PNNL

Abstract

RATIONALE The high-resolution measurement capability of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for exploring the molecular composition of soil, plant, aquatic, and petroleum samples. This demand has driven a need for informatics tools to explore and analyze FT-MS data in a robust and reproducible manner. METHODS FREDA is an interactive web application developed to enable spectrometrists to format, process, and explore their FT-MS data without the need for statistical programming expertise. FREDA was built to explore outputs from a molecular identification tool, like CoreMS, and provide a suite of methods to filter data, compute chemical properties of peaks, statistically compare samples and groups of samples, conduct exploratory data analysis, and download the results with a report detailing all steps conducted. RESULTS To demonstrate the utility of FREDA, an example analysis was conducted using FT-MS data from a soil microbiology study of samples collected at two elevations at Rattlesnake Mountain in Washington state. Differences between the two elevations are observed using Kendrick, Gibbs Free Energy, and van Krevelen plots. G-tests are used to quantify a significant difference between the groups. All analyses and plots are conducted using only the FREDA application. CONCLUSIONS FREDA is an open-source and readily available web application that allows users to explore and make statistically valid conclusions about their FT-MS data. The application is available online (https://map.emsl.pnnl.gov/app/freda) with a tutorial web series (https://youtu.be/k5HLE2kNSBY?si=yB6sGoyvzxrFf5MP) and freely accessible code on Github (https://github.com/EMSL-Computing/FREDA).