PTMProphet

PTM site localization probabilities with PTMProphet

Version

PTMProphet v5.01

Usage

philosopher ptmprophet [flags] [file]

Flags

--mods

Specify modifications to be localized (e.g. STY:79.9663,MW:15.9949 to localize phosphorylation and oxidation)

--keepold

Retain old PTMProphet results in the pepXML file

--massdiffmode

Use the Mass Difference and localize

--minprob

Use specified minimum probability to evaluate peptides

--mztol

Use specified +/- MS2 mz tolerance on site specific ions (default 0.1)

--output

Output prefix file name

--ppmtol

use specified +/- MS1 ppm tolerance on peptides which may have a slight offset depending on search parameters (default 1)

--verbose

produce Warnings to help troubleshoot potential PTM shuