Articles producció científica> Enginyeria Electrònica, Elèctrica i Automàtica

What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging

  • Datos identificativos

    Identificador: imarina:9271502
    Autores:
    Baquer, GerardSemente, LlucMahamdi, ToufikCorreig, XavierRafols, PereGarcia-Altares, Maria
    Resumen:
    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.
  • Otros:

    Autor según el artículo: Baquer, Gerard; Semente, Lluc; Mahamdi, Toufik; Correig, Xavier; Rafols, Pere; Garcia-Altares, Maria;
    Departamento: Enginyeria Electrònica, Elèctrica i Automàtica
    Autor/es de la URV: Baquer Gómez, Gerard Sergi / Correig Blanchar, Francesc Xavier / Garcia-Altares Pérez, Maria / Mahamdi, Toufik / Ràfols Soler, Pere / Sementé Fernández, Lluc
    Palabras clave: Tissue-sections Software R package Protein identification Molecular identification Molecular annotation Metabolomics Matrix application Mass spectrometry imaging Liquid-chromatography Ion mobility spectrometry Identification confidence levels High-spatial-resolution Drug distribution Desorption ionization Assisted-laser-desorption/ionization
    Resumen: 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.
    Áreas temáticas: Spectroscopy General biochemistry,genetics and molecular biology Condensed matter physics Biochemistry, genetics and molecular biology (miscellaneous) Biochemistry, genetics and molecular biology (all) Analytical chemistry
    Acceso a la licencia de uso: https://creativecommons.org/licenses/by/3.0/es/
    Direcció de correo del autor: maria.garcia-altares@urv.cat pere.rafols@urv.cat toufik.mahamdi@urv.cat lluc.semente@estudiants.urv.cat lluc.semente@estudiants.urv.cat gerard.baquer@estudiants.urv.cat gerard.baquer@estudiants.urv.cat xavier.correig@urv.cat
    Identificador del autor: 0000-0002-9240-4058 0000-0002-4433-4972 0000-0002-4433-4972 0000-0002-6902-3054
    Fecha de alta del registro: 2024-09-07
    Versión del articulo depositado: info:eu-repo/semantics/publishedVersion
    URL Documento de licencia: https://repositori.urv.cat/ca/proteccio-de-dades/
    Referencia al articulo segun fuente origial: Mass Spectrometry Reviews.
    Referencia de l'ítem segons les normes APA: Baquer, Gerard; Semente, Lluc; Mahamdi, Toufik; Correig, Xavier; Rafols, Pere; Garcia-Altares, Maria; (2022). What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging. Mass Spectrometry Reviews, (), -. DOI: 10.1002/mas.21794
    Entidad: Universitat Rovira i Virgili
    Año de publicación de la revista: 2022
    Tipo de publicación: Journal Publications
  • Palabras clave:

    Analytical Chemistry,Biochemistry, Genetics and Molecular Biology (Miscellaneous),Condensed Matter Physics,Spectroscopy
    Tissue-sections
    Software
    R package
    Protein identification
    Molecular identification
    Molecular annotation
    Metabolomics
    Matrix application
    Mass spectrometry imaging
    Liquid-chromatography
    Ion mobility spectrometry
    Identification confidence levels
    High-spatial-resolution
    Drug distribution
    Desorption ionization
    Assisted-laser-desorption/ionization
    Spectroscopy
    General biochemistry,genetics and molecular biology
    Condensed matter physics
    Biochemistry, genetics and molecular biology (miscellaneous)
    Biochemistry, genetics and molecular biology (all)
    Analytical chemistry
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