compareMS2 is a tool for direct comparison of tandem mass spectrometry (MS/MS) datasets, typically from LC-MS/MS, in proteomics or metabolomics, defining a distance as a function of the share of similar spectra. Applications span biomedicine, phylogenetics, forensics, ecology and food science.
compareMS2 calculates the similarity between tandem mass spectrometry datasets and visualizes the results in a phylogenetic tree. * Only mass spectrometry data is needed * Relative distances between samples immediately become clear * A Graphical User Interface simplifies usage * Optionally, sample files can be mapped to species names * Phylogenetic trees can be saved in several graphics file formats for direct use in publications * Input consists of MS2 data in MGF format * Output file formats are compatible with common phylogenetic tree software (for instance [MEGA](https://www.megasoftware.net/)) for further analysis and visualization
National Institute of Standards and Technology
compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets
Molecular phylogenetics by direct comparison of tandem mass spectra