rMSIKeyIon: An Ion Filtering R Package for Untargeted Analysis of Metabolomic LDI-MS Images

Metabolites
Esteban Del CastilloXavier Correig

Abstract

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 ...Continue Reading

References

Apr 26, 2011·Journal of Proteomics·Tyler GreerLingjun Li
Aug 2, 2011·Journal of Proteome Research·Jocelyne BruandVineet Bafna
Mar 23, 2012·Nature Reviews. Molecular Cell Biology·Gary J PattiGary Siuzdak
May 1, 2012·Integrative Biology : Quantitative Biosciences From Nano to Macro·Do Yup LeeTrent Northen
Jun 16, 2012·BMC Medical Research Methodology·Morten W Fagerland
Jun 30, 2012·Journal of Proteomics·Emrys A JonesLiam A McDonnell
Jul 3, 2013·Current Opinion in Pharmacology·Lavinia MorosiEnrico Davoli
Nov 26, 2013·Analytical Chemistry·Tytus D MakAlbert J Fornace
Feb 4, 2014·PloS One·Manuela Martins-GreenMargarita Curras-Collazo
May 18, 2016·Analytical Chemistry·Alberto CasseseBenjamin Balluff
Oct 30, 2016·Proceedings of the National Academy of Sciences of the United States of America·Walid M AbdelmoulaBoudewijn P F Lelieveldt
Apr 4, 2017·Bioinformatics·Pere RàfolsXavier Correig
May 17, 2017·Chemical Science·Paolo IngleseRobert C Glen
Nov 16, 2017·Nucleic Acids Research·David S WishartAugustin Scalbert
Jul 28, 2018·Journal of Lipid Research·Estefanía Moreno-GordalizaM Milagros Gómez-Gómez

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Citations

Mar 9, 2020·Metabolomics : Official Journal of the Metabolomic Society·Keiron O'Shea, Biswapriya B Misra

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Software Mentioned

rMSIKeyIon
rMSIKeyIon R package
rMSI package
FlexImaging
Compass
MSI
rMSIKeyIons
rMSIKeyIon package
R package
R

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