3.GUI: a pairwise spectrum view

This GUI enables the manual inspection of how spectra actually look alike and can be downloaded here.

1-Start the application: GUI can be started by running a command prompt in a folder that contains spectrum_similarity_pairwise_GUI-X.Y.Z.jar (X.Y.Z shows the current version number). On the command prompt, the following line needs to be executed:

java -jar spectrum_similarity_pairwise_GUI-0.1.jar


2-Introduce the files:

The required inputs

  • Two folders containing spectra that are compared (specA and specB, and must be mgf files)
  • A text file containing calculated scores
  • Indices of spectrum titles from these two spectra folders in a given text file


3-Create: Click on the CREATE button to start visualizing pairwise spectra.

after create

A pairwise spectra can be inspected either as bubble spectra (see above) or mirrored spectra (see below).

mirror spectra

FILTERING: Each visualization can be also inspected by applying noise filtering. Clicking the NoiseFilter button applies an adaptive noise filtering from pride-asa-pipeline. The resulted remaining percentage can be automatically given.


Alternatively, the sliding bar allows the removal of low-intense peaks corresponding to the remaining percentage of peaks in a given spectrum.


Note that column colors and spectrum colors in visualization match.