
Lucas PL, Mathieu-Rivet E, Song PCT, Oltmanns A, Loutelier-Bourhis C, Plasson C, Afonso C, Hippler M, Lerouge P, Mati-Baouche N, Bardor M. Multiple xylosyltransferases heterogeneously xylosylate protein N-linked glycans in Chlamydomonas reinhardtii. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:230-245. [PMID: 31777161 DOI: 10.1111/tpj.14620] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/24/2019] [Accepted: 11/05/2019] [Indexed: 05/08/2023]
Abstract
Nowadays, little information is available regarding the N-glycosylation pathway in the green microalga Chlamydomonas reinhardtii. Recent investigation demonstrated that C. reinhardtii synthesizes linear oligomannosides. Maturation of these oligomannosides results in N-glycans that are partially methylated and carry one or two xylose residues. One xylose residue was demonstrated to be a core β(1,2)-xylose. Recently, N-glycoproteomic analysis performed on glycoproteins secreted by C. reinhardtii demonstrated that the xylosyltransferase A (XTA) was responsible for the addition of the core β(1,2)-xylose. Furthermore, another xylosyltransferase candidate named XTB was suggested to be involved in the xylosylation in C. reinhardtii. In the present study, we focus especially on the characterization of the structures of the xylosylated N-glycans from C. reinhardtii taking advantage of insertional mutants of XTA and XTB, and of the XTA/XTB double-mutant. The combination of mass spectrometry approaches allowed us to identify the major N-glycan structures bearing one or two xylose residues. They confirm that XTA is responsible for the addition of the core β(1,2)-xylose, whereas XTB is involved in the addition of the xylose residue onto the linear branch of the N-glycan as well as in the partial addition of the core β(1,2)-xylose suggesting that this transferase exhibits a low substrate specificity. Analysis of the double-mutant suggests that an additional xylosyltransferase is involved in the xylosylation process in C. reinhardtii. Additional putative candidates have been identified in the C. reinhardtii genome. Altogether, these results pave the way for a better understanding of the C. reinhardtii N-glycosylation pathway.
Collapse
Affiliation(s)
- Pierre-Louis Lucas
- Laboratoire Glyco-MEV EA4358, Normandie University, UNIROUEN, Rouen, France
- Normandie University, UNIROUEN, SFR NORVEGE, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Normandie University, UNIROUEN, Rouen, France
| | - Elodie Mathieu-Rivet
- Laboratoire Glyco-MEV EA4358, Normandie University, UNIROUEN, Rouen, France
- Normandie University, UNIROUEN, SFR NORVEGE, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Normandie University, UNIROUEN, Rouen, France
| | - Philippe C T Song
- Institute for Research and Innovation in Biomedicine (IRIB), Normandie University, UNIROUEN, Rouen, France
- Normandie University, UNIROUEN, Plate-Forme de Protéomique PISSARO, Rouen, France
| | - Anne Oltmanns
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
| | | | - Carole Plasson
- Laboratoire Glyco-MEV EA4358, Normandie University, UNIROUEN, Rouen, France
- Normandie University, UNIROUEN, SFR NORVEGE, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Normandie University, UNIROUEN, Rouen, France
| | - Carlos Afonso
- Normandie University, UNIROUEN, INSA Rouen, CNRS, COBRA, Rouen, France
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Patrice Lerouge
- Laboratoire Glyco-MEV EA4358, Normandie University, UNIROUEN, Rouen, France
- Normandie University, UNIROUEN, SFR NORVEGE, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Normandie University, UNIROUEN, Rouen, France
| | - Narimane Mati-Baouche
- Laboratoire Glyco-MEV EA4358, Normandie University, UNIROUEN, Rouen, France
- Normandie University, UNIROUEN, SFR NORVEGE, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Normandie University, UNIROUEN, Rouen, France
| | - Muriel Bardor
- Laboratoire Glyco-MEV EA4358, Normandie University, UNIROUEN, Rouen, France
- Normandie University, UNIROUEN, SFR NORVEGE, Rouen, France
- Institute for Research and Innovation in Biomedicine (IRIB), Normandie University, UNIROUEN, Rouen, France
- Institut Universitaire de France (IUF), Paris, France
| |
Collapse
|
18
|
Wei J, Tang Y, Bai Y, Zaia J, Costello CE, Hong P, Lin C. Toward Automatic and Comprehensive Glycan Characterization by Online PGC-LC-EED MS/MS. Anal Chem 2020; 92:782-791. [PMID: 31829560 PMCID: PMC7082718 DOI: 10.1021/acs.analchem.9b03183] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Despite the recent advances in mass spectrometry (MS)-based methods for glycan structural analysis, characterization of glycomes remains a significant analytical challenge, in part due to the widespread presence of isomeric structures and the need to define the many structural variables for each glycan. Interpretation of the complex tandem mass spectra of glycans is often laborious and requires substantial expertise. Broad adoption of MS methods for glycomics, within and outside the glycoscience community, has been hindered by the shortage of bioinformatics tools for rapid and accurate glycan sequencing. Here, we developed an online porous graphitic carbon liquid chromatography (PGC-LC)-electronic excitation dissociation (EED) MS/MS method that takes advantage of the superior isomer resolving power of PGC and the structural details provided by EED MS/MS for characterization of glycan mixtures. We also made improvements to GlycoDeNovo, our de novo glycan sequencing algorithm, so that it can automatically and accurately identify glycan topologies from EED tandem mass spectra acquired online. The majority of linkages can also be determined de novo, although in some cases, biological insight may be needed to fully define the glycan structure. Application of this method to the analysis of N-glycans released from ribonuclease B not only revealed the presence of 18 high-mannose structures, including new isomers not previously reported, but also provided relative quantification for each isomeric structure. With fully automated data acquisition and topology analysis, the approach presented here holds great potential for automated and comprehensive glycan characterization.
