proteobench.io.parsing.utils module#

Utilities for parsing modifications.

proteobench.io.parsing.utils.add_fixed_mod(proforma: str, mod_name: str, aas: str) → str[source]#

Add a single fixed modification to a peptide in ProForma format.

Parameters:

  • proforma (str) – Peptide in ProForma format.

  • mod_name (str) – Name of the modification to add as a fixed modification.

  • aas (str) – The amino acid whereon the fixed modifications should be registered.

Returns:

The modified peptide in ProForma format.

Return type:

str

proteobench.io.parsing.utils.add_maxquant_fixed_modifications(params: ProteoBenchParameters, result_perf: DataFrame) → DataFrame[source]#

Format MaxQuant modifications.

Parameters:

  • params (ProteoBenchParameters) – ProteoBenchParameters object from MaxQuant results. Contains modifications in fixed_mods attribute.

  • result_perf (pd.DataFrame) – The benchmarking results.

Returns:

Results of benchmarking with parsed modifications.

Return type:

pd.DataFrame

Notes

params.fixed_mods uses ProForma-like notation ("C[Carbamidomethyl]", comma-separated). Empty values (no fixed modifications), terminal modifications (e.g. "Protein N-term[Acetyl]"), and unrecognised tokens are skipped rather than raised, so a submission is never blocked by modification formatting.