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Sorokin AA, Pekov SI, Zavorotnyuk DS, Shamraeva MM, Bormotov DS, Popov IA. Modern machine-learning applications in ambient ionization mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38671553 DOI: 10.1002/mas.21886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024]
Abstract
This article provides a comprehensive overview of the applications of methods of machine learning (ML) and artificial intelligence (AI) in ambient ionization mass spectrometry (AIMS). AIMS has emerged as a powerful analytical tool in recent years, allowing for rapid and sensitive analysis of various samples without the need for extensive sample preparation. The integration of ML/AI algorithms with AIMS has further expanded its capabilities, enabling enhanced data analysis. This review discusses ML/AI algorithms applicable to the AIMS data and highlights the key advancements and potential benefits of utilizing ML/AI in the field of mass spectrometry, with a focus on the AIMS community.
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Affiliation(s)
- Anatoly A Sorokin
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Stanislav I Pekov
- Mass Spectrometry Laboratory, Skolkovo Institute of Science and Technology, Moscow, Russia
- Translational Medicine Laboratory, Siberian State Medical University, Tomsk, Russia
- Department for Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Denis S Zavorotnyuk
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mariya M Shamraeva
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Denis S Bormotov
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Igor A Popov
- Laboratory of Molecular Medical Diagnostics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Translational Medicine Laboratory, Siberian State Medical University, Tomsk, Russia
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Kumar BS. Recent Developments and Application of Mass Spectrometry Imaging in N-Glycosylation Studies: An Overview. Mass Spectrom (Tokyo) 2024; 13:A0142. [PMID: 38435075 PMCID: PMC10904931 DOI: 10.5702/massspectrometry.a0142] [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: 12/12/2023] [Accepted: 01/06/2024] [Indexed: 03/05/2024] Open
Abstract
Among the most typical posttranslational modifications is glycosylation, which often involves the covalent binding of an oligosaccharide (glycan) to either an asparagine (N-linked) or a serine/threonine (O-linked) residue. Studies imply that the N-glycan portion of a glycoprotein could serve as a particular disease biomarker rather than the protein itself because N-linked glycans have been widely recognized to evolve with the advancement of tumors and other diseases. N-glycans found on protein asparagine sites have been especially significant. Since N-glycans play clearly defined functions in the folding of proteins, cellular transport, and transmission of signals, modifications to them have been linked to several illnesses. However, because these N-glycans' production is not template driven, they have a substantial morphological range, rendering it difficult to distinguish the species that are most relevant to biology and medicine using standard techniques. Mass spectrometry (MS) techniques have emerged as effective analytical tools for investigating the role of glycosylation in health and illness. This is due to developments in MS equipment, data collection, and sample handling techniques. By recording the spatial dimension of a glycan's distribution in situ, mass spectrometry imaging (MSI) builds atop existing methods while offering added knowledge concerning the structure and functionality of biomolecules. In this review article, we address the current development of glycan MSI, starting with the most used tissue imaging techniques and ionization sources before proceeding on to a discussion on applications and concluding with implications for clinical research.
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Kumar BS. Recent developments and applications of ambient mass spectrometry imaging in pharmaceutical research: an overview. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 16:8-32. [PMID: 38088775 DOI: 10.1039/d3ay01267k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The application of ambient mass spectrometry imaging "MSI" is expanding in the areas of fundamental research on drug delivery and multiple phases of the process of identifying and developing drugs. Precise monitoring of a drug's pharmacological workflows, such as intake, distribution, metabolism, and discharge, is made easier by MSI's ability to determine the concentrations of the initiating drug and its metabolites across dosed samples without losing spatial data. Lipids, glycans, and proteins are just a few of the many phenotypes that MSI may be used to concurrently examine. Each of these substances has a particular distribution pattern and biological function throughout the body. MSI offers the perfect analytical tool for examining a drug's pharmacological features, especially in vitro and in vivo effectiveness, security, probable toxic effects, and putative molecular pathways, because of its high responsiveness in chemical and physical environments. The utilization of MSI in the field of pharmacy has further extended from the traditional tissue examination to the early stages of drug discovery and development, including examining the structure-function connection, high-throughput capabilities in vitro examination, and ex vivo research on individual cells or tumor spheroids. Additionally, an enormous array of endogenous substances that may function as tissue diagnostics can be scanned simultaneously, giving the specimen a highly thorough characterization. Ambient MSI techniques are soft enough to allow for easy examination of the native sample to gather data on exterior chemical compositions. This paper provides a scientific and methodological overview of ambient MSI utilization in research on pharmaceuticals.