Collapse
Affiliation(s)
- Juan Wei
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Yang Tang
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Pengyu Hong
- Department of Computer Science, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
| |
Collapse
|
19
|
Jin C, Harvey DJ, Struwe WB, Karlsson NG. Separation of Isomeric O-Glycans by Ion Mobility and Liquid Chromatography–Mass Spectrometry. Anal Chem 2019; 91:10604-10613. [DOI: 10.1021/acs.analchem.9b01772] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - David J. Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Weston B. Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Chemistry Research laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
20
|
Jeanne Dit Fouque K, Fernandez-Lima F. Recent advances in biological separations using trapped ion mobility spectrometry – mass spectrometry. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.04.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
21
|
Sahota N, AbuSalim DI, Wang ML, Brown CJ, Zhang Z, El-Baba TJ, Cook SP, Clemmer DE. A microdroplet-accelerated Biginelli reaction: mechanisms and separation of isomers using IMS-MS. Chem Sci 2019; 10:4822-4827. [PMID: 31160956 PMCID: PMC6509997 DOI: 10.1039/c9sc00704k] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 03/28/2019] [Indexed: 01/17/2023] Open
Abstract
Electrospray ionization (ESI) combined with ion mobility spectrometry (IMS) and mass spectrometry (MS) techniques is used to examine the Biginelli reaction in an ensemble of ions generated from droplets.
Electrospray ionization (ESI) combined with ion mobility spectrometry (IMS) and mass spectrometry (MS) techniques is used to examine the Biginelli reaction in an ensemble of ions generated from droplets. We find evidence for rapid dihydropyrimidinone formation from condensation of ethyl acetoacetate, benzaldehyde, and urea on the very short timescales associated with the electrospray process (∼10 μs to ∼1.0 ms). Control bulk-solution reactions show no product formation even after several days. This implies that the in-droplet reaction rate is enhanced by an astonishing factor. Examination of the reaction conditions and characterization of the intermediates en route to product shows evidence for variations in the reaction mechanism. IMS separation shows that the Knoevenagel condensation intermediate from benzaldehyde and ethyl acetoacetate exists as both the cis- and trans-isomer, in a ∼5 to 1 ratio. We suggest that the dramatic acceleration arises because of increased reagent confinement as electrosprayed droplets shrink. The ability of IMS-MS to resolve intermediates (including isomers) provides a new means of understanding reaction pathways.
Collapse
Affiliation(s)
- Navneet Sahota
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Deyaa I AbuSalim
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Melinda L Wang
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Christopher J Brown
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Zhicaho Zhang
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Tarick J El-Baba
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - Silas P Cook
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| | - David E Clemmer
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , IN 47405-7102 , USA . ;
| |
Collapse
|
22
|
Mucha E, Stuckmann A, Marianski M, Struwe WB, Meijer G, Pagel K. In-depth structural analysis of glycans in the gas phase. Chem Sci 2019; 10:1272-1284. [PMID: 30809341 PMCID: PMC6357860 DOI: 10.1039/c8sc05426f] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/04/2019] [Indexed: 12/26/2022] Open
Abstract
Although there have been substantial improvements in glycan analysis over the past decade, the lack of both high-resolution and high-throughput methods hampers progress in glycomics. This perspective article highlights the current developments of liquid chromatography, mass spectrometry, ion-mobility spectrometry and cryogenic IR spectroscopy for glycan analysis and gives a critical insight to their individual strengths and limitations. Moreover, we discuss a novel concept in which ion mobility-mass spectrometry and cryogenic IR spectroscopy is combined in a single instrument such that datasets consisting of m/z, collision cross sections and IR fingerprints can be obtained. This multidimensional data will then be compared to a comprehensive reference library of intact glycans and their fragments to accurately identify unknown glycans on a high-throughput scale with minimal sample requirements. Due to the complementarity of the obtained information, this novel approach is highly diagnostic and also suitable for the identification of larger glycans; however, the workflow and instrumentation is straightforward enough to be implemented into a user-friendly setup.
Collapse
Affiliation(s)
- Eike Mucha
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany . .,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Alexandra Stuckmann
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany . .,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| | - Mateusz Marianski
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
| | - Weston B Struwe
- Oxford Glycobiology Institute , Department of Biochemistry , University of Oxford , OX1 3QU Oxford , UK
| | - Gerard Meijer
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany .
| | - Kevin Pagel
- Fritz Haber Institute of the Max Planck Society , Department of Molecular Physics , Faradayweg 4-6 , 14195 Berlin , Germany . .,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Takustraße 3 , 14195 Berlin , Germany
| |
Collapse
|
23
|
Li S, Zhou Y, Xiao K, Li J, Tian Z. Selective fragmentation of the N-glycan moiety and protein backbone of ribonuclease B on an Orbitrap Fusion Lumos Tribrid mass spectrometer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:2031-2039. [PMID: 30152909 DOI: 10.1002/rcm.8273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/23/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE The functional study and application of an intact glycoprotein require the structural characterization of both the protein backbone and the glycan moiety; the former has been successfully demonstrated with selective fragmentation of the protein backbone in CID and ExD; whether the latter can be achieved with selective fragmentation of the glycan moiety remains to be explored. METHODS RNase B solution was electrosprayed and its intact glycoforms of GlcNAc2 Mann (n = 5-9) with the highest abundance (charge state z = 16) were isolated individually and fragmented using CID, ETD, HCD, ETciD, and EThcD on the Orbitrap Fusion Lumos Tribrid mass spectrometer; the dissociation parameters were optimized for selective fragmentation of the N-glycan moiety and protein backbone as well as high sequence coverage. The obtained spectra were interpreted using the protein and N-glycan database search engines ProteinGoggle and GlySeeker, respectively. RESULTS With exploration of different dissociation parameters for all the five methods, selective fragmentation of the N-glycan moiety (the protein backbone staying intact) was observed in both HCD and EThcD at low collisional energies, but only a few matched product ions were observed; more comprehensive fragmentation was observed at high collisional energies (the protein backbone lost). Selective protein backbone fragmentation was observed in all the five dissociation methods. CONCLUSIONS For comprehensive structural characterization of intact N-glycoproteins using tandem mass spectrometry, the composition and topology of the N-glycan moiety can be identified using HCD and EThcD complementarily at low and high energies; while the amino acid sequence and glycosite can be identified using CID, ETD, HCD, ETciD, and EThcD with their optimal dissociation parameters.
