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Luo RY, Comstock K, Ding C, Wu AH, Lynch KL. Comparison of liquid chromatography-high-resolution tandem mass spectrometry (MS 2) and multi-stage mass spectrometry (MS 3) for screening toxic natural products. J Mass Spectrom Adv Clin Lab 2023; 30:38-44. [PMID: 37876549 PMCID: PMC10590993 DOI: 10.1016/j.jmsacl.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/22/2023] [Accepted: 09/27/2023] [Indexed: 10/26/2023] Open
Abstract
Background Liquid chromatography-high-resolution mass spectrometry (LC-HR-MS) has emerged as a powerful analytical technology for compound screening in clinical toxicology. To evaluate the potential of LC-HR-MS3 in detecting toxic natural products, a spectral library of 85 natural products (79 alkaloids) that contains both MS2 and MS3 mass spectra was constructed and used to identify the natural products. Samples were analyzed using an LC-HR-MS3 method and the generated data were matched to the spectral library to identify the natural products. Methods To test the performance of the LC-HR-MS3 method in different sample matrices, the 85 natural product standards were divided into three groups to separate structural isomers and avoid ion suppression effects caused by co-elution of multiple analytes. The grouped analytes were spiked into drug-free serum and drug-free urine to produce contrived clinical samples. Results The compound identification results of the 85 natural products in urine and serum samples were obtained. The match scores using both MS2 and MS3 mass spectra and those using only MS2 mass spectra were compared at 10 different analyte concentrations. The two types of data analysis provided identical identification results for the majority of the analytes (96% in serum, 92% in urine), whereas, for the remaining analytes, the MS2-MS3 tree data analysis had better performance in identifying them at lower concentrations. Conclusion This study shows that in comparison to LC-HR-MS (MS2), LC-HR-MS3 can increase the performance in identification of a small group of the toxic natural products tested in serum and urine specimens.
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Affiliation(s)
- Ruben Yiqi Luo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | | | - Alan H.B. Wu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kara L. Lynch
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
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Hou X, Wang Y, Bu D, Wang Y, Sun S. EMNGly: predicting N-linked glycosylation sites using the language models for feature extraction. Bioinformatics 2023; 39:btad650. [PMID: 37930896 PMCID: PMC10627407 DOI: 10.1093/bioinformatics/btad650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/14/2023] [Indexed: 11/08/2023] Open
Abstract
MOTIVATION N-linked glycosylation is a frequently occurring post-translational protein modification that serves critical functions in protein folding, stability, trafficking, and recognition. Its involvement spans across multiple biological processes and alterations to this process can result in various diseases. Therefore, identifying N-linked glycosylation sites is imperative for comprehending the mechanisms and systems underlying glycosylation. Due to the inherent experimental complexities, machine learning and deep learning have become indispensable tools for predicting these sites. RESULTS In this context, a new approach called EMNGly has been proposed. The EMNGly approach utilizes pretrained protein language model (Evolutionary Scale Modeling) and pretrained protein structure model (Inverse Folding Model) for features extraction and support vector machine for classification. Ten-fold cross-validation and independent tests show that this approach has outperformed existing techniques. And it achieves Matthews Correlation Coefficient, sensitivity, specificity, and accuracy of 0.8282, 0.9343, 0.8934, and 0.9143, respectively on a benchmark independent test set.
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Affiliation(s)
- Xiaoyang Hou
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Wang
- Syneron Technology, Guangzhou 510000, China
| | - Dongbo Bu
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaojun Wang
- College of Information and Electrical Engineering, China Agricultural University, Beijing 100083, China
| | - Shiwei Sun
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2019-2020. MASS SPECTROMETRY REVIEWS 2022:e21806. [PMID: 36468275 DOI: 10.1002/mas.21806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2020. Also included are papers that describe methods appropriate to analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. The review is basically divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of arrays. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other areas such as medicine, industrial processes and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. The reported work shows increasing use of incorporation of new techniques such as ion mobility and the enormous impact that MALDI imaging is having. MALDI, although invented nearly 40 years ago is still an ideal technique for carbohydrate analysis and advancements in the technique and range of applications show little sign of diminishing.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
- Department of Chemistry, University of Oxford, Oxford, Oxfordshire, United Kingdom
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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: 61] [Impact Index Per Article: 30.5] [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.
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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
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Multistage mass spectrometry with intelligent precursor selection for N-glycan branching pattern analysis. Carbohydr Polym 2020; 237:116122. [DOI: 10.1016/j.carbpol.2020.116122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 02/10/2020] [Accepted: 03/03/2020] [Indexed: 12/28/2022]
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