Output files

Depending on the options you choose, the following files will be created. All PSMs, peptides, and proteins are not yet filtered at any false discovery rate (FDR) level and contain both target and decoy identifications.

Main output files:

File	Description
<prefix>.tsv	Main output file with rescored PSMs and their new scores
<prefix>.report.html	HTML report with interactive plots showing the results and some quality control metrics.

Log and configuration files:

File	Description
<prefix>.log.txt	Log file with information about the run
<prefix>.log.html	HTML version of the log file
<prefix>.full-config.json	Full configuration file with all the parameters used as configured in the user-provided configuration file, the command line or graphical interface, and the default values.
<prefix>.feature_names.tsv	List of the features and their descriptions
<prefix>.intermediate.tsv	Created automatically if the process crashes during feature generation or rescoring. Contains all PSMs with successfully added features up to the crash point. Can be used to resume processing with -p <prefix>.intermediate.tsv -t tsv.
<prefix>.weights.tsv	Feature weights, showing feature usage in the rescoring run.

Identification result tables:

The post-rescoring score, q-value, and PEP at each identification level, as plain TSV files. The protein-level table is only written if the PSM file provides a protein_list.

File	Description
<prefix>.psms.tsv	PSMs and their rescored score, at PSM-level FDR.
<prefix>.peptidoforms.tsv	Peptidoforms (sequence and modifications, no charge) and their score, at peptidoform-level FDR.
<prefix>.peptides.tsv	Peptides (stripped sequence) and their score, at peptide-level FDR.
<prefix>.proteins.tsv	Protein groups and their score, at protein group-level FDR.

If max_psm_rank_output is set to more than 1, these tables (and the main PSM list output) hold multiple ranks per spectrum, and their q-values/PEPs are computed treating each rank as an independent row rather than through proper spectrum competition (not statistically rigorous FDR control). max_psm_rank_output > 1 is intended for surfacing ambiguous results (e.g. multiple candidate peptidoforms per spectrum from Mumble), not for a corrected identification count.