Collapse
Affiliation(s)
- Shasha Li
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Yue Zhou
- Thermo Fisher Scientific, Shanghai, 201206, China
| | - Kaijie Xiao
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Jing Li
- Thermo Fisher Scientific, Shanghai, 201206, China
| | - Zhixin Tian
- School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Tang Y, Pu Y, Gao J, Hong P, Costello CE, Lin C. De Novo Glycan Sequencing by Electronic Excitation Dissociation and Fixed-Charge Derivatization. Anal Chem 2018; 90:3793-3801. [PMID: 29443510 DOI: 10.1021/acs.analchem.7b04077] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Detailed glycan structural characterization is frequently achieved by collisionally activated dissociation (CAD) based sequential tandem mass spectrometry (MS n) analysis of permethylated glycans. However, it is challenging to implement MS n ( n > 2) during online glycan separation, and this has limited its application to analysis of complex glycan mixtures from biological samples. Further, permethylation can reduce liquid chromatographic (LC) resolution of isomeric glycans. Here, we studied the electronic excitation dissociation (EED) fragmentation behavior of native glycans with a reducing-end fixed charge tag and identified key spectral features that are useful for topology and linkage determination. We also developed a de novo glycan sequencing software that showed remarkable accuracy in glycan topology elucidation based on the EED spectra of fixed charge-derivatized glycans. The ability to obtain glycan structural details at the MS2 level, without permethylation, via a combination of fixed charge derivatization, EED, and de novo spectral interpretation, makes the present approach a promising tool for comprehensive and rapid characterization of glycan mixtures.
Collapse
Affiliation(s)
- Yang Tang
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States.,Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Yi Pu
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States.,Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Jinshan Gao
- Department of Chemistry and Biochemistry , Montclair State University , Montclair , New Jersey 07043 , United States
| | - Pengyu Hong
- Department of Computer Science, Brandeis University , Waltham , Massachusetts 02453 , United States
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States.,Department of Chemistry , Boston University , Boston , Massachusetts 02215 , United States
| | - Cheng Lin
- Center for Biomedical Mass Spectrometry , Boston University School of Medicine , Boston , Massachusetts 02118 , United States
| |
Collapse
|
26
|
Re S, Watabe S, Nishima W, Muneyuki E, Yamaguchi Y, MacKerell AD, Sugita Y. Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase. Sci Rep 2018; 8:1644. [PMID: 29374210 PMCID: PMC5786100 DOI: 10.1038/s41598-018-20012-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/10/2018] [Indexed: 12/18/2022] Open
Abstract
Ion mobility mass spectrometry (IM-MS) is a technique capable of investigating structural changes of biomolecules based on their collision cross section (CCS). Recent advances in IM-MS allow us to separate carbohydrate isomers with subtle conformational differences, but the relationship between CCS and atomic structure remains elusive. Here, we characterize conformational ensembles of gas-phase N-glycans under the electrospray ionization condition using molecular dynamics simulations with enhanced sampling. We show that the separation of CCSs between isomers reflects folding features of N-glycans, which are determined both by chemical compositions and protonation states. Providing a physicochemical basis of CCS for N-glycans helps not only to interpret IM-MS measurements but also to estimate CCSs of complex glycans.
Collapse
Affiliation(s)
- Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shigehisa Watabe
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Wataru Nishima
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Eiro Muneyuki
- Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, 21201, USA
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| |
Collapse
|
27
|
Masellis C, Khanal N, Kamrath MZ, Clemmer DE, Rizzo TR. Cryogenic Vibrational Spectroscopy Provides Unique Fingerprints for Glycan Identification. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2217-2222. [PMID: 28643189 PMCID: PMC5693781 DOI: 10.1007/s13361-017-1728-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 05/30/2017] [Accepted: 05/31/2017] [Indexed: 05/23/2023]
Abstract
The structural characterization of glycans by mass spectrometry is particularly challenging. This is because of the high degree of isomerism in which glycans of the same mass can differ in their stereochemistry, attachment points, and degree of branching. Here we show that the addition of cryogenic vibrational spectroscopy to mass and mobility measurements allows one to uniquely identify and characterize these complex biopolymers. We investigate six disaccharide isomers that differ in their stereochemistry, attachment point of the glycosidic bond, and monosaccharide content, and demonstrate that we can identify each one unambiguously. Even disaccharides that differ by a single stereogenic center or in the monosaccharide sequence order show distinct vibrational fingerprints that would clearly allow their identification in a mixture, which is not possible by ion mobility spectrometry/mass spectrometry alone. Moreover, this technique can be applied to larger glycans, which we demonstrate by distinguishing isomeric branched and linear pentasaccharides. The creation of a database containing mass, collision cross section, and vibrational fingerprint measurements for glycan standards should allow unambiguous identification and characterization of these biopolymers in mixtures, providing an enabling technology for all fields of glycoscience. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Chiara Masellis
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, 1015, Lausanne, Switzerland
| | - Neelam Khanal
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Michael Z Kamrath
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, 1015, Lausanne, Switzerland
- , TOFWERK AG, Uttingenstrasse 22, 3600, Thun, Switzerland
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Thomas R Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, 1015, Lausanne, Switzerland.
| |
Collapse
|
28
|
Snyder CM, Zhou X, Karty JA, Fonslow BR, Novotny MV, Jacobson SC. Capillary electrophoresis-mass spectrometry for direct structural identification of serum N-glycans. J Chromatogr A 2017; 1523:127-139. [PMID: 28989033 DOI: 10.1016/j.chroma.2017.09.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 09/01/2017] [Accepted: 09/03/2017] [Indexed: 10/18/2022]
Abstract
Through direct coupling of capillary electrophoresis (CE) to mass spectrometry (MS) with a sheathless interface, we have identified 77 potential N-glycan structures derived from human serum. We confirmed the presence of N-glycans previously identified by indirect methods, e.g., electrophoretic mobility standards, obtained 31 new N-glycan structures not identified in our prior work, differentiated co-migrating structures, and determined specific linkages on isomers featuring sialic acids. Serum N-glycans were cleaved from proteins, neutralized via methylamidation, and labeled with the fluorescent tag 8-aminopyrene-1,3,6-trisulfonic acid, which renders the glycan fluorescent and provides a -3 charge for electrophoresis and negative-mode MS detection. The neutralization reaction also stabilizes the labile sialic acids. In addition to methylamidation, native charges from sialic acids were neutralized through reaction with 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium to amidate α2,6-linked sialic acids in the presence of ammonium chloride and form lactones with α2,3-linked sialic acids. This neutralization effectively labels each type of sialic acid with a unique mass to determine specific linkages on sialylated N-glycans. For both neutralization schemes, we compared the results from microchip electrophoresis and CE.
