filter

A custom algorithm for MS/MS data filtering and multi-level false discovery rate estimation.

Usage

philosopher filter [flags]

Flags

--ion

Peptide ion FDR level (default 0.01).

--mapmods

Map modifications.

--models

Print model distribution for the analyzed pepXML.

--pep

Peptide FDR level (default 0.01)

--pepProb

top peptide probability threshold for the FDR filtering (default 0.7)

--pepxml

Path to the pepXML file or the path to a directory containing a set of pepXML files.

--picked

Apply the picked FDR algorithm before the protein scoring.

--prot

Protein FDR level (default 0.01).

--protProb

Protein probability threshold for the FDR filtering (not used with the razor algorithm) (default 0.5).

--protxml

Path to the protXML file path.

--psm

PSM FDR level (default 0.01).

--razor

Uses razor peptides for protein FDR scoring.

--sequential

Alternative algorithm that estimates FDR using both filtered PSM and Protein lists to boost identifications.

--cappedsequential

Alternative algorithm that estimates FDR using both filtered PSM and Protein lists using a threshold cap from first pass.

--tag

The decoy prefix used on decoy sequences (default "rev_").

--weight

Threshold for defining peptide uniqueness (default 1).

Examples

Process a single pepXML file using the standard filter values.

philosopher filter --pepxml interact.pepxml

Process several pepXML files and one protXML file using the standard filter values.

philosopher filter --pepxml results/ --protxml interact.protxml

Process all pepXML files and the protXML file called sample.protxml found in the result folder. The program will employ the razor algorithm during the FDR filtering and at the end will save the analyzed data in binary format for posterior processing and reporting.

philosopher filter --pepxml results/ --protxml results/sample.protxml --razor