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 Software Tools


We use GitHub to share computational pipelines. You can check us out at KujawinskiLaboratory


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


We developed a boutique database for metabolomics data. This code is freely-available at GitHub and is described in Longnecker et al. (2015). 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.

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 (2006). This code is implemented in MATLAB and is freely-available at GitHub. The README file describes how to use the program.

Laboratory Protocols

We make our protocols public here on; we welcome comments and questions on the protocols that are posted.