Collapse
Affiliation(s)
- Christa M Snyder
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - Xiaomei Zhou
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | | | - Milos V Novotny
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States
| | - Stephen C Jacobson
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, United States.
| |
Collapse
|
29
|
Vanier G, Lucas PL, Loutelier-Bourhis C, Vanier J, Plasson C, Walet-Balieu ML, Tchi-Song PC, Remy-Jouet I, Richard V, Bernard S, Driouich A, Afonso C, Lerouge P, Mathieu-Rivet E, Bardor M. Heterologous expression of the N-acetylglucosaminyltransferase I dictates a reinvestigation of the N-glycosylation pathway in Chlamydomonas reinhardtii. Sci Rep 2017; 7:10156. [PMID: 28860654 PMCID: PMC5578997 DOI: 10.1038/s41598-017-10698-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/14/2017] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic N-glycosylation pathways are dependent of N-acetylglucosaminyltransferase I (GnTI), a key glycosyltransferase opening the door to the formation of complex-type N-glycans by transferring a N-acetylglucosamine residue onto the Man5GlcNAc2 intermediate. In contrast, glycans N-linked to Chlamydomonas reinhardtii proteins arise from a GnTI-independent Golgi processing of oligomannosides giving rise to Man5GlcNAc2 substituted eventually with one or two xylose(s). Here, complementation of C. reinhardtii with heterologous GnTI was investigated by expression of GnTI cDNAs originated from Arabidopsis and the diatom Phaeodactylum tricornutum. No modification of the N-glycans was observed in the GnTI transformed cells. Consequently, the structure of the Man5GlcNAc2 synthesized by C. reinhardtii was reinvestigated. Mass spectrometry analyses combined with enzyme sequencing showed that C. reinhardtii proteins carry linear Man5GlcNAc2 instead of the branched structure usually found in eukaryotes. Moreover, characterization of the lipid-linked oligosaccharide precursor demonstrated that C. reinhardtii exhibit a Glc3Man5GlcNAc2 dolichol pyrophosphate precursor. We propose that this precursor is then trimmed into a linear Man5GlcNAc2 that is not substrate for GnTI. Furthermore, cells expressing GnTI exhibited an altered phenotype with large vacuoles, increase of ROS production and accumulation of starch granules, suggesting the activation of stress responses likely due to the perturbation of the Golgi apparatus.
Collapse
Affiliation(s)
- Gaëtan Vanier
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, EA 4358, 76000, Rouen, France.,UMR FARE 614, Fractionnement des AgroRessources et Environnement, Chaire AFERE, Université de Reims-Champagne-Ardenne, INRA, 51686, Reims Cedex, France
| | - Pierre-Louis Lucas
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, EA 4358, 76000, Rouen, France
| | - Corinne Loutelier-Bourhis
- Normandie Univ, UNIROUEN, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen, CNRS, 76000, Rouen, France
| | - Jessica Vanier
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, EA 4358, 76000, Rouen, France
| | - Carole Plasson
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, EA 4358, 76000, Rouen, France
| | - Marie-Laure Walet-Balieu
- Normandie Univ, UNIROUEN, Plate-Forme de Protéomique PISSARO, 76000, Rouen, France.,Normandie Univ, UNIROUEN, Institut de Recherche et d'Innovation Biomédicale (IRIB), 76000, Rouen, France
| | - Philippe Chan Tchi-Song
- Normandie Univ, UNIROUEN, Plate-Forme de Protéomique PISSARO, 76000, Rouen, France.,Normandie Univ, UNIROUEN, Institut de Recherche et d'Innovation Biomédicale (IRIB), 76000, Rouen, France
| | - Isabelle Remy-Jouet
- Normandie Univ, UNIROUEN, Inserm UMR 1096, Plateforme BOSS, 76000, Rouen, France
| | - Vincent Richard
- Normandie Univ, UNIROUEN, Inserm UMR 1096, Plateforme BOSS, 76000, Rouen, France
| | - Sophie Bernard
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, EA 4358, 76000, Rouen, France.,Normandie Univ, UNIROUEN, Plate-forme, PRIMACEN, Cell Imaging Platform of Normandy, 76000, Rouen, France
| | - Azeddine Driouich
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, EA 4358, 76000, Rouen, France.,Normandie Univ, UNIROUEN, Plate-forme, PRIMACEN, Cell Imaging Platform of Normandy, 76000, Rouen, France
| | - Carlos Afonso
- Normandie Univ, UNIROUEN, COBRA, UMR 6014 et FR 3038, Université de Rouen, INSA de Rouen, CNRS, 76000, Rouen, France
| | - Patrice Lerouge
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, EA 4358, 76000, Rouen, France
| | - Elodie Mathieu-Rivet
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, EA 4358, 76000, Rouen, France
| | - Muriel Bardor
- Normandie Univ, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire végétale, EA 4358, 76000, Rouen, France. .,Institut Universitaire de France (I.U.F.) 1, rue Descartes, 75231, Paris, Cedex 05, France.
| |
Collapse
|
30
|
Borovcová L, Hermannová M, Pauk V, Šimek M, Havlíček V, Lemr K. Simple area determination of strongly overlapping ion mobility peaks. Anal Chim Acta 2017; 981:71-79. [DOI: 10.1016/j.aca.2017.05.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/01/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
|
31
|
Hofmann J, Pagel K. Glykananalyse mittels Ionenmobilitäts-Massenspektrometrie. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Johanna Hofmann
- Abteilung Molekülphysik; Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Deutschland
| | - Kevin Pagel
- Institut für Chemie und Biochemie; Freie Universität Berlin; Takustraße 3 Deutschland
| |
Collapse
|
32
|
Hofmann J, Pagel K. Glycan Analysis by Ion Mobility-Mass Spectrometry. Angew Chem Int Ed Engl 2017; 56:8342-8349. [DOI: 10.1002/anie.201701309] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/03/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Johanna Hofmann
- Abteilung Molekülphysik; Fritz-Haber-Institut der Max-Planck-Gesellschaft; Faradayweg 4-6 14195 Berlin Germany
| | - Kevin Pagel
- Institut für Chemie und Biochemie; Freie Universität Berlin; Takustraße 3 Germany
| |
Collapse
|
33
|
Glaskin RS, Khatri K, Wang Q, Zaia J, Costello CE. Construction of a Database of Collision Cross Section Values for Glycopeptides, Glycans, and Peptides Determined by IM-MS. Anal Chem 2017; 89:4452-4460. [PMID: 28323417 PMCID: PMC5766263 DOI: 10.1021/acs.analchem.6b04146] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An ion mobility quadrupole time-of-flight mass spectrometer was used to examine the gas-phase structures of a set of glycopeptides resulting from proteolytic digestion of the well-characterized glycoproteins bovine ribonuclease B, human transferrin, bovine fetuin and human α1-acid glycoprotein, the corresponding deglycosylated peptides, and the glycans released by the endoglycosidase PNGase F. When closely related glycoforms did not occur naturally, exoglycosidases were used to achieve stepwise removal of individual saccharide units from the nonreducing termini of the multiantennary structures. Collision cross sections (CCS) were calculated and plotted as a function of mass-to-charge ratio. Linear trendlines were observed for the glycoforms of individual N-linked glycopeptides, the deglycosylated peptides, and the released, deutero-reduced permethylated glycans. For the glycoforms of a given glycopeptide or set of derivatized glycans, the slope of the line connecting CCS values remained similar for the [M+3H]3+ ions observed as the glycan antennae were shortened by stepwise exoglycosidase treatments; this trend was consistent regardless of the peptide length or the saccharide removed. The results form the basis for a database of CCS values and the CCS increments that correspond to changes in glycoform compositions.
