iProphet

Multi-level integrative analysis of shotgun proteomic data with iProphet

Version

iProphet v5.01

Usage

philosopher iprophet [flags] [files]

Flags

--cat

Specify file listing peptide categories.

--decoy

Specify the decoy tag.

--nonsi

Do not use NSI model.

--nonrs

Do not use NRS model.

--nonsm

Do not use NSM model.

--nonsp

Do not use NSP model.

--sharpnse

Use more discriminating model for NSE in SWATH mode (default: Enabled, use NONSE to disable).

--length

Use Peptide Length model.

--minProb

Specify minimum probability of results to report.

--nonss

Do not use NSS model.

--nofpkm

Do not use FPKM model.

--nonse

Do not use NSE model.

--output

Specify output name (default "iproph.pep.xml").

--threads

Specify threads to use (default 1).

Example

Run iProphet on several files pepXML files using 6 threads.

philosopher iprophet --threads 6 combined_samples_1.pepxml combined_samples_2.pepxml combined_samples_3.pepxml

FAQ

Do I need TPP installed to run this?

No