A Case Report of Switching from Specific Vendor-Based to R-Based Pipelines for Untargeted LC-MS Metabolomics Fernández Ochoa, Álvaro Quirantes Piné, Rosa Borrás-Linares, Isabel Cádiz Gurrea, María de la Luz PRECISESADS Clinical Consortium Alarcón-Riquelme, Marta E. Brunius, Carl Segura-Carretero, Antonio metabolomics data pre-processing mass spectrometry Data pre-processing of the LC-MS data is a critical step in untargeted metabolomics studies in order to achieve correct biological interpretations. Several tools have been developed for pre-processing, and these can be classified into either commercial or open source software. This case report aims to compare two specific methodologies, Agilent Profinder vs. R pipeline, for a metabolomic study with a large number of samples. Specifically, 369 plasma samples were analyzed by HPLC-ESI-QTOF-MS. The collected data were pre-processed by both methodologies and later evaluated by several parameters (number of peaks, degree of missingness, quality of the peaks, degree of misalignments, and robustness in multivariate models). The vendor software was characterized by ease of use, friendly interface and good quality of the graphs. The open source methodology could more e ectively correct the drifts due to between and within batch e ects. In addition, the evaluated statistical methods achieved better classification results with higher parsimony for the open source methodology, indicating higher data quality. Although both methodologies have strengths and weaknesses, the open source methodology seems to be more appropriate for studies with a large number of samples mainly due to its higher capacity and versatility that allows combining di erent packages, functions, and methods in a single environment. 2024-09-17T11:09:02Z 2024-09-17T11:09:02Z 2020-01-08 journal article Fernández Ochoa, A. et. al. Metabolites 2020, 10, 28. [https://doi.org/10.3390/metabo10010028] https://hdl.handle.net/10481/94611 10.3390/metabo10010028 eng info:eu-repo/grantAgreement/EC/FP7/2007-2013 http://creativecommons.org/licenses/by/4.0/ open access Atribución 4.0 Internacional MDPI