As spectrum prediction tools are becoming increasingly more accurate, in case a spectral library for a specific proteome is not available, we can accurately simulate a spectral library instead.
Implement functionality to simulate a spectral library using Prosit. Evaluate whether we want to access the web API they provide (slow but no maintenance for us, does not complicate installation) or whether we want to integrate Prosit into ANN-SoLo directly (fast but makes ANN-SoLo more complex).
[x] Predict a spectral library from a FASTA file.
[x] Predict a spectral library for decoys generated from a FASTA file.
[ ] Combine an experimental spectral library and a predicted spectral library.
As spectrum prediction tools are becoming increasingly more accurate, in case a spectral library for a specific proteome is not available, we can accurately simulate a spectral library instead.
Implement functionality to simulate a spectral library using Prosit. Evaluate whether we want to access the web API they provide (slow but no maintenance for us, does not complicate installation) or whether we want to integrate Prosit into ANN-SoLo directly (fast but makes ANN-SoLo more complex).