Repositori institucional URV
| URV's Author/s: | Correig Blanchar, Francesc Xavier / Del Castillo Pérez, Esteban / Ràfols Soler, Pere / Ramírez González, Noelia / Santafé Martínez, Manuel / Sementé Fernández, Lluc / Torres Gene, Sonia |
| Author, as appears in the article.: | Del Castillo E; Sementé L; Torres S; Ràfols P; Ramírez N; Martins-Green M; Santafe M; Correig X |
| Author's mail: | 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 |
| Author identifier: | 0000-0002-9240-4058 0000-0002-5462-5108 0000-0002-6902-3054 0000-0002-1743-656X |
| Journal publication year: | 2019 |
| Publication Type: | Journal Publications |
| ISSN: | 22181989 |
| e-ISSN: | 2218-1989 |
| 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 |
| Papper original source: | Metabolites. 9 (8): |
| Abstract: | © 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. |
| Article's DOI: | 10.3390/metabo9080162 |
| Link to the original source: | https://www.mdpi.com/2218-1989/9/8/162 |
| Papper version: | info:eu-repo/semantics/publishedVersion |
| licence for use: | thttps://creativecommons.org/licenses/by/3.0/es/ |
| Department: | Enginyeria Electrònica, Elèctrica i Automàtica Ciències Mèdiques Bàsiques |
| Licence document URL: | https://repositori.urv.cat/ca/proteccio-de-dades/ |
| Thematic Areas: | Molecular biology Medicina ii Farmacia Endocrinology, diabetes and metabolism Ciências biológicas ii Ciências biológicas i Biotecnología Biochemistry & molecular biology Biochemistry |
| Keywords: | Metabolomics imaging Mass spectrometry imaging Ion selection algorithms Biostatistics mass spectrometry imaging ion selection algorithms biostatistics |
| Entity: | Universitat Rovira i Virgili |
| Record's date: | 2024-06-22 |
| Journal volume: | 9 |
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