Collapse
Affiliation(s)
| | - Kshitij Khatri
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118-2646, United States
| | | | - Joseph Zaia
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118-2646, United States
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118-2646, United States
| |
Collapse
|
34
|
Liu Y, Cong X, Liu W, Laganowsky A. Characterization of Membrane Protein-Lipid Interactions by Mass Spectrometry Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:579-586. [PMID: 27924494 DOI: 10.1007/s13361-016-1555-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/06/2016] [Accepted: 11/03/2016] [Indexed: 05/21/2023]
Abstract
Lipids in the biological membrane can modulate the structure and function of integral and peripheral membrane proteins. Distinguishing individual lipids that bind selectively to membrane protein complexes from an ensemble of lipid-bound species remains a daunting task. Recently, ion mobility mass spectrometry (IM-MS) has proven to be invaluable for interrogating the interactions between protein and individual lipids, where the complex undergoes collision induced unfolding followed by quantification of the unfolding pathway to assess the effect of these interactions. However, gas-phase unfolding experiments for membrane proteins are typically performed on the entire ensemble (apo and lipid bound species), raising uncertainty to the contribution of individual lipids and the species that are ejected in the unfolding process. Here, we describe the application of mass spectrometry ion mobility mass spectrometry (MS-IM-MS) for isolating ions corresponding to lipid-bound states of a model integral membrane protein, ammonia channel (AmtB) from Escherichia coli. Free of ensemble effects, MS-IM-MS reveals that bound lipids are ejected as neutral species; however, no correlation was found between the lipid-induced stabilization of complex and their equilibrium binding constants. In comparison to data obtained by IM-MS, there are surprisingly limited differences in stability measurements from IM-MS and MS-IM-MS. The approach described here to isolate ions of membrane protein complexes will be useful for other MS methods, such as surface induced dissociation or collision induced dissociation to determine the stoichiometry of hetero-oligomeric membrane protein complexes. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Yang Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Xiao Cong
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Wen Liu
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
| | - Arthur Laganowsky
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA.
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA.
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan, TX, 77807, USA.
| |
Collapse
|
35
|
Morrison KA, Bendiak BK, Clowers BH. Enhanced Mixture Separations of Metal Adducted Tetrasaccharides Using Frequency Encoded Ion Mobility Separations and Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:664-677. [PMID: 27796835 DOI: 10.1007/s13361-016-1505-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 05/16/2023]
Abstract
Using five isomeric tetrasaccharides in combination with seven multivalent metals, the impact on mobility separations and resulting CID spectra were examined using a hybrid ion mobility atmospheric pressure drift tube system coupled with a linear ion trap. By enhancing the duty cycle of the drift tube system using a linearly chirped frequency, the collision-induced dissociation spectra were encoded in the mobility domain according to the drift times of each glycan isomer precursor. Differential fragmentation patterns correlated with precursor drift times ensured direct assignment of fragments with precursor structure whether as individual standards or in a mixture of isomers. In addition to certain metal ions providing higher degrees of separation than others, in select cases more than one arrival time distribution was observed for a single pure carbohydrate isomer. These observations suggest the existence of alternative coordination sites within a single monomeric species, but more interesting was the observation of different fragmentation ion yields for carbohydrate dimers formed through metal adduction. Positive-ion data were also compared with negative-ion species, where dimer formation did not occur and single peaks were observed for each isomeric tetrasaccharide-alditol. This enhanced analytical power has implications not only for carbohydrate molecules but also for a wide variety of complex mixtures of molecules where dissociation spectra may potentially be derived from combinations of monomeric, homodimeric, and heterodimeric species having identical nominal m/z values. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Kelsey A Morrison
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164, USA
| | - Brad K Bendiak
- Department of Cell and Developmental Biology and Program in Structural Biology and Biochemistry, University of Colorado Health Sciences Center, Mail Stop 8108, 12801 E 17th Ave., Aurora, CO, 80045, USA
| | - Brian H Clowers
- Department of Chemistry, Washington State University, PO Box 644630, Pullman, WA, 99164, USA.
| |
Collapse
|
36
|
Abstract
Glycosylation is one of the most common and essential protein modifications. Glycans conjugated to biomolecules modulate the function of such molecules through both direct recognition of glycan structures and indirect mechanisms that involve the control of protein turnover rates, stability, and conformation. The biological attributes of glycans in numerous biological processes and implications in a number of diseases highlight the necessity for comprehensive characterization of protein glycosylation. This chapter reviews cutting-edge methods and tools developed to facilitate quantitative glycomics. This chapter highlights the different methods employed for the release and purification of glycans from biological samples. The most effective labeling methods developed for sensitive quantitative glycomics are also described and discussed. The chromatographic approaches that have been used effectively in glycomics are also highlighted.
Collapse
Affiliation(s)
- L Veillon
- Texas Tech University, Lubbock, TX, United States
| | - S Zhou
- Texas Tech University, Lubbock, TX, United States
| | - Y Mechref
- Texas Tech University, Lubbock, TX, United States.
| |
Collapse
|
37
|
Zhang X, Romm M, Zheng X, Zink EM, Kim YM, Burnum-Johnson KE, Orton DJ, Apffel A, Ibrahim YM, Monroe ME, Moore RJ, Smith JN, Ma J, Renslow RS, Thomas DG, Blackwell AE, Swinford G, Sausen J, Kurulugama RT, Eno N, Darland E, Stafford G, Fjeldsted J, Metz TO, Teeguarden JG, Smith RD, Baker ES. SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids. CLINICAL MASS SPECTROMETRY 2016; 2:1-10. [PMID: 29276770 PMCID: PMC5739065 DOI: 10.1016/j.clinms.2016.11.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with high reproducibility (CV 6 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure.
