MetFrag

MetFrag2.2 (Webapp, CL(Java), R package)

Overview:

• Looks up online databases to identify peaks, given an input list of databases
• Has a statistical score associated with each returned result (Equation 1 in the related publication), presumably a score related to “accuracy” or “confidence” in the result, ranging from 0 to 1 (not confident at all, to maximum confidence).
• All 3 versions seem very easy to use (but necessarily easy to set up)

MetFragCL

• 2 text file (.txt) inputs: a peak list file, which contains data to be processed, and a parameter file, which contains parameter specifications in the format that MetFragCL requires
• Can use the mzml2metfrag tool to generate the parameter file in the required format
• Looks up an online database (e.g. Pubchem), and returns a spreadsheet (.xls)
• pre-compiled .jar file (java based), directly downloaded
• Tested working on Mac with JDK 12.0.1 OSX, using the example datasets

Available Databases

• PubChem
• HMDB
• KEGG
• derivatized KEGG (generated by in silico TMS and MeOx derivatization).
• CheBI
• MetaCyc
• ChemSpider
• FOR-IDENT
• LipidMaps
• Your own database in csv, psv or sdf formats
• MetFrag's own proprietary database.