config.toml parameters

General Parameters

• output: Path to output folder; if it does not exist, it will be generated
• threads: Number of CPU threads used by the ProSIMSIt pipeline
• tmt_ms_level: Select MS2 or MS3, depending on how you perform TMT quantification

Input Parameters:

• maxquant_results: Path to /combined/txt/ output folder with MaxQuant results
• spectra: Path to folder containing the .raw or .mzML files
• spectra_type: Mass spec file format, mzml or raw

Prosit-specific parameters

• intensity_model: Utilized Prosit intensity model for Oktoberfest; we recommend "Prosit_2020_intensity_TMT" or "Prosit_2024_intensity_PTMs_gl"
• irt_model: Utilized Prosit retention time model for Oktoberfest; we recommend "Prosit_2020_irt_TMT" or "rosit_2024_irt_PTMs_gl"
• prediction_server: Koina instance utilized by Oktoberfest, e.g. "koina.wilhelmlab.org:443"
• ssl: Keep on "true" if using public Koina instances
• ms_analyzer: "ot" for Orbitrap or "it" for Ion Trap

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: Enzyme used for database search, e.g. "trypsinp" for "Trypsin/P"