Tim Leefmann1, Stephan Frickenhaus1,2,3, Boris P Koch1,2. 1. Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany. 2. University of Applied Sciences, An der Karlstadt 8, 27568, Bremerhaven, Germany. 3. Centre for Industrial Mathematics, University of Bremen, Bibliothekstraße 5, 28359, Bremen, Germany.
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 publication-quality 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.
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 publication-quality 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.
Authors: Yury V Zhernov; Andrey I Konstantinov; Alexander Zherebker; Eugene Nikolaev; Alexey Orlov; Mikhail I Savinykh; Galina V Kornilaeva; Eduard V Karamov; Irina V Perminova Journal: Environ Res Date: 2020-10-14 Impact factor: 6.498
Authors: Lisa M Bramer; Amanda M White; Kelly G Stratton; Allison M Thompson; Daniel Claborne; Kirsten Hofmockel; Lee Ann McCue Journal: PLoS Comput Biol Date: 2020-03-16 Impact factor: 4.475