ProteinProphet

Statistical validation of protein identifications

Version

ProteinProphet v5.2.1

Usage

philosopher proteinprophet [flags] [files]

Flags

--iprophet

Input is from iProphet.

--maxppmdiff

Maximum peptide mass difference in ppm (default 20).

--minprob

PeptideProphet probability threshold (default 0.05).

--nonsp

Do not use NSP model.

--output

Output name (default "interact.prot.xml").

--unmapped

Report results for UNMAPPED proteins.

Example

Execute a standard analysis on a pepXML file called sample.pepxml.

philosopher proteinprophet sample.pepxml

FAQ

Do I need TPP installed for running this ?

No