First pass at creating an ISA-TAB file from the following publication: Farag, M., Porzel, A., Schmidt, J. & Wessjohann, L. Metabolite profiling and fingerprinting of commercial cultivars of Humulus lupulus L. (hop) - a comparision of MS and NMR methods in metabolomics Metabolomics 8, 492-507, (2012) DOI 10.1007/s11306-011-0335-y
information extraction from manuscript: -organism: -metabolite profiling in plant cones -metabolite profiling in resin derived from plant
5 assays: mass spectrometry : GC-MS (positive mode acquisition only: In General, there is only one ionisation polarity in GC) LC-MS (positive mode acquisition only ? -> to confirm) UPLC-MS (positive mode AND negative mode) ESI-FTICR-MS (positive mode AND negative mode)
nmr spectroscopy: 1D 1H-NMR 2D 1H-13C NMR (not represented)
wherever possible: ontology tagging using {NCBITaxonomy, Plant Ontology,CHEBI,OBI,GAZ,PSI-MS,Unit Ontology,}
TODO:
check all files (cdf or mzml for ms, native files or nmrml files for nmr)
submit to CHEBI the following chemical:
methanol-d4
acetone-d6
Hexamethyldisiloxane (CAS 107-46-0)
lithium formiate
add funder/grant information (absent from the manuscript). Done.