Fig. 2.
The generation of molecular networks via spectral alignment. (A) A schematic representation of how the molecular networks are generated. The values are representative of cosine scores from 0 to 1, where 1 indicates identical spectra and 0 means no similarity whatsoever. In our data, we found that a cosine cutoff of 0.5 resulted in molecular networks that could be interpreted. The thickness of the edges (blue lines connecting nodes) indicates the level of similarity. (B) A Cytoscape visualization of the surfactin single adduct cluster from B. subtilis 3610. The full MS/MS network is shown in Fig. 3A. Nodes with red border are represented in C. (C) An example of four spectra from the molecular network shown in B that show a strong cosine score.