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Affiliation(s)
- Bharath Sampath Kumar
- Independent researcher, 21, B2, 27th Street, Lakshmi Flats, Nanganallur, Chennai 600061, India.
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Baquer G, Sementé L, Ràfols P, Martín-Saiz L, Bookmeyer C, Fernández JA, Correig X, García-Altares M. rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation. J Cheminform 2023; 15:80. [PMID: 37715285 PMCID: PMC10504721 DOI: 10.1186/s13321-023-00756-2] [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: 04/03/2023] [Accepted: 08/29/2023] [Indexed: 09/17/2023] Open
Abstract
Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) spatially resolves the chemical composition of tissues. Lipids are of particular interest, as they influence important biological processes in health and disease. However, the identification of lipids in MALDI-MSI remains a challenge due to the lack of chromatographic separation or untargeted tandem mass spectrometry. Recent studies have proposed the use of MALDI in-source fragmentation to infer structural information and aid identification. Here we present rMSIfragment, an open-source R package that exploits known adducts and fragmentation pathways to confidently annotate lipids in MALDI-MSI. The annotations are ranked using a novel score that demonstrates an area under the curve of 0.7 in ROC analyses using HPLC-MS and Target-Decoy validations. rMSIfragment applies to multiple MALDI-MSI sample types and experimental setups. Finally, we demonstrate that overlooking in-source fragments increases the number of incorrect annotations. Annotation workflows should consider in-source fragmentation tools such as rMSIfragment to increase annotation confidence and reduce the number of false positives.
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Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain.
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain.
| | - Lucía Martín-Saiz
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Christoph Bookmeyer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Institute of Hygiene, University of Münster, Münster, Germany
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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Hu H, Laskin J. Emerging Computational Methods in Mass Spectrometry Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203339. [PMID: 36253139 PMCID: PMC9731724 DOI: 10.1002/advs.202203339] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/17/2022] [Indexed: 05/10/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful analytical technique that generates maps of hundreds of molecules in biological samples with high sensitivity and molecular specificity. Advanced MSI platforms with capability of high-spatial resolution and high-throughput acquisition generate vast amount of data, which necessitates the development of computational tools for MSI data analysis. In addition, computation-driven MSI experiments have recently emerged as enabling technologies for further improving the MSI capabilities with little or no hardware modification. This review provides a critical summary of computational methods and resources developed for MSI data analysis and interpretation along with computational approaches for improving throughput and molecular coverage in MSI experiments. This review is focused on the recently developed artificial intelligence methods and provides an outlook for a future paradigm shift in MSI with transformative computational methods.
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Affiliation(s)
- Hang Hu
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN47907USA
| | - Julia Laskin
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN47907USA
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Baquer G, Sementé L, Mahamdi T, Correig X, Ràfols P, García-Altares M. What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2022:e21794. [PMID: 35822576 DOI: 10.1002/mas.21794] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) has become a widespread analytical technique to perform nonlabeled spatial molecular identification. The Achilles' heel of MSI is the annotation and identification of molecular species due to intrinsic limitations of the technique (lack of chromatographic separation and the difficulty to apply tandem MS). Successful strategies to perform annotation and identification combine extra analytical steps, like using orthogonal analytical techniques to identify compounds; with algorithms that integrate the spectral and spatial information. In this review, we discuss different experimental strategies and bioinformatics tools to annotate and identify compounds in MSI experiments. We target strategies and tools for small molecule applications, such as lipidomics and metabolomics. First, we explain how sample preparation and the acquisition process influences annotation and identification, from sample preservation to the use of orthogonal techniques. Then, we review twelve software tools for annotation and identification in MSI. Finally, we offer perspectives on two current needs of the MSI community: the adaptation of guidelines for communicating confidence levels in identifications; and the creation of a standard format to store and exchange annotations and identifications in MSI.
