FluoroMatch – Covers entire non-targeted PFAS workflow

FluoroMatch 4.3 updated on 11/09/23

1. Isotopic Support (great thanks to Michael Kummer, and David Schiessel!):
   1. Filter by percent abundance of isotope
   2. Kauffman Plots with reference database
   3. Working on Sophisticated Formula Prediction (coming very soon!)
2. Dramatic Library Expansion (great thanks to Jacqueline Bangma, Mark Strynar, Carrie McDonough, David Dukes, and Sheng Liu):
   1. 8,874 new rule based fragmentation across 29 compound classes (see b and d)
   2. Biotransformation Products from Enzymatically Treated Standards
   3. Biotransformation products using Biotransformer and structure-fragment relationship prediction (200,000+)
   4. Chemical compounds related to industrial effluent characterized at the EPA
3. New filters
   1. Filter by feature number, m/z, retention time range, isotope percentages...
   2. Filter by flagged features
4. IonDecon (great thanks to Michael Kummer, Kathy Hunt (Vogon Labs), and Olivier Chevallier!):
   1. This is a seperate software but now allows FluoroMatch to support All-Ions data: IonDecon (all-ions deconvolution) – Innovative Omics (working to integrate into FluoroMatch to increase throughput, coming soon!)

1. A New Interface with new features (give great thanks to Bernard Brooks!):
   1. Important/relevant weblinks
   2. Loading bars which track the progress of all steps (file conversion, peak picking, annotation, visualization files)
   3. New parameters which can reduce file size and speed up processing (intensity cutoffs for file conversion and annotation, retention time range for file conversion, etc.)
   4. debugging functionality to rerun only the annotation step after peak picking if there was an issue
   5. automatic saving of parameters for next time it is used
2. Statistics integration (great thanks to David Godri and Bernard!):
   1. New "groupings parameter" on the interface for automatic group detection
   2. ANOVA, Volcano Plot, PCA, Violin Plot, Heatmap, etc. calculations and visualizations
3. Targeted peak detection, just upload a peaklist and targeted peak detection will be performed and added to the non-targeted peak table. For example, add your list of standards (m/z and retention times) or your list of knowns you want to make sure to capture can be uploaded every time you run the software. Could also be used for retention time predicted databases for searching.
4. Chromatogram (EIC) and MS1 visualizations (great thanks to Michael Kummer and Nandarani Abril). Visualize chromatograms interactively for every feature in the visualizer along with MS1 spectra with isotopic labeling.
5. Python integration into the FluoroMatch ecosystem (thanks to Eric Siegel, Michael Kummer, and Nandarani Abril)
6. R v4.2.1 integration into the FluoroMatch ecosystem (thanks to Bernard Brooks)
7. New libraries (labeled standards and transformation products):
   1. PFAS transformation products especially glucuronic acids (certain libraries are turned off until publication/discussion, but will be turned on shortly) (great thanks to the Carrie McDonough group, and Sheng Liu of Krystal Pollitt's group)
   2. A subset of labeled standards (thank you to Jackie Bangma and James McCord)

FluoroMatch Flow 3.0

FluoroMatch Flow 2.6

Click this button in the upper menu of each video to view each playlist item

The following document is kept to date with issues / errors that can arise while using FluoroMatch software.

• Manual / TroubleShooting / Known Issues

Feel free to email jeremykoelmel@innovativeomics.com if you encounter a new issue, have suggested edits, or want to provide feedback. The following link is for editing the manual and providing feedback.

• Manual / TroubleShooting / Known Issues - editable

We appreciate your input to improve our software.

For Developers Only, the Distribution for Users Should be Downloaded from the Innovative Omics Software webpage

• Core-Match GitHub

Jeremy P. Koelmel, Paul Stelben, David Godri, Jiarong Qi, Carrie A. McDonough, David A. Dukes, Juan J. Aristizabal-Henao, John A. Bowden, Sandi Sternberg, Emma E. Rennie, Krystal J. Godri Pollitt, Interactive software for visualization of nontargeted mass spectrometry data—FluoroMatch visualizer, Exposome. (2022), 2(1) doi: 10.1093/exposome/osac006

Koelmel, J.P. §, Stelben, P.J. §, McDonough, C.A., Dukes, D.A., Aristizabal-Henao, J.J., Nason, S.L., Li, Y., Sternberg, S., Lin, E., Beckmann, M., Williams, A.J., Draper, J., Finch, J.P., Munk, J.K., Deigl, C., Rennie, E.E., Bowden, J.A.*, Godri Pollitt, K.J.*: FluoroMatch 2.0 – Making Automated and Comprehensive Non-Targeted PFAS Annotation a Reality. Anal. Bioanal. Chem. (2021).

Koelmel, J.P., Paige, M.K., Aristizabal-Henao, J.J., Robey, N.M., Nason, S.L., Stelben, P.J., Li, Y., Kroeger, N.M., Napolitano, M.P., Savvaides, T., Vasiliou, V., Rostkowski, P., Garrett, T.J., Lin, E., Deigl, C., Jobst, K., Townsend, T.G., Godri Pollitt, K.J.*, Bowden, J.A.*: Toward Comprehensive Per- and Polyfluoroalkyl Substances Annotation Using FluoroMatch Software and Intelligent High-Resolution Tandem Mass Spectrometry Acquisition. Anal. Chem. 92, 11186–11194 (2020).

D. Kessner, M. Chambers, R. Burke, D. Agus, and P. Mallick: ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Bioinformatics. (2008) 24(21): 2534–2536. doi: 10.1093/bioinformatics/btn323

T. Pluskal, S. Castillo, A. Villar-Briones, M. Orešič, MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data, BMC Bioinformatics 11:395 (2010). PMID: 20650010