RefMet: A Reference list of Metabolite names

The main objective of RefMet is to provide a standardized reference nomenclature for both discrete metabolite structures and metabolite species identified by spectroscopic techniques in metabolomics experiments. This is an essential prerequisite for the ability to compare and contrast metabolite data across different experiments and studies. The use of identifiers such as PubChem compound id's and InChiKeys offers only a partial solution because these identifiers will vary depending on parameters such as the salt form and degree of stereochemical detail. In addition, many metabolite species, especially lipids, are not reported by MS methods as discrete structures but rather as isobaric mixtures (such as PC 34:1 and TG 54:2). To this end, a list of over 600,000 names from a set of over 2,900 MS and NMR studies on the Metabolomics Workbench has been used as a starting point to generate a highly curated analytical chemistry-centric list of common names for metabolite structures and isobaric species. Additionally, the vast majority of these names have been linked to a metabolite classification system using a combination of LIPID MAPS and ClassyFire classification methods. A name-conversion user interface is provided where users can submit a list of metabolite names and map them to the corresponding Refmet names. This is a work-in-progress with the caveat that many metabolite names generated by metabolomics experiments will not currently map to RefMet identifiers. Nevertheless, RefMet has the ability to greatly increase the data-sharing potential of metabolomics experiments and facilitate "meta-analysis" and systems biology objectives for the majority of commonly encountered metabolite species.

• Browse/Search/Download Refmet
  
• View Refmet classification
  
• Core structures of RefMet sub classes
  
• Convert(map) a list of metabolite names to RefMet nomenclature
  
• Help on RefMet
  
• Lipid Notation in RefMet and lipid m/z calculation tools
  
• Mobile phone apps (App. links are active on phones only. Save the URLs below as icons on your home screen):
  • NMDR metabolite summary app. Search over 2,000 studies in NMDR by anlytical technique, sample source, species and metabolite class. Retrieve a summary table sorted by frequency of detection of metabolite species, linked to structures and individual NMDR study information.
  • RefMet search app. Search RefMet by (partial) name and/or neutral mass.
  • RefMet name conversion app. Convert a metabolite name to RefMet nomenclature. Display structure. Calculate m/z.
  • RefMet MS search app. Search RefMet with m/z value.
  • Lipid mass/formula app. Calculate lipid neutral mass and m/z for over 160 lipid species.
  • View Screenshot
    
• RefMet R package on Github
  • This R package enables users to map a list of metabolite names (from a text file or a data frame column) to RefMet nomenclature in batch mode, gain access to RefMet metadata for metabolites and perform plotting and saving functions.
• A Python script to standardize metabolite names to RefMet nomenclature
  • REFMET_post.py(zipped)Convert a file with metabolite names to a file containing RefMet names and associated metadata, using Python.
• An R script to standardize metabolite names to RefMet nomenclature
  • refmet_convert.R(zipped)Convert a data frame column with metabolite names to RefMet names and associated metadata, using R.
• Run as Shiny app on local R installation
  • RefMet name search Shiny App
    
  • RefMet MS search Shiny App
    
• Reference: RefMet: a reference nomenclature for metabolomics (Nature Methods, 2020)