I am using spectraST frequently to build spectral libraries and also the corresponding decoy libraries. Usually these libraries are build by randomly shuffling sequences or adding amino acids to the peptide sequence. Thus, during the downstream processing of search results with peptide or protein prophet decoys can not be mapped to the correct protein, when using a forward/reverse fasta file.
I was not worried about this before but, since recently started to use the philosopher pipeline for FDR filtering on protein level, I am not sure whether those decoy peptides will transfer correctly to the protein level?
I know that I can use the option to include unmapped peptides in the prophets but I don't know how those peptides would be distributed to the correct proteins? I guess the easiest way to ensure correct mapping would be an option to export a fasta file together with the decoy generation which includes the concatenated modified peptide sequences for each protein. Does anyone know if such an option present in spectraST?