Collapse
Affiliation(s)
- Xing Zhang
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Michelle Romm
- Agilent Technologies, Santa Clara, CA, United States
| | - Xueyun Zheng
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erika M Zink
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Young-Mo Kim
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Kristin E Burnum-Johnson
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Daniel J Orton
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Alex Apffel
- Agilent Technologies, Santa Clara, CA, United States
| | - Yehia M Ibrahim
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Matthew E Monroe
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ronald J Moore
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jordan N Smith
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jian Ma
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Ryan S Renslow
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Dennis G Thomas
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | | | | | - John Sausen
- Agilent Technologies, Santa Clara, CA, United States
| | | | - Nathan Eno
- Agilent Technologies, Santa Clara, CA, United States
| | - Ed Darland
- Agilent Technologies, Santa Clara, CA, United States
| | | | | | - Thomas O Metz
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Justin G Teeguarden
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.,Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Richard D Smith
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Erin S Baker
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| |
Collapse
|
38
|
Harper B, Neumann EK, Stow SM, May JC, McLean JA, Solouki T. Determination of ion mobility collision cross sections for unresolved isomeric mixtures using tandem mass spectrometry and chemometric deconvolution. Anal Chim Acta 2016; 939:64-72. [PMID: 27639144 PMCID: PMC5744691 DOI: 10.1016/j.aca.2016.07.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 01/23/2023]
Abstract
Ion mobility (IM) is an important analytical technique for determining ion collision cross section (CCS) values in the gas-phase and gaining insight into molecular structures and conformations. However, limited instrument resolving powers for IM may restrict adequate characterization of conformationally similar ions, such as structural isomers, and reduce the accuracy of IM-based CCS calculations. Recently, we introduced an automated technique for extracting "pure" IM and collision-induced dissociation (CID) mass spectra of IM overlapping species using chemometric deconvolution of post-IM/CID mass spectrometry (MS) data [J. Am. Soc. Mass Spectrom., 2014, 25, 1810-1819]. Here we extend those capabilities to demonstrate how extracted IM profiles can be used to calculate accurate CCS values of peptide isomer ions which are not fully resolved by IM. We show that CCS values obtained from deconvoluted IM spectra match with CCS values measured from the individually analyzed corresponding peptides on uniform field IM instrumentation. We introduce an approach that utilizes experimentally determined IM arrival time (AT) "shift factors" to compensate for ion acceleration variations during post-IM/CID and significantly improve the accuracy of the calculated CCS values. Also, we discuss details of this IM deconvolution approach and compare empirical CCS values from traveling wave (TW)IM-MS and drift tube (DT)IM-MS with theoretically calculated CCS values using the projected superposition approximation (PSA). For example, experimentally measured deconvoluted TWIM-MS mean CCS values for doubly-protonated RYGGFM, RMFGYG, MFRYGG, and FRMYGG peptide isomers were 288.8 Å(2), 295.1 Å(2), 296.8 Å(2), and 300.1 Å(2); all four of these CCS values were within 1.5% of independently measured DTIM-MS values.
Collapse
Affiliation(s)
- Brett Harper
- Institute of Biomedical Studies, Baylor University, Waco, TX 76798, USA
| | - Elizabeth K Neumann
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA
| | - Sarah M Stow
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN 37235, USA; Center for Innovative Technology, Nashville, TN 37235, USA
| | - Jody C May
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN 37235, USA; Center for Innovative Technology, Nashville, TN 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA; Vanderbilt Institute of Chemical Biology, Nashville, TN 37235, USA; Vanderbilt Institute for Integrative Biosystems Research and Education, Nashville, TN 37235, USA; Center for Innovative Technology, Nashville, TN 37235, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798, USA.
| |
Collapse
|
39
|
Gray C, Thomas B, Upton R, Migas L, Eyers C, Barran P, Flitsch S. Applications of ion mobility mass spectrometry for high throughput, high resolution glycan analysis. Biochim Biophys Acta Gen Subj 2016; 1860:1688-709. [DOI: 10.1016/j.bbagen.2016.02.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/21/2022]
|
40
|
Struwe WB, Benesch JL, Harvey DJ, Pagel K. Collision cross sections of high-mannose N-glycans in commonly observed adduct states--identification of gas-phase conformers unique to [M-H](-) ions. Analyst 2016; 140:6799-803. [PMID: 26159123 DOI: 10.1039/c5an01092f] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We report collision cross sections (CCS) of high-mannose N-glycans as [M + Na](+), [M + K](+), [M + H](+), [M + Cl](-), [M + H2PO4](-) and [M - H](-) ions, measured by drift tube (DT) ion mobility-mass spectrometry (IM-MS) in helium and nitrogen gases. Further analysis using traveling wave (TW) IM-MS reveal the existence of distinct conformers exclusive to [M - H](-) ions.
Collapse
Affiliation(s)
- W B Struwe
- Department of Chemistry, University of Oxford, Oxford, UKOX1 3TA.
| | | | | | | |
Collapse
|
41
|
Huang Y, Dodds ED. Ion-neutral collisional cross sections of carbohydrate isomers as divalent cation adducts and their electron transfer products. Analyst 2016. [PMID: 26225371 DOI: 10.1039/c5an01093d] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As the gravity of glycoscience continues to amass, a commensurate demand for rapid, sensitive, and structurally comprehensive glycoanalytical tools has arisen. Among the most elusive but desirable analytical capabilities is the ability to expeditiously and unambiguously detect, distinguish, and resolve carbohydrates that differ only in their constitutional isomerism and/or stereoisomerism. While ion mobility spectrometry (IMS) has proven a highly promising tool for such analyses, the facility of this method to discriminate larger oligosaccharides is still somewhat limited. In an effort to expand the capabilities of IMS to discriminate among carbohydrate isomers, the present investigation was focused on IMS studies of four trisaccharide isomers, four pentasaccharide isomers, and two hexasaccharide isomers, each as group II metal ion adducts and their corresponding gas-phase electron transfer (ET) products. These studies were also evaluated in the context of previously investigated group I metal ion adducts of the same saccharides. The orientationally averaged ion-neutral collisional cross sections (CCSs) of the various carbohydrate/metal ion adducts were found to be dependent on the structures of specific carbohydrate isomers, sensitive to the electronic characteristics of the bound cation, and responsive to the attachment of an additional electron (in the case of divalent metal ion adducts). Overall, these results underscore the utility of metal ions for probing carbohydrate structure in concert with IMS, and the capacity of gas-phase ion chemistry to expand the menu of such probes.
