Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

Provides tools for assigning molecular formulas from exact masses obtained by ultrahigh-resolution mass spectrometry. The methodology follows the workflow described in Leefmann et al. (2019) . The package supports the inspection, filtering and visualization of molecular formula data and includes utilities for calculating common molecular parameters (e.g., double bond equivalents, DBE). A graphical user interface is available via the 'shiny'-based 'ume' application.

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

👉

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")

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)

Installation

install.packages("ume")

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!