title: geoRge: A Computational Tool To Detect the Presence of Stable Isotope Labeling in LC/MS-Based Untargeted Metabolomics.
abstract: Studying the flow of chemical moieties through the complex set of metabolic reactions that happen in the cell is essential to understanding the alterations in homeostasis that occur in disease. Recently, LC/MS-based untargeted metabolomics and isotopically labeled metabolites have been used to facilitate the unbiased mapping of labeled moieties through metabolic pathways. However, due to the complexity of the resulting experimental data sets few computational tools are available for data analysis. Here we introduce geoRge, a novel computational approach capable of analyzing untargeted LC/MS data from stable isotope-labeling experiments. geoRge is written in the open language R and runs on the output structure of the XCMS package, which is in widespread use. As opposed to the few existing tools, which use labeled samples to track stable isotopes by iterating over all MS signals using the theoretical mass difference between the light and heavy isotopes, geoRge uses unlabeled and labeled biologically equivalent samples to compare isotopic distributions in the mass spectra. Isotopically enriched compounds change their isotopic distribution as compared to unlabeled compounds. This is directly reflected in a number of new m/z peaks and higher intensity peaks in the mass spectra of labeled samples relative to the unlabeled equivalents. The automated untargeted isotope annotation and relative quantification capabilities of geoRge are demonstrated by the analysis of LC/MS data from a human retinal pigment epithelium cell line (ARPE-19) grown on normal and high glucose concentrations mimicking diabetic retinopathy conditions in vitro. In addition, we compared the results of geoRge with the outcome of X(13)CMS, since both approaches rely entirely on XCMS parameters for feature selection, namely m/z and retention time values. To ensure data traceability and reproducibility, and enabling for comparison with other existing and future approaches, raw LC/MS files have been deposited in MetaboLights (MTBLS213) and geoRge is available as an R script at https://github.com/jcapelladesto/geoRge.
authors.affiliation: Centre for Omic Sciences, Universitat Rovira i Virgili , Avinguda Universitat 1, 43204 Reus, Spain.|Institut d'Investigacio Sanitaria Pere i Virgili (IISPV), Avinguda Universitat 1, 43204 Reus, Spain.|Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Monforte de Lemos 3-5, 28029 Madrid, Spain.
authors.forename: Jordi
authors.initials: J
authors.lastname: Capellades
authors.affiliation: Centre for Omic Sciences, Universitat Rovira i Virgili , Avinguda Universitat 1, 43204 Reus, Spain.|Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Monforte de Lemos 3-5, 28029 Madrid, Spain.
authors.forename: Miriam
authors.initials: M
authors.lastname: Navarro
authors.affiliation: Centre for Omic Sciences, Universitat Rovira i Virgili , Avinguda Universitat 1, 43204 Reus, Spain.|Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Monforte de Lemos 3-5, 28029 Madrid, Spain.
authors.forename: Sara
authors.initials: S
authors.lastname: Samino
authors.affiliation: Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Monforte de Lemos 3-5, 28029 Madrid, Spain.|Diabetes and Metabolism Research Unit, Institut de Recerca Hospital Universitari Vall d'Hebron (VHIR) , Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.
authors.forename: Marta
authors.initials: M
authors.lastname: Garcia-Ramirez
authors.affiliation: Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Monforte de Lemos 3-5, 28029 Madrid, Spain.|Diabetes and Metabolism Research Unit, Institut de Recerca Hospital Universitari Vall d'Hebron (VHIR) , Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Hernandez
authors.affiliation: Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Monforte de Lemos 3-5, 28029 Madrid, Spain.|Diabetes and Metabolism Research Unit, Institut de Recerca Hospital Universitari Vall d'Hebron (VHIR) , Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Simo
authors.affiliation: Centre for Omic Sciences, Universitat Rovira i Virgili , Avinguda Universitat 1, 43204 Reus, Spain.|Department of Electronic Engineering, Universitat Rovira i Virgili , Avinguda Paisos Catalans 26, 43007 Tarragona, Spain.|Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Monforte de Lemos 3-5, 28029 Madrid, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Vinaixa
authors.affiliation: Centre for Omic Sciences, Universitat Rovira i Virgili , Avinguda Universitat 1, 43204 Reus, Spain.|Department of Electronic Engineering, Universitat Rovira i Virgili , Avinguda Paisos Catalans 26, 43007 Tarragona, Spain.|Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) , Monforte de Lemos 3-5, 28029 Madrid, Spain.
authors.forename: Oscar
authors.initials: O
authors.lastname: Yanes
mesh_terms: D002478:Cells, Cultured; D002851:Chromatography, High Pressure Liquid; D006801:Humans; D007553:Isotope Labeling; D013058:Mass Spectrometry; D055432:Metabolomics; D008968:Molecular Conformation; D012984:Software