Collapse
Affiliation(s)
- Yuting Huang
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
| | | |
Collapse
|
42
|
Harvey DJ, Scarff CA, Edgeworth M, Struwe WB, Pagel K, Thalassinos K, Crispin M, Scrivens J. Travelling-wave ion mobility and negative ion fragmentation of high-mannose N-glycans. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:219-35. [PMID: 26956389 PMCID: PMC4821469 DOI: 10.1002/jms.3738] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/01/2015] [Accepted: 12/02/2015] [Indexed: 05/02/2023]
Abstract
The isomeric structure of high-mannose N-glycans can significantly impact biological recognition events. Here, the utility of travelling-wave ion mobility mass spectrometry for isomer separation of high-mannose N-glycans is investigated. Negative ion fragmentation using collision-induced dissociation gave more informative spectra than positive ion spectra with mass-different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra, and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed, but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers or anomers were being separated. Collision cross sections of the isomers in positive and negative fragmentation mode were estimated from travelling-wave ion mobility mass spectrometry data using dextran glycans as calibrant. More complete collision cross section data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N-glycans released from the well-characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross-sectional data, details of the negative ion collision-induced dissociation spectra of all resolved isomers are discussed.
Collapse
Affiliation(s)
- David J. Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
| | - Charlotte A. Scarff
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
- Current address, Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew Edgeworth
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
| | - Weston B. Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
- Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Kevin Pagel
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse. 3, 14159 Berlin, Germany
- Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, 14195 Berlin, Germany
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jim Scrivens
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
| |
Collapse
|
43
|
Harvey DJ, Crispin M, Bonomelli C, Scrivens JH. Ion Mobility Mass Spectrometry for Ion Recovery and Clean-Up of MS and MS/MS Spectra Obtained from Low Abundance Viral Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015. [PMID: 26204966 PMCID: PMC4811024 DOI: 10.1007/s13361-015-1163-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Many samples of complex mixtures of N-glycans released from small amounts of material, such as glycoproteins from viruses, present problems for mass spectrometric analysis because of the presence of contaminating material that is difficult to remove by conventional methods without involving sample loss. This study describes the use of ion mobility for extraction of glycan profiles from such samples and for obtaining clean CID spectra when targeted m/z values capture additional ions from those of the target compound. N-glycans were released enzymatically from within SDS-PAGE gels, from the representative recombinant glycoprotein, gp120 of the human immunodeficiency virus, and examined by direct infusion electrospray in negative mode followed by ion mobility with a Waters Synapt G2 mass spectrometer (Waters MS-Technologies, Manchester, UK). Clean profiles of singly, doubly, and triply charged N-glycans were obtained from samples in cases where the raw electrospray spectra displayed only a few glycan ions as the result of low sample concentration or the presence of contamination. Ion mobility also enabled uncontaminated CID spectra to be obtained from glycans when their molecular ions displayed coincidence with ions from fragments or multiply charged ions with similar m/z values. This technique proved to be invaluable for removing extraneous ions from many CID spectra. The presence of such ions often produces spectra that are difficult to interpret. Most CID spectra, even those from abundant glycan constituents, benefited from such clean-up, showing that the extra dimension provided by ion mobility was invaluable for studies of this type.
Collapse
Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK.
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Camille Bonomelli
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Jim H Scrivens
- Department of Biological Sciences, University of Warwick, Coventry, CV47AL, UK
| |
Collapse
|
44
|
Baker ES, Burnum-Johnson KE, Ibrahim YM, Orton DJ, Monroe ME, Kelly RT, Moore RJ, Zhang X, Théberge R, Costello CE, Smith RD. Enhancing bottom-up and top-down proteomic measurements with ion mobility separations. Proteomics 2015; 15:2766-76. [PMID: 26046661 DOI: 10.1002/pmic.201500048] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/06/2015] [Accepted: 06/02/2015] [Indexed: 11/06/2022]
Abstract
Proteomic measurements with greater throughput, sensitivity, and structural information are essential for improving both in-depth characterization of complex mixtures and targeted studies. While LC separation coupled with MS (LC-MS) measurements have provided information on thousands of proteins in different sample types, the introduction of a separation stage that provides further component resolution and rapid structural information has many benefits in proteomic analyses. Technical advances in ion transmission and data acquisition have made ion mobility separations an opportune technology to be easily and effectively incorporated into LC-MS proteomic measurements for enhancing their information content. Herein, we report on applications illustrating increased sensitivity, throughput, and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements.
Collapse
Affiliation(s)
- Erin Shammel Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Yehia M Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ryan T Kelly
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Xing Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Roger Théberge
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Catherine E Costello
- Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| |
Collapse
|
45
|
Zhu F, Trinidad JC, Clemmer DE. Glycopeptide Site Heterogeneity and Structural Diversity Determined by Combined Lectin Affinity Chromatography/IMS/CID/MS Techniques. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1092-102. [PMID: 25840811 PMCID: PMC4475505 DOI: 10.1007/s13361-015-1110-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 05/10/2023]
Abstract
Glycopeptides from a tryptic digest of chicken ovomucoid were enriched using a simplified lectin affinity chromatography (LAC) platform, and characterized by high-resolution mass spectrometry (MS) as well as ion mobility spectrometry (IMS)-MS. The LAC platform effectively enriched the glycoproteome, from which a total of 117 glycopeptides containing 27 glycan forms were identified for this protein. IMS-MS analysis revealed a high degree of glycopeptide site heterogeneity. Comparison of the IMS distributions of the glycopeptides from different charge states reveals that higher charge states allow more structures to be resolved. Presumably the repulsive interactions between charged sites lead to more open configurations, which are more readily separated compared with the more compact, lower charge state forms of the same groups of species. Combining IMS with collision induced dissociation (CID) made it possible to determine the presence of isomeric glycans and to reconstruct their IMS profiles. This study illustrates a workflow involving hybrid techniques for determining glycopeptide site heterogeneity and evaluating structural diversity of glycans and glycopeptides.
