Thank you, Julianus, for your reply and explanation - I will try this out then as I was also not sure what’s the issue as index files should be there…the error message essentially says that files are not found in the location (although they exist).
Will have a go with CometAdapter! Thank you for your kind help
ERROR OMSSAAdapter 0:76 Failing process stdout: [OMSSAAdapter took 0.06 s (wall), 0.02 s (CPU), 0.02 s (system), 0.00 s (user); Peak Memory Usage: 23 MB.]
ERROR OMSSAAdapter 0:76 Failing process stderr: [Input database ‘D:\Research work\Mass spectrometry\References\s_pyo_sfHS.fasta.psq’ not found (the file ‘D:\Research work\Mass spectrometry\References\s_pyo_sfHS.fasta.psq’ could not be found). Make sure it exists (and check ‘OpenMS.ini:id_db_dir’ if you used relative paths. Aborting!, Unable to find database ‘D:\Research work\Mass spectrometry\References\s_pyo_sfHS.fasta.psq’ (searched all folders). Did generate the PSQ file (see OMSSAAdapter documentation).]
ERROR OMSSAAdapter 0:76 Return code: 6
ERROR OMSSAAdapter 0:76 Execute failed: Failed to execute node OMSSAAdapter