JGI/LBNL Metabolomics - Standard LC-MS/MS ESI Method - Polar HILIC-Z v1

This protocol describes the standard LC-MS/MS ESI method developed at Lawrence Berkeley National Laboratory (LBNL) by JGI Metabolomics and EGSB's Northen Lab to analyze polar metabolites (e.g. amino acids, nucleic acids, sugars, organic acids, primary metabolites, etc.) using normal phase chromatography (HILIC-Z) coupled to a Thermo Orbitrap Mass Spectrometer with ESI source. This robust method of detection is easily reproduced and adapted onto similar LC-MS/MS systems to achieve consistent outcomes across mass spectrometry datasets, foster inter-lab and inter-experiment comparability, and enable effective data integration and analysis. Since its inception in 2018, this method has been used to analyze tens of thousands of experimental samples, with many of these datasets publicly available in the MassIVE data repository1,2. This method has also been used to run thousands of compound standards to collect characteristic retention time, m/z and fragmentation spectra. This forms the basis of Berkeley Lab's Environmental Metabolite Atlas (EMA), a database used for confident annotation of metabolites and publicly available through GNPS/GNPS23.