exhaustive Ultra Formula Annotation (UFAx) by the Integrated Data Science Laboratory for Metabolomics and Exposomics (IDSL.ME) is an R package to annotate a number of peaks from the IDSL.IPA peaklists using an exhaustive chemical enumeration-based approach. This package can perform elemental composition calculations using the following 15 elements : C, B, Br, Cl, K, S, Si, N, H, As, F, I, Na, O, and P.
IDSL.UFAx applies a hursitic approach to enumerate vast chemical spaces (<1027 molecular formulas). Although the IDSL.UFAx approach is computationally expensive, it is very suitable for elemental composition of unknown chromatographic peaks when the chemical space is unidentifiable. The IDSL.UFAx enumeration approach is a controlled combinatorial explosion to find molecular formulas for chromatographic peaks that were left un-assigned by a molecular formula source and enumerated chemical space approaches embedded in the IDSL.UFA package. IDSL.UFAx utilizes combinatorial subset sum solutions using 15 selected atoms for one m/z value. However, depending on the complexity of the assigned chemical space, IDSL.UFAx may be slow and should only be used for one file at a time.
install.packages("IDSL.UFAx")
Note: The IDSL.UFAx package has dependencies on RcppAlgos and gmp R packages. In some instance to install these two packages, you may need to run the following command on a linux terminal.
sudo apt-get install libgmp-dev
To annotate your mass spectrometry data (mzXML, mzML, netCDF), mass spectrometry data should be processed using the IDSL.IPA workflow to acquire chromatographic information of the peaks (m/z-RT). When the chromatographic information of individual peaklists were generated using the IDSL.IPA workflow, download the UFAx parameter spreadsheet and select the parameters accordingly and then use this spreadsheet as the input for the IDSL.UFAx workflow:
library(IDSL.UFAx)
UFAx_workflow("Address of the UFAx parameter spreadsheet")
[1] Fakouri Baygi, S., Banerjee S. K., Chakraborty P., Kumar, Y. Barupal, D.K. IDSL.UFA assigns high confidence molecular formula annotations for untargeted LC/HRMS datasets in metabolomics and exposomics. Analytical Chemistry, 2022, 94(39), 13315–13322.
[2] Fakouri Baygi, S., Kumar, Y. Barupal, D.K. IDSL. IPA characterizes the organic chemical space in untargeted LC/HRMS datasets. Journal of proteome research, 2022, 21(6), 1485-1494.