config.toml parameters

General Parameters

• output: Path to output folder; if it does not exist, it will be generated
• threads = ""
• tmt_ms_level = "<ms2/ms3>"

Input Parameters:

• maxquant_results = "<Path to MaxQuant combined/txt/>"
• spectra = ""
• spectra_type = "<raw/mzml>"

Prosit-specific parameters

• intensity_model = "<Prosit_2020_intensity_TMT/>"
• irt_model = "<Prosit_2020_irt_TMT>"
• prediction_server = "koina.wilhelmlab.org:443"
• ssl = true
• ms_analyzer = "<ot/it>"

SIMSI-specific parameters

• stringency: Clustering stringency used by MaRaCluster for SIMSI-Transfer; recommended to be kept at 10
• max_pep: Maximum Posterior Error Probability (PEP) in % of an identification to be considered for Transfer; recommended to be kept at 5

Picked Protein Group FDR specific parameters

• fasta = "<Path to .fasta file used for database search>"
• enzyme = ""