Hi everyone,
I’m currently using MetaboAnalystR to perform metabolite annotation, but I’ve run into a challenge with MS² deconvolution. My raw data is from an AIF (all-ion fragmentation) DIA method. Unfortunately, MetaboAnalystR only supports deconvolution for SWATH‑DIA and DDA data.
I’m wondering if a workaround might be helpful:
Use MS‑DIAL to perform MS² deconvolution on my AIF DIA data and obtain both MS1 peak tables and MS² annotation results.
Then, feed the MS1 peak intensity table and associated p-values (from MetaboAnalystR statistical analysis) together with the MS‑DIAL annotation output into MetaboAnalystR—similar to how the PerformMS2ResultsFormatting() function handles MS‑Finder results, e.g.:
library(MetaboAnalystR)
PerformMS2ResultsFormatting(
file_path = “./Structure_result_2072.txt”,
type = “msfinder”,
MS1_features_list = “./peaks_ms1_msdial.txt”
)
Would it work to substitute MS‑Finder output with MS‑DIAL output? Has anyone tried using MS‑DIAL’s MS2Dec‑deconvoluted spectra from AIF DIA merged into MetaboAnalystR’s MS1 feature table?
My specific questions are:
Are there any successful cases or tips for integrating MS‑DIAL deconvolution results from AIF DIA into MetaboAnalystR?
Any advice on parameter settings in MS‑DIAL (for AIF) to optimize compatibility with MetaboAnalystR?
Thanks for your help!