Untargeted Metabolomics Analysis

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Dear all,

My lab is starting a new metabolomics activity, mainly focusing on untargeted analysis. We recently installed a Synapt XS and have begun performing analysis on trial sets of serum samples, acquiring data in HDMSe. After data acquisition, we move all the raw files to Progenesis QI, starting with some compound identification using ChemSpider and KEGG, and then using Progenesis Metascope and a biomolecules database (already available in our resources). We would then like to proceed with pathway analysis and networking using other platforms but have encountered some issues with the type of data acquired, as HDMSe data seems to not be compatible with multiple platforms.

My first question is, based on your experience, what is the best identification method and database for biomarker analysis and discovery? Additionally, which platform would be best for processing HDMSe data outside Progenesis QI or after an initial screening in Progenesis QI?

Thank you very much in advance.