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 (http://dx.doi.org/10.1021/ac0600306). 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.
We are in the process of making our protocols public here on protocols.io; we welcome comments and questions on the protocols that are posted.