Hello,
I am trying to identify the best tool within MetaboAnalyst (web version) for annotating an untargeted LC-MS/MS (negative mode) dataset. I have seen several viable options but would like advice on what might work best.
My LC-MS/MS data are already tabulated (.csv) with columns of mass-to-charge ratio, retention time (minutes), reference ion, then peak intensities per sample. I have three experimental variables and replicate samples. I have access to the original spectra files but am trying to find a workflow I can jump into with the tabulated data, but most similar discussions I have found here seem focused on LC-MS Spectra processing.
Of the MetaboAnalyst options, I first looked at Functional Analysis [LC-MS] > A peak intensity table. My data are from gut microbial communities but this tool requires the user specify a single (prokaryote) KEGG pathway library for comparison. Additionally, this tool does not take the reference ion information into account, working just off of m/z and the context supplied by the library.
I then looked at Peak Annotation [MS2-DDS/DIA] > Multiple Tandem Spectra, but this tool requests file types I am unfamiliar with (.mgf and .msp) from MS-DIAL specifically, seemingly outputs from that workflow.
I’m looking for a tool to generate putative annotations from the data I have against, ideally, multiple databases, and am not concerned with extra support for multivariate or statistical analyses. Is there a tool I’m missing (or misinterpreting) available on MetaboAnalyst that can accomplish this, or am I jumping the gun on a few preparatory steps?
Thank you