Articles producció científica> Enginyeria Electrònica, Elèctrica i Automàtica

rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization

  • Identification data

    Identifier: imarina:7473807
    Authors:
    Baquer, GerardSemente, LlucGarcia-Altares, MariaLee, Young JinChaurand, PierreCorreig, XavierRafols, Pere
    Abstract:
    Mass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform non-targeted spatial metabolomics. However, the compounds used to promote desorption and ionization of the analyte during acquisition cause spectral interferences in the low mass range that hinder downstream data processing in metabolomics applications. Thus, it is advisable to annotate and remove matrix-related peaks to reduce the number of redundant and non-biologically-relevant variables in the dataset. We have developed rMSIcleanup, an open-source R package to annotate and remove signals from the matrix, according to the matrix chemical composition and the spatial distribution of its ions. To validate the annotation method, rMSIcleanup was challenged with several images acquired using silver-assisted laser desorption ionization MSI (AgLDI MSI). The algorithm was able to correctly classify m/z signals related to silver clusters. Visual exploration of the data using Principal Component Analysis (PCA) demonstrated that annotation and removal of matrix-related signals improved spectral data post-processing. The results highlight the need for including matrix-related peak annotation tools such as rMSIcleanup in MSI workflows.
  • Others:

    Author, as appears in the article.: Baquer, Gerard; Semente, Lluc; Garcia-Altares, Maria; Lee, Young Jin; Chaurand, Pierre; Correig, Xavier; Rafols, Pere
    Department: Enginyeria Electrònica, Elèctrica i Automàtica
    e-ISSN: 1758-2946
    URV's Author/s: Baquer Gómez, Gerard Sergi / Correig Blanchar, Francesc Xavier / Garcia-Altares Pérez, Maria / Ràfols Soler, Pere / Sementé Fernández, Lluc
    Keywords: Spectral processing Spatial metabolomics Small-molecule analysis Silver-assisted laser/desorption ionization Resolution Overlapping-signal detection Ms Matrix annotation Mass spectrometry imaging Fingermarks Desorption-ionization
    Abstract: Mass spectrometry imaging (MSI) has become a mature, widespread analytical technique to perform non-targeted spatial metabolomics. However, the compounds used to promote desorption and ionization of the analyte during acquisition cause spectral interferences in the low mass range that hinder downstream data processing in metabolomics applications. Thus, it is advisable to annotate and remove matrix-related peaks to reduce the number of redundant and non-biologically-relevant variables in the dataset. We have developed rMSIcleanup, an open-source R package to annotate and remove signals from the matrix, according to the matrix chemical composition and the spatial distribution of its ions. To validate the annotation method, rMSIcleanup was challenged with several images acquired using silver-assisted laser desorption ionization MSI (AgLDI MSI). The algorithm was able to correctly classify m/z signals related to silver clusters. Visual exploration of the data using Principal Component Analysis (PCA) demonstrated that annotation and removal of matrix-related signals improved spectral data post-processing. The results highlight the need for including matrix-related peak annotation tools such as rMSIcleanup in MSI workflows.
    Thematic Areas: Química Physical and theoretical chemistry Library and information sciences Computer science, interdisciplinary applications Computer science, information systems Computer science applications Computer graphics and computer-aided design Ciencias sociales Chemistry, multidisciplinary Biotecnología
    licence for use: https://creativecommons.org/licenses/by/3.0/es/
    Author's mail: maria.garcia-altares@urv.cat pere.rafols@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
    Author identifier: 0000-0002-9240-4058 0000-0002-4433-4972 0000-0002-4433-4972 0000-0002-6902-3054
    Record's date: 2024-11-09
    Papper version: info:eu-repo/semantics/publishedVersion
    Link to the original source: https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00449-0
    Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
    Papper original source: Journal Of Cheminformatics. 12 (1): 45-
    APA: Baquer, Gerard; Semente, Lluc; Garcia-Altares, Maria; Lee, Young Jin; Chaurand, Pierre; Correig, Xavier; Rafols, Pere (2020). rMSIcleanup: an open-source tool for matrix-related peak annotation in mass spectrometry imaging and its application to silver-assisted laser desorption/ionization. Journal Of Cheminformatics, 12(1), 45-. DOI: 10.1186/s13321-020-00449-0
    Article's DOI: 10.1186/s13321-020-00449-0
    Entity: Universitat Rovira i Virgili
    Journal publication year: 2020
    Publication Type: Journal Publications
  • Keywords:

    Chemistry, Multidisciplinary,Computer Graphics and Computer-Aided Design,Computer Science Applications,Computer Science, Information Systems,Computer Science, Interdisciplinary Applications,Library and Information Sciences,Physical and Theoretical Chemistry
    Spectral processing
    Spatial metabolomics
    Small-molecule analysis
    Silver-assisted laser/desorption ionization
    Resolution
    Overlapping-signal detection
    Ms
    Matrix annotation
    Mass spectrometry imaging
    Fingermarks
    Desorption-ionization
    Química
    Physical and theoretical chemistry
    Library and information sciences
    Computer science, interdisciplinary applications
    Computer science, information systems
    Computer science applications
    Computer graphics and computer-aided design
    Ciencias sociales
    Chemistry, multidisciplinary
    Biotecnología
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