LCMSpector: A simple open-source viewer for targeted hyphenated mass spectrometry analysis

Mateusz Fido, Etienne Hoesli, Elisa Cappio Barazzone, Renato Zenobi and Emma Slack

PLOS Computational Biology, 2025, vol. 21, issue 12, 1-18

Abstract: The ubiquitousness of hyphenated mass spectrometry techniques across life sciences has made researchers around the world aware of their analytical power. However, the analysis of multidimensional high-complexity mass spectrometry data remains virtually impossible for non-specialists. LCMSpector is a standalone graphical user interface application for straightforward analysis of targeted mass spectrometry data, distributed under the MIT license and available free of charge for Windows, MacOS, and Linux. The user can upload and process the data entirely locally on their machine by specifying the desired mass-to-charge ratios of the targeted compound ions and simply clicking “Process”. It allows for the processing of multiple files simultaneously, freely modifying and exporting graphs in real time, and calculating compound concentrations based on calibration standards. We show the versatility and applicability of LCMSpector to different kinds of mass spectrometry data by analyzing a series of publicly available datasets from various samples recorded on instruments from multiple vendors and by different research teams.Author summary: Mass spectrometry coupled with chromatography is among the most powerful analytical techniques used in the life sciences today. However, the generated datasets are large and complex, requiring specialized software or custom scripts for analysis. Therefore, data viewing and treatment in mass spectrometry create a barrier to entry for non-specialists within the field. Open-source, user-friendly tools for inspecting raw data, enabling evaluation of both chromatographic and mass spectrometric information, are lacking. Here we present LCMSpector, an easy-to-use graphical application for visualizing and analyzing hyphenated mass spectrometry data, available on Windows, MacOS, and Linux. Using several public datasets, we demonstrate how LCMSpector’s comprehensive raw data viewing features aid targeted analysis of metabolic products. We benchmarked our application against software with similar functionality and conducted a small-scale usability study to evaluate adoption by non-specialists. The results indicate that LCMSpector lowers the technical barrier of entry and improves efficiency for researchers analyzing hyphenated mass spectrometry data. We hope this open-source software benefits the life science community and grows into a robust tool across subfields, such as metabolomics, proteomics, glycomics, and other “omics” employing hyphenated mass spectrometry.

Date: 2025
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1013095

DOI: 10.1371/journal.pcbi.1013095

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