The results file report_specnets.txt is created in the directory where the analysis was started (using specnets('myparameters.params'); from the Matlab command prompt). This multi-column text file is a standard tab-separated set of results per spectrum, easily accessed using standard tools such as Microsoft Excel, OpenOffice or your favorite text editor. The values of the different columns in this output file are described below.
In addition to results_specnets.txt, the Spectral Networks package also outputs the spectral networks graphs in a format suitable for visualization with Graphviz. In particular, the graph for the spectral network with index I in results_specnets.txt can be found in graphs/specnet_I.txt.
| Column header | Description |
|---|---|
| Network index | Index of the spectral network containing the spectrum. |
| Spectrum index | Index of the spectrum in the filtered set of spectra. |
| Spectrum filename | Name of the input file followed by the spectrum index inside the input file (separated by ':'). |
| Peptide | Peptide annotation assigned to the spectrum. |
| Propagation level | Number of iterations of the propagation algorithm required to annotate the spectrum. |
| Perc EI (score) | Percentage of intensity explained by the assigned peptide in the scored version of the spectrum. |
| Perc TP (score) | Percentage of b/y-ions found in the scored version of the spectrum. |
| Perc EI (MS/MS) | Percentage of intensity explained by the assigned peptide in the original MS/MS version of the spectrum. |
| Protein | Protein assignment for the spectrum. |