title: Comparison of peak-picking workflows for untargeted liquid chromatography/high-resolution mass spectrometry metabolomics data analysis.
abstract: BACKGROUND
  Data analysis is a key step in mass spectrometry based untargeted metabolomics, starting with the generation of generic peak lists from raw liquid chromatography/mass spectrometry (LC/MS) data. Due to the use of various algorithms by different workflows, the results of different peak-picking strategies often differ widely.
  
  
  METHODS
  Raw LC/HRMS data from two types of biological samples (bile and urine), as well as a standard mixture of 84 metabolites, were processed with four peak-picking softwares: Peakview®, Markerview™, MetabolitePilot™ and XCMS Online. The overlaps between the results of each peak-generating method were then investigated. To gauge the relevance of peak lists, a database search using the METLIN online database was performed to determine which features had accurate masses matching known metabolites as well as a secondary filtering based on MS/MS spectral matching.
  
  
  RESULTS
  In this study, only a small proportion of all peaks (less than 10%) were common to all four software programs. Comparison of database searching results showed peaks found uniquely by one workflow have less chance of being found in the METLIN metabolomics database and are even less likely to be confirmed by MS/MS.
  
  
  CONCLUSIONS
  It was shown that the performance of peak-generating workflows has a direct impact on untargeted metabolomics results. As it was demonstrated that the peaks found in more than one peak detection workflow have higher potential to be identified by accurate mass as well as MS/MS spectrum matching, it is suggested to use the overlap of different peak-picking workflows as preliminary peak lists for more rugged statistical analysis in global metabolomics investigations.
authors.affiliation: Université du Québec à Montréal, Chemistry Department/Pharmaqam, Montreal, QC, Canada.
authors.forename: Atefeh
authors.initials: A
authors.lastname: Rafiei
authors.forename: Lekha
authors.initials: L
authors.lastname: Sleno
mesh_terms: D000818:Animals; D001646:Bile / Q000737:chemistry; D002853:Chromatography, Liquid / Q000379:methods*; D062126:Databases, Chemical; D004285:Dogs; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D012984:Software; D053719:Tandem Mass Spectrometry / Q000379:methods*