UltraMassExplorer: a browser‐based application for the evaluation of high‐resolution mass spectrometric data

Abstract

Rationale: High-resolution mass spectrometry (HRMS) with high sample throughput has become an important analytical tool for the analysis of highly complex samples and data processing has become a major challenge for the user community. Evaluating direct-infusion HRMS data without automated tools for batch processing can be a time-consuming step in the analytical pipeline. Therefore, we developed a new browser-based software tool for processing HRMS data. Methods:The software, named UltraMassExplorer (UME), was written in the R programming language using the shiny library to build the graphical user interface.The performance of the integrated formula library search algorithm was tested using HRMS data derived from analyses of up to 50 extracts of marine dissolved organic matter. Results:The software supports the processing of lists of calibrated masses of neutral, protonated or deprotonated molecules, with masses of up to 700 Da and a mass accuracy <3 ppm. In the performance test, the number of assigned peaks per second increased with the number of submitted peaks and reached a maximum rate of 4745 assigned peaks per second.Conclusions: UME offers a complete data evaluation pipeline comprising a fast molecular formula assignment algorithm allowing for the swift reanalysis of complete datasets, advanced filter functions and the export of data, metadata and publicationquality graphics. Unique to UME is a fast and interactive connection between data and their visual representation. UME provides a new platform enabling an increased transparency, customization, documentation and comparability of datasets.

Antiviral activity of natural humic substances and shilajit materials against HIV-1: Relation to structure

“…Molecular compositions were assigned using the open source browser-based application UltraMassExplorer created by Leefmann et al ( http://dockersrv1.awi.de:3838/ume ) ( Leefmann et al, 2019 ). The pivot table with all assigned formulae is presented in Supplementary file Table S5 .…”

Mathematical chromatography deciphers the molecular fingerprints of dissolved organic matter

“…As of the publication of this article, community-driven software only covers molecular formula assignment and basic exploration of variance for direct-infusion data. 19,20 To fully exploit the potential of HPLC-HRMS, such tools could be expanded upon to include data analysis routines that isolate systematic variation from HPLC-HRMS datasets.…”

Interlaboratory comparison of humic substances compositional space as measured by Fourier transform ion cyclotron resonance mass spectrometry (IUPAC Technical Report)

“…Where laboratories a and c determined 499 and 213 compositions, respectively, laboratories b, d, and e found significantly fewer of these compositions, lower by a factor of 10. The abundant CHOS compounds could also be originated from impurities, e.g., surfactants [24].…”

“…However, the dynamic range and sensitivity are specific features of the instruments and depend mainly on the ion optics, ICR cell geometry, and the homogeneity of the magnetic field [30]. In addition, the lifetime of ions depends drastically on the ion accumulation parameters [24]. The latter were not standardized in this study due to the different architecture of the instruments used by the participating laboratories.…”