An R package for UltraMassExplorer (UME)

UME has been under active development since 2019 and provides a comprehensive workflow for ultrahigh-resolution mass spectrometry data analysis of complex organic matter.

The package comprises about 70 documented functions and supports workflows ranging from molecular formula assignment to visualization and reporting.

Ressources

All package versions

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Github for public releases

👉 https://github.com/boriskoch/ume

Active development takes place in AWI GitLab.

UME shiny app

👉 https://www.awi.de/en/ume

Complete manual

👉 The UME Vignette

browseVignettes("ume")

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Quick tour

Predefined molecular formula libraries

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

Zenodo DOI: https://doi.org/10.5281/zenodo.17606457

Download within the ume package:

lib <- download_library(library = "lib_02.rds")

Molecular formula assignment

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)

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Installation

install.packages("ume")

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Create custom molecular formula library

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

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

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