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compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets



Rob Marissen, Jeroen Laros, Josef Rasinger, Madhushri Varunjikar, Ben Neely, Magnus Palmblad


It has long been known that biological species can be identified from mass spectrometry data alone. Ten years ago, we described a method and software tool, compareMS2, for calculating a distance between sets of tandem mass spectra, as routinely collected in proteomics. This method has seen use in species identification and mixture characterization in food and feed products, as well as other applications. Here, we present the first major update of this software, including a new metric, a graphical user interface and additional functionality. The data have been deposited to ProteomeXchange with dataset identifier PXD034932.
ACS Journal of Proteome Research


compareMS2, distance metric, molecular phylogenetics, quality control, spectral clustering, distance metric, tandem mass spectrometry


Marissen, R. , Laros, J. , Rasinger, J. , Varunjikar, M. , Neely, B. and Palmblad, M. (2022), compareMS2 2.0: An Improved Software for Comparing Tandem Mass Spectrometry Datasets, ACS Journal of Proteome Research, [online],, (Accessed April 17, 2024)
Created September 29, 2022, Updated November 29, 2022