title: MetMSLine: an automated and fully integrated pipeline for rapid processing of high-resolution LC-MS metabolomic datasets.
abstract: MetMSLine represents a complete collection of functions in the R programming language as an accessible GUI for biomarker discovery in large-scale liquid-chromatography high-resolution mass spectral datasets from acquisition through to final metabolite identification forming a backend to output from any peak-picking software such as XCMS. MetMSLine automatically creates subdirectories, data tables and relevant figures at the following steps: (i) signal smoothing, normalization, filtration and noise transformation (PreProc.QC.LSC.R); (ii) PCA and automatic outlier removal (Auto.PCA.R); (iii) automatic regression, biomarker selection, hierarchical clustering and cluster ion/artefact identification (Auto.MV.Regress.R); (iv) Biomarker-MS/MS fragmentation spectra matching and fragment/neutral loss annotation (Auto.MS.MS.match.R) and (v) semi-targeted metabolite identification based on a list of theoretical masses obtained from public databases (DBAnnotate.R).
  
  
  METHODS
  All source code and suggested parameters are available in an un-encapsulated layout on http://wmbedmands.github.io/MetMSLine/. Readme files and a synthetic dataset of both X-variables (simulated LC-MS data), Y-variables (simulated continuous variables) and metabolite theoretical masses are also available on our GitHub repository.
authors.affiliation: Department of Biomarkers, Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC), F-69372 Cedex 08, Lyon, France.
authors.forename: William M B
authors.initials: WM
authors.lastname: Edmands
authors.affiliation: Department of Biomarkers, Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC), F-69372 Cedex 08, Lyon, France.
authors.forename: Dinesh K
authors.initials: DK
authors.lastname: Barupal
authors.affiliation: Department of Biomarkers, Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC), F-69372 Cedex 08, Lyon, France.
authors.forename: Augustin
authors.initials: A
authors.lastname: Scalbert
mesh_terms: D001331:Automation; D002853:Chromatography, Liquid / Q000379:methods*; D016208:Databases, Factual; D066264:Datasets as Topic; D001330:Electronic Data Processing / Q000379:methods*; D006801:Humans; D055432:Metabolomics; D011381:Programming Languages; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*