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DatabaseSuitability

Calculates the suitability of a database which was used a for peptide identification search. Also reports the quality of LC-MS spectra.

The metric this tool uses to determine the suitability of a database is based on a de novo model. Therefore it is crucial that your workflow is set up the right way. Above you can see an example.
Most importantly the peptide identification search needs to be done with a combination of the database in question and a de novo "database".
To generate the de novo "database":

For re-ranking all cases where a peptide hit only found in the de novo "database" scores above a peptide hit found in the actual database are checked. In all these cases the cross-correlation scores of those peptide hits are compared. If they are similar enough, the database hit will be re-ranked to be on top of the de novo hit. You can control how much of cases with similar scores will be re-ranked by using the reranking_cutoff_percentile.
For this to work it is important PeptideIndexer ran before. However it is also crucial that no FDR was performed. This tool does this itself and will crash if a q-value is found. You can still control the FDR that you want to establish using the corresponding flag.

Note
For identification search the recommended search engine is Comet because the Comet cross-correlation score is recommended for re-ranking.
If you use other search engines re-ranking will be turned off automatically. You can still enforce re-ranking by using the 'force' flag.
In this case the tool will use the default score of your search engine. This can result in undefined behaviour. Be warned.

The results are written directly into the console. But you can provide an optional tsv output file where the most important results will be exported to.

This tool uses the metrics and algorithms first presented in:
Assessing protein sequence database suitability using de novo sequencing. Molecular & Cellular Proteomics. January 1, 2020; 19, 1: 198-208. doi:10.1074/mcp.TIR119.001752.
Richard S. Johnson, Brian C. Searle, Brook L. Nunn, Jason M. Gilmore, Molly Phillips, Chris T. Amemiya, Michelle Heck, Michael J. MacCoss.

The command line parameters of this tool are:

INI file documentation of this tool: