Ross, D. H.; Chang, C.; Vasquez, J.; Overstreet, R.; Schultz, K.; Metz, T.; Bade, J.

Pseudomonas putida strain KT2440 is a crucial model organism for synthetic biology and bioengineering applications, yet there currently exists no comprehensive metabolomics database comparable to those available for other model organisms. This gap hinders the use of untargeted metabolomics for exploratory analyses in this system. We developed the P. putida metabolome reference database (PPMDB v1) to address this limitation by consolidating metabolite information from multiple sources and expanding coverage through computational predictions. The database was constructed by curating metabolites from BioCyc, BiGG, and other literature sources, then computationally expanding this collection using BioTransformer environmental transformation predictions to generate additional predicted metabolites. We enhanced the database's utility for molecular annotation in metabolomics studies by incorporating analytical properties including collision cross-sections, tandem mass spectra, and gas-phase infrared spectra. These analytical properties were gathered from existing measurement data or predicted using computational tools. We further augmented the database through inclusion of reaction information and pathway annotations, facilitating biological interpretation of metabolomics data. This publicly available resource fills a critical gap in P. putida research infrastructure, supporting metabolite annotation and biological interpretation in untargeted metabolomics studies and enabling in-depth exploratory analyses of this important synthetic biology platform at the molecular level.