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.

Main output files:

File

Description

<prefix>.psms.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

Rescoring engine files:

File

Description

<prefix>.<mokapot/percolator>.psms.txt

PSMs and their new scores at PSM-level FDR.

<prefix>.<mokapot/percolator>.peptides.txt

Peptides and their new scores at peptide-level FDR.

<prefix>.<mokapot/percolator>.proteins.txt

Proteins and their new scores at protein-level FDR.

<prefix>.<mokapot/percolator>.decoy.psms.txt

Decoy PSMs and their new scores at PSM-level FDR.

<prefix>.<mokapot/percolator>.decoy.peptides.txt

Decoy peptides and their new scores at peptide-level FDR.

<prefix>.<mokapot/percolator>.decoy.proteins.txt

Decoy proteins and their new scores at protein-level FDR.

<prefix>.<mokapot/percolator>.weights.txt

Feature weights, showing feature usage in the rescoring run

If no rescoring engine is selected, if Percolator was selected, or in DEBUG mode, the following files will also be written:

File

Description

<prefix>.pin

PSMs with all features for rescoring