During the recent workshop at the EuBIC-MS Winter School, it was suggested by several participants to output the shared and unique spectra from compareMS2. The easiest way to do this is probably to output three additional files in the 1-vs-1 comparison mode, one with the spectra from dataset 1 that are not similar to any spectrum in dataset 2, one with the spectra from dataset 2 that are not similar to any spectrum in dataset 1, and one with all the spectra from both dataset 1 and dataset 2 that are similar to at least one spectrum in the other dataset.
During the recent workshop at the EuBIC-MS Winter School, it was suggested by several participants to output the shared and unique spectra from compareMS2. The easiest way to do this is probably to output three additional files in the 1-vs-1 comparison mode, one with the spectra from dataset 1 that are not similar to any spectrum in dataset 2, one with the spectra from dataset 2 that are not similar to any spectrum in dataset 1, and one with all the spectra from both dataset 1 and dataset 2 that are similar to at least one spectrum in the other dataset.