Articles producció científica> Enginyeria Electrònica, Elèctrica i Automàtica

RMsikeyion: An ion filtering r package for untargeted analysis of metabolomic LDI-MS images

  • Dades identificatives

    Identificador: imarina:5813226
    Autors:
    Del Castillo ESementé LTorres SRàfols PRamírez NMartins-Green MSantafe MCorreig X
    Resum:
    © 2019 by the authors. Licensee MDPI, Basel, Switzerland. Many MALDI-MS imaging experiments make a case versus control studies of different tissue regions in order to highlight significant compounds affected by the variables of study. This is a challenge because the tissue samples to be compared come from different biological entities, and therefore they exhibit high variability. Moreover, the statistical tests available cannot properly compare ion concentrations in two regions of interest (ROIs) within or between images. The high correlation between the ion concentrations due to the existence of different morphological regions in the tissue means that the common statistical tests used in metabolomics experiments cannot be applied. Another difficulty with the reliability of statistical tests is the elevated number of undetected MS ions in a high percentage of pixels. In this study, we report a procedure for discovering the most important ions in the comparison of a pair of ROIs within or between tissue sections. These ROIs were identified by an unsupervised segmentation process, using the popular k-means algorithm. Our ion filtering algorithm aims to find the up or down-regulated ions between two ROIs by using a combination of three parameters: (a) the percentage of pixels in which a particular ion is not detected, (b) the Mann–Whitney U ion concentration test, and (c) the ion concentration fold-change. The undetected MS signals (null peaks) are discarded from the histogram before the calculation of (b) and (c) parameters. With this methodology, we found the important ions between the different segments of a mouse brain tissue sagittal section and determined some lipid compounds (mainly triacylglycerols and phosphatidylcholines) in the liver of mice exposed to thirdhand
  • Altres:

    Autor segons l'article: Del Castillo E; Sementé L; Torres S; Ràfols P; Ramírez N; Martins-Green M; Santafe M; Correig X
    Departament: Enginyeria Electrònica, Elèctrica i Automàtica Ciències Mèdiques Bàsiques
    e-ISSN: 2218-1989
    Autor/s de la URV: Correig Blanchar, Francesc Xavier / Del Castillo Pérez, Esteban / Ràfols Soler, Pere / Ramírez González, Noelia / Santafé Martínez, Manuel / Sementé Fernández, Lluc / Torres Gene, Sonia
    Paraules clau: Metabolomics imaging Mass spectrometry imaging Ion selection algorithms Biostatistics mass spectrometry imaging ion selection algorithms biostatistics
    Resum: © 2019 by the authors. Licensee MDPI, Basel, Switzerland. Many MALDI-MS imaging experiments make a case versus control studies of different tissue regions in order to highlight significant compounds affected by the variables of study. This is a challenge because the tissue samples to be compared come from different biological entities, and therefore they exhibit high variability. Moreover, the statistical tests available cannot properly compare ion concentrations in two regions of interest (ROIs) within or between images. The high correlation between the ion concentrations due to the existence of different morphological regions in the tissue means that the common statistical tests used in metabolomics experiments cannot be applied. Another difficulty with the reliability of statistical tests is the elevated number of undetected MS ions in a high percentage of pixels. In this study, we report a procedure for discovering the most important ions in the comparison of a pair of ROIs within or between tissue sections. These ROIs were identified by an unsupervised segmentation process, using the popular k-means algorithm. Our ion filtering algorithm aims to find the up or down-regulated ions between two ROIs by using a combination of three parameters: (a) the percentage of pixels in which a particular ion is not detected, (b) the Mann–Whitney U ion concentration test, and (c) the ion concentration fold-change. The undetected MS signals (null peaks) are discarded from the histogram before the calculation of (b) and (c) parameters. With this methodology, we found the important ions between the different segments of a mouse brain tissue sagittal section and determined some lipid compounds (mainly triacylglycerols and phosphatidylcholines) in the liver of mice exposed to thirdhand smoke.
    Àrees temàtiques: Molecular biology Medicina ii Farmacia Endocrinology, diabetes and metabolism Ciências biológicas ii Ciências biológicas i Biotecnología Biochemistry & molecular biology Biochemistry
    Accès a la llicència d'ús: thttps://creativecommons.org/licenses/by/3.0/es/
    ISSN: 22181989
    Adreça de correu electrònic de l'autor: noelia.ramirez@urv.cat pere.rafols@urv.cat manuel.santafe@urv.cat xavier.correig@urv.cat esteban.delcastillo@urv.cat lluc.semente@estudiants.urv.cat lluc.semente@estudiants.urv.cat
    Identificador de l'autor: 0000-0002-9240-4058 0000-0002-5462-5108 0000-0002-6902-3054 0000-0002-1743-656X
    Data d'alta del registre: 2024-06-22
    Volum de revista: 9
    Versió de l'article dipositat: info:eu-repo/semantics/publishedVersion
    Enllaç font original: https://www.mdpi.com/2218-1989/9/8/162
    Referència a l'article segons font original: Metabolites. 9 (8):
    Referència de l'ítem segons les normes APA: Del Castillo E; Sementé L; Torres S; Ràfols P; Ramírez N; Martins-Green M; Santafe M; Correig X (2019). RMsikeyion: An ion filtering r package for untargeted analysis of metabolomic LDI-MS images. Metabolites, 9(8), -. DOI: 10.3390/metabo9080162
    URL Document de llicència: https://repositori.urv.cat/ca/proteccio-de-dades/
    DOI de l'article: 10.3390/metabo9080162
    Entitat: Universitat Rovira i Virgili
    Any de publicació de la revista: 2019
    Tipus de publicació: Journal Publications
  • Paraules clau:

    Biochemistry,Biochemistry & Molecular Biology,Endocrinology, Diabetes and Metabolism,Molecular Biology
    Metabolomics imaging
    Mass spectrometry imaging
    Ion selection algorithms
    Biostatistics
    mass spectrometry imaging
    ion selection algorithms
    biostatistics
    Molecular biology
    Medicina ii
    Farmacia
    Endocrinology, diabetes and metabolism
    Ciências biológicas ii
    Ciências biológicas i
    Biotecnología
    Biochemistry & molecular biology
    Biochemistry
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