title: Intensity drift removal in LC/MS metabolomics by common variance compensation.
abstract: Liquid chromatography coupled to mass spectrometry (LC/MS) has become widely used in Metabolomics. Several artefacts have been identified during the acquisition step in large LC/MS metabolomics experiments, including ion suppression, carryover or changes in the sensitivity and intensity. Several sources have been pointed out as responsible for these effects. In this context, the drift effects of the peak intensity is one of the most frequent and may even constitute the main source of variance in the data, resulting in misleading statistical results when the samples are analysed. In this article, we propose the introduction of a methodology based on a common variance analysis before the data normalization to address this issue. This methodology was tested and compared with four other methods by calculating the Dunn and Silhouette indices of the quality control classes. The results showed that our proposed methodology performed better than any of the other four methods. As far as we know, this is the first time that this kind of approach has been applied in the metabolomics context.
  
  
  METHODS
  The source code of the methods is available as the R package intCor at http://b2slab.upc.edu/software-and-downloads/intensity-drift-correction/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain.
authors.forename: Francesc
authors.initials: F
authors.lastname: Fernández-Albert
authors.affiliation: Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain.
authors.forename: Rafael
authors.initials: R
authors.lastname: Llorach
authors.affiliation: Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain.
authors.forename: Mar
authors.initials: M
authors.lastname: Garcia-Aloy
authors.affiliation: Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain.
authors.forename: Andrey
authors.initials: A
authors.lastname: Ziyatdinov
authors.affiliation: Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Andres-Lacueva
authors.affiliation: Department d'Enginyeria de Sistemes, Automàtica i Informàtica Industrial, Universitat Politècnica de Catalunya, CIBER-BBN, Biomarkers & Nutrimetabolomic Lab., Department of Nutrition and Food Science-XaRTA, INSA, Faculty of Pharmacy, Food and Nutrition Torribera Campus, University of Barcelona, Av. Prat de la Riba 171, 08921, Sta Coloma de Gramenet and INGENIO-CONSOLIDER Program, FUN-C-Food CSD2007-063, Av Joan XXIII s/n 08028, Barcelona, Spain.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Perera
mesh_terms: D000704:Analysis of Variance; D056808:Biostatistics / Q000379:methods*; D002853:Chromatography, Liquid / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D055432:Metabolomics / Q000379:methods*; D025341:Principal Component Analysis; D011786:Quality Control