A case report of switching from specific vendor-based to R-based pipelines for untargeted LC-MS metabolomics
Journal article, 2020

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 effectively correct the drifts due to between and within batch effects. 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 different packages, functions, and methods in a single environment.

Data pre-processing

Mass spectrometry


R packages

Liquid chromatography

Vendor software


Álvaro Fernández-Ochoa

Research and Development of Functional Food Centre (CIDAF)

Universidad de Granada

Rosa Quirantes-Piné

Research and Development of Functional Food Centre (CIDAF)

Isabel Borrás-Linares

Research and Development of Functional Food Centre (CIDAF)

María de la Luz Cádiz-Gurrea

Universidad de Granada

Research and Development of Functional Food Centre (CIDAF)

Marta E.Alarcón Riquelme

Universidad de Granada

Carl Brunius

Chalmers, Biology and Biological Engineering, Food and Nutrition Science

Antonio Segura-Carretero

Research and Development of Functional Food Centre (CIDAF)

Universidad de Granada


2218-1989 (ISSN) 22181989 (eISSN)

Vol. 10 1 28

Subject Categories

Software Engineering

Media Engineering

Bioinformatics and Systems Biology



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