Software Tools

GitHub

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

Autotuner

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.

domdb

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

protocols.io

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

• Solid phase extraction of dissolved organic matter from seawater
• Internal metabolite extraction for targeted and untargeted metabolomics
• BC derivatization for dissolved marine metabolites (original version and updated version)
• There are also protocols for collecting dissolved/total organic matter, cleaning glassware, and processing samples to determine the efficiency organic matter is captured using solid phase extraction.