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Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Toufik Mahamdi
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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Barupal DK, Mahajan P, Fakouri-Baygi S, Wright RO, Arora M, Teitelbaum SL. CCDB: A database for exploring inter-chemical correlations in metabolomics and exposomics datasets. ENVIRONMENT INTERNATIONAL 2022; 164:107240. [PMID: 35461097 PMCID: PMC9195052 DOI: 10.1016/j.envint.2022.107240] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 05/18/2023]
Abstract
Inter-chemical correlations in metabolomics and exposomics datasets provide valuable information for studying relationships among chemicals reported for human specimens. With an increase in the number of compounds for these datasets, a network graph analysis and visualization of the correlation structure is difficult to interpret. We have developed the Chemical Correlation Database (CCDB), as a systematic catalogue of inter-chemical correlation in publicly available metabolomics and exposomics studies. The database has been provided via an online interface to create single compound-centric views. We have demonstrated various applications of the database to explore: 1) the chemicals from a chemical class such as Per- and Polyfluoroalkyl Substances (PFAS), polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), phthalates and tobacco smoke related metabolites; 2) xenobiotic metabolites such as caffeine and acetaminophen; 3) endogenous metabolites (acyl-carnitines); and 4) unannotated peaks for PFAS. The database has a rich collection of 35 human studies, including the National Health and Nutrition Examination Survey (NHANES) and high-quality untargeted metabolomics datasets. CCDB is supported by a simple, interactive and user-friendly web-interface to retrieve and visualize the inter-chemical correlation data. The CCDB has the potential to be a key computational resource in metabolomics and exposomics facilitating the expansion of our understanding about biological and chemical relationships among metabolites and chemical exposures in the human body. The database is available at www.ccdb.idsl.me site.
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Affiliation(s)
- Dinesh Kumar Barupal
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA.
| | - Priyanka Mahajan
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Sadjad Fakouri-Baygi
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Robert O Wright
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Manish Arora
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
| | - Susan L Teitelbaum
- Department of Environmental Medicine and Public Health, Institute for Exposomic Research, Icahn School of Medicine at Mount Sinai, 17 E 102nd St, CAM Building, New York 10029, USA
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Zhu Y, Zang Q, Luo Z, He J, Zhang R, Abliz Z. An Organ-Specific Metabolite Annotation Approach for Ambient Mass Spectrometry Imaging Reveals Spatial Metabolic Alterations of a Whole Mouse Body. Anal Chem 2022; 94:7286-7294. [PMID: 35548855 DOI: 10.1021/acs.analchem.2c00557] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Rapid and accurate metabolite annotation in mass spectrometry imaging (MSI) can improve the efficiency of spatially resolved metabolomics studies and accelerate the discovery of reliable in situ disease biomarkers. To date, metabolite annotation tools in MSI generally utilize isotopic patterns, but high-throughput fragmentation-based identification and biological and technical factors that influence structure elucidation are active challenges. Here, we proposed an organ-specific, metabolite-database-driven approach to facilitate efficient and accurate MSI metabolite annotation. Using data-dependent acquisition (DDA) in liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to generate high-coverage product ions, we identified 1620 unique metabolites from eight mouse organs (brain, liver, kidney, heart, spleen, lung, muscle, and pancreas) and serum. Following the evaluation of the adduct form difference of metabolite ions between LC-MS and airflow-assisted desorption electrospray ionization (AFADESI)-MSI and deciphering organ-specific metabolites, we constructed a metabolite database for MSI consisting of 27,407 adduct ions. An automated annotation tool, MSIannotator, was then created to conduct metabolite annotation in the MSI dataset with high efficiency and confidence. We applied this approach to profile the spatially resolved landscape of the whole mouse body and discovered that metabolites were distributed across the body in an organ-specific manner, which even spanned different mouse strains. Furthermore, the spatial metabolic alteration in diabetic mice was delineated across different organs, exhibiting that differentially expressed metabolites were mainly located in the liver, brain, and kidney, and the alanine, aspartate, and glutamate metabolism pathway was simultaneously altered in these three organs. This approach not only enables robust metabolite annotation and visualization on a body-wide level but also provides a valuable database resource for underlying organ-specific metabolic mechanisms.
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Affiliation(s)
- Ying Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Qingce Zang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhigang Luo
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jiuming He
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.,Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China.,Center for Imaging and Systems Biology, College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
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