FluoroMatch IM Tutorial 2: Running the Software

Download the software at: https://innovativeomics.com/software/fluoromatch-im This tutorial covers mzML conversion and 4D peak picked table attributes. And then covers running the R script, the interface, and the parameters. https://innovativeomics.com/software/fluoromatch-im FluoroMatch (IM) provides interactive visualizations combining mass spectrometric evidence (CCS, drift time, retention time, and accurate mass) to discern PFAS homologous series and structures from non-targeted datasets. Simply upload your feature table (for example after using Agilent Mass Profiler), the CCS libraries, and homologous series file, select your parameters and run. FluoroMatch IM does CCS matching across 5000+ PFAS contained in the CCS library. Results can be opened in FluoroMatch IM Visualizer and visualizations include normalized mass defect plots, retention time versus accurate mass plots, CCS/drift time versus accurate mass plots, 3D plots including retention time, m/z, and drift time, and tables of annotations and metadata. All graphs and tables are interactive and have cross-filtering such that when a user selects a feature or homologous series, all other visuals highlight the feature or series of interest. Check out this page for examples of our interactive datasets generated which can be shared online! Collaborations: We are excited to publish this work, want to join us? If you have interesting Ion Mobility data for PFAS or if you have CCS libraries you are willing to share, contact us! Updates since last release: Drastically Expanded CCS libraries (256 from standards, 6,138 predicted) (Rachel Smolinski and Jeremy Koelmel compiled and validated, Erin Baker and John McClean lab developed databases): Environ. Sci. Technol. 2022, 56, 12, 9133–9143 Environ. Sci. Technol. 2025, 59, 13, 6636–6648 David Weil from Agilent https://tarheels.live/bakerlab/databases/ Added visualization by abundance (with on and off toggle, including in 3D) (Jeremy Koelmel and David Godri) Added column showing whether CCS Match was from a predicted or standard or experimental CCS value, also ranked and scored hits depending on which source they were from (Rachel Smolinski and Jeremy Koelmel). If the top hit is predicted B+ otherwise A/A-. Finally added a parameter which will increase search tolerance for predicted CCS values (+/-5% matching error, based on publication showing 90% of the 50 PFAS validation set fell within this range https://pubs.acs.org/doi/10.1021/acs.est.2c00201) Advanced formula prediction: added more robust formula prediction (error capture) (Jeremy Koelmel and David Schiessel) Added homologous series voting (formula prediction based on formulas across all members of a series) (Paul Stelben coder) Added kernel density region for EPA PFAS in Kaufmann space. Kaufmann isolines for filtering candidates to only those which fall within the PFAS region (0.94 recommended default). Used to determine likely PFAS candidates even without database matching (Michael Kummer coder) Added video tutorials (new running the IM software, R Code, and Visualizer)