An R package for UltraMassExplorer (UME)

👉 The complete UME manual (Vignette)

Usage - quick tour

Download predefined UME formula library (Zenodo)

The official UME molecular formula libraries (lib_02.rds, lib_05.rds)
are available at:

👉 https://doi.org/10.5281/zenodo.17606457

You can download them within ume: lib <- download_library(library = "lib_02.rds")

Molecular formula assignment

data(peaklist_demo)

mfd <- ume_assign_formulas( pl = peaklist_demo, formula_library = lib, pol = "neg", ma_dev = 0.5, verbose = TRUE )

Formula filter process

mfd_filt <- ume_filter_formulas(mfd = mfd, normalization = "none", c_iso_check = T, dbe_o_max = 10, p_max = 0, s_max = 1, n_max = 2, verbose = TRUE )

Data summary

ds <- calc_data_summary(mfd_filt)

Visualization examples

Plot mass spectrum

uplot_ms(pl = peaklist_demo, label = "file")

Plot van Krevelen diagram

uplot_vk(mfd_filt)

Plot evaluation of carbon istope abundance:

uplot_isotope_precision(mfd_filt)

Installation

***

In case you already loaded a previous version of ume:

detach("package:ume", unload = TRUE)

install.packages("remotes") remotes::install_git(url = "https://gitlab.awi.de/bkoch/ume.git")

Create your custom molecular formula library

Be aware that this step requires a lot of memory and processing time!

lib <- create_ume_formula_library(max_formula = "C1000[13C1]H3000[15N1]N6O1000P3S3[34S1]", min_formula = "C1H1", max_mass = 250, heu_filter = TRUE, verbose = T)