This software is a non-official implementation of the paper "The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution" by S. Majewski, M. A. Ciach, M. Startek, W. Niemyska, B. Miasojedow and A. Gambin.

Default solver is based on a problem-specific genetic algorithm. This allows for numerical stability and high speed.

Figure: t-distributed Stochastic Neighbor Embedding of MS1 ESI-QTOF spectra with precomputed matrix Wasserstein distances. The colormaps gives the mass of each molecule (point) expressed in Daltons.

Run mass spectral deconvolution algorithm on an empirical spectrum and a folder containing the theoretical spectra. Paths to theoretical spectra should be specified in molecule_list.txt. A concrete example of dataset is provided in example-msd/ folder.

deconvms path/to/empirical/spectrum.txt path/to/molecule_list.txt path/to/molecules/folder --niter 50000

Compute Wasserstein dissimilarity between two mass spectra:

wassms path/to/first/record/file.txt path/to/second/record/file.txt --m W

Compute Euclidean distance between two mass spectra:

wassms path/to/first/record/file.txt path/to/second/record/file.txt --m E

Compile the project with g++:

make release

This will create the two executable files wassms and deconvms.

The project is built on top of Eigen, whose path is assumed to be stored in a Eigen3_DIR variable.