Collapse
Affiliation(s)
| | - Jonathan C. Trinidad
- Corresponding authors. J.C.T.: ; Tel: (812) 856-4126. D.E.C.: ; Tel: (812) 855-8259
| | - David E. Clemmer
- Corresponding authors. J.C.T.: ; Tel: (812) 856-4126. D.E.C.: ; Tel: (812) 855-8259
| |
Collapse
|
46
|
Hermannová M, Iordache AM, Slováková K, Havlíček V, Pelantová H, Lemr K. Arrival time distributions of product ions reveal isomeric ratio of deprotonated molecules in ion mobility-mass spectrometry of hyaluronan-derived oligosaccharides. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:854-63. [PMID: 26169140 DOI: 10.1002/jms.3596] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 03/11/2015] [Accepted: 03/16/2015] [Indexed: 05/16/2023]
Abstract
Hyaluronic acid is a naturally occurring linear polysaccharide with substantial medical potential. In this work, discrimination of tyramine-based hyaluronan derivatives was accessed by ion mobility-mass spectrometry of deprotonated molecules and nuclear magnetic resonance spectroscopy. As the product ion mass spectra did not allow for direct isomer discrimination in mixture, the reductive labeling of oligosaccharides as well as stable isotope labeling was performed. The ion mobility separation of parent ions together with the characteristic fragmentation for reduced isomers providing unique product ions allowed us to identify isomers present in a mixture and determine their mutual isomeric ratio. The determination used simple recalculation of arrival time distribution areas of unique ions to areas of deprotonated molecules. Mass spectrometry data were confirmed by nuclear magnetic resonance spectroscopy.
Collapse
Affiliation(s)
| | - Andreea-Maria Iordache
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17.listopadu 12, Olomouc, 771 46, Czech Republic
| | - Kristína Slováková
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17.listopadu 12, Olomouc, 771 46, Czech Republic
| | - Vladimír Havlíček
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17.listopadu 12, Olomouc, 771 46, Czech Republic
- Institute of Microbiology, ASCR, v.v.i., Videnska 1083, 142 20, Czech Republic
| | - Helena Pelantová
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17.listopadu 12, Olomouc, 771 46, Czech Republic
- Institute of Microbiology, ASCR, v.v.i., Videnska 1083, 142 20, Czech Republic
| | - Karel Lemr
- Regional Centre of Advanced Technologies and Materials, Department of Analytical Chemistry, Faculty of Science, Palacký University, 17.listopadu 12, Olomouc, 771 46, Czech Republic
- Institute of Microbiology, ASCR, v.v.i., Videnska 1083, 142 20, Czech Republic
| |
Collapse
|
47
|
Niu S, Ruotolo BT. Collisional unfolding of multiprotein complexes reveals cooperative stabilization upon ligand binding. Protein Sci 2015; 24:1272-81. [PMID: 25970849 DOI: 10.1002/pro.2699] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 04/13/2015] [Accepted: 04/29/2015] [Indexed: 12/19/2022]
Abstract
Cooperative binding mechanisms are a common feature in biology, enabling a diverse range of protein-based molecular machines to regulate activities ranging from oxygen uptake to cellular membrane transport. Much, however, is not known about such cooperative binding mechanisms, including how such events typically add to the overall stability of such protein systems. Measurements of such cooperative stabilization events are challenging, as they require the separation and resolution of individual protein complex bound states within a mixture of potential stoichiometries to individually assess protein stabilities. Here, we report ion mobility-mass spectrometry results for the concanavalin A tetramer bound to a range of polysaccharide ligands. We use collision induced unfolding, a relatively new methodology that functions as a gas-phase analog of calorimetry experiments in solution, to individually assess the stabilities of concanavalin A bound states. By comparing the differences in activation voltage required to unfold different concanavalin A-ligand stoichiometries, we find evidence suggesting a cooperative stabilization of concanavalin A occurs upon binding most carbohydrate ligands. We critically evaluate this observation by assessing a broad range of ligands, evaluating the unfolding properties of multiple protein charge states, and by comparing our gas-phase results with those obtained from calorimetry experiments carried out in solution.
Collapse
Affiliation(s)
- Shuai Niu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| |
Collapse
|
48
|
Huang Y, Dodds ED. Discrimination of Isomeric Carbohydrates as the Electron Transfer Products of Group II Cation Adducts by Ion Mobility Spectrometry and Tandem Mass Spectrometry. Anal Chem 2015; 87:5664-8. [PMID: 25955237 DOI: 10.1021/acs.analchem.5b00759] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The rapid and unambiguous distinction of isomeric carbohydrate structures persists as a tremendous analytical challenge. This paper reports the first exploitation of carbohydrate/metal ion interactions in concert with gas-phase ion chemistry to improve discrimination of oligosaccharide isomers by both ion mobility spectrometry and tandem mass spectrometry. This is demonstrated for two isomeric pentasaccharides and two isomeric hexasaccharides, each studied in an underivatized form as their calcium ion adducts, barium ion adducts, and gas-phase electron transfer products thereof. With appropriate selection of the charge carrier, transfer of a single electron to the carbohydrate metal ion adducts resulted in isomer-distinguishing shifts in their ion/neutral collision cross sections and the appearance of unique features in their vibrational activation/dissociation spectra. These findings suggest novel and elegant gas-phase strategies for rapid differentiation of isomeric oligosaccharides.
Collapse
Affiliation(s)
- Yuting Huang
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Eric D Dodds
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0304, United States
| |
Collapse
|
49
|
Affiliation(s)
- Jody C. May
- Department
of Chemistry,
Center for Innovative Technology, Vanderbilt Institute for Chemical
Biology, Vanderbilt Institute for Integrative Biosystems Research
and Education , Vanderbilt University, Nashville, Tennessee 37235, United States
| | - John A. McLean
- Department
of Chemistry,
Center for Innovative Technology, Vanderbilt Institute for Chemical
Biology, Vanderbilt Institute for Integrative Biosystems Research
and Education , Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
50
|
Maurer MM, Donohoe GC, Valentine SJ. Advances in ion mobility-mass spectrometry instrumentation and techniques for characterizing structural heterogeneity. Analyst 2015; 140:6782-98. [PMID: 26114255 DOI: 10.1039/c5an00922g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Enabling IM-MS instrumentation and techniques for characterizing sample structural heterogeneity have developed rapidly over the last five years.
Collapse
Affiliation(s)
- Megan M. Maurer
- C. Eugene Bennett Department of Chemistry
- West Virginia University
- Morgantown
- USA
| | - Gregory C. Donohoe
- C. Eugene Bennett Department of Chemistry
- West Virginia University
- Morgantown
- USA
| | | |
Collapse
|