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

Abstract

Rational: 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, respectively, 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 number of submitted peaks and reached a maximum rate 4,745 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 its visual representation. UME provides a new platform enabling an increased transparency, customization, documentation and comparability of datasets