title: Fast parametric time warping of peak lists.
abstract: Alignment of peaks across samples is a difficult but unavoidable step in the data analysis for all analytical techniques containing a separation step like chromatography. Important application examples are the fields of metabolomics and proteomics. Parametric time warping (PTW) has already shown to be very useful in these fields because of the highly restricted form of the warping functions, avoiding overfitting. Here, we describe a new formulation of PTW, working on peak-picked features rather than on complete profiles. Not only does this allow for a much more smooth integration in existing pipelines, it also speeds up the (already among the fastest) algorithm by orders of magnitude. Using two publicly available datasets we show the potential of the new approach. The first set is a LC-DAD dataset of grape samples, and the second an LC-MS dataset of apple extracts.
  
  
  METHODS
  Parametric time warping of peak lists is implemented in the ptw package, version 1.9.1 and onwards, available from Github (https://github.com/rwehrens/ptw) and CRAN (http://cran.r-project.org). The package also contains a vignette, providing more theoretical details and scripts to reproduce the results below.
  
  
  BACKGROUND
  ron.wehrens@wur.nl.
authors.affiliation: Biometris, Wageningen UR, Wageningen, The Netherlands, Educational Institute for Molecular Sciences and Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
authors.forename: Ron
authors.initials: R
authors.lastname: Wehrens
authors.affiliation: Biometris, Wageningen UR, Wageningen, The Netherlands, Educational Institute for Molecular Sciences and Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands Biometris, Wageningen UR, Wageningen, The Netherlands, Educational Institute for Molecular Sciences and Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
authors.forename: Tom G
authors.initials: TG
authors.lastname: Bloemberg
authors.affiliation: Biometris, Wageningen UR, Wageningen, The Netherlands, Educational Institute for Molecular Sciences and Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
authors.forename: Paul H C
authors.initials: PH
authors.lastname: Eilers
mesh_terms: D000465:Algorithms; D002338:Carotenoids / Q000032:analysis*; D002853:Chromatography, Liquid / Q000379:methods*; D013058:Mass Spectrometry / Q000379:methods*; D055432:Metabolomics / Q000379:methods; D040901:Proteomics / Q000379:methods; D027843:Vitis / Q000737:chemistry*
chemical_list: D002338:Carotenoids