Identifies peptides in MS/MS spectra.

pot. predecessor tools	→ ProSE →	pot. successor tools
any signal-/preprocessing tool (in mzML or Bruker .d format)	→ ProSE →	IDFilter or any protein/peptide processing tool

@em This search engine is mainly for educational/benchmarking/prototyping use cases.
It lacks behind in speed and/or quality of results when compared to state-of-the-art search engines.

@note Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using @ref TOPP_IDFileConverter if necessary.
@note Open-search mode is automatically determined by the precursor mass tolerance: enabled when tolerance exceeds 1 Da or 1000 ppm. No explicit open-search parameter is needed. This is logged at runtime and recorded in the output search parameters as UserParam 'open_search'.
@note Decoy handling: either enable '-Search:decoys' to generate decoys internally, or provide a FASTA database that already contains decoy proteins (e.g., from DecoyDatabase). In both cases, the decoy accession prefix must match '-Search:decoy_prefix' (default: "DECOY_").

<B>The command line parameters of this tool are:</B>
@verbinclude TOPP_ProSE.cli
<B>INI file documentation of this tool:</B>
@htmlinclude TOPP_ProSE.html