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Software Tools

Compound Identification Algorithm

The formula assignment algorithm will calculate elemental formulas from mass-to-charge data generated by an ultrahigh resolution mass spectrometer. The program, Compound Identification Algorithm (CIA), is described in Kujawinski and Behn ( This code is implemented in MATLAB and is freely-available at GitHub. The README file describes how to use the program.


We developed a boutique database for metabolomics data. This code is freely-available at GitHub and is described in this manuscript. The database organizes LC-MS data and metadata to allow efficient querying of data from our metabolomics experiments. The wiki at GitHub describes how to use the software.


This package is designed to help facilitate data processing in untargeted metabolomics. This code is freely-available on Bioconductor and McLean and Kujawinski (2020) provides details on the code.

Laboratory Protocols

We are in the process of making our protocols public here on; we welcome comments and questions on the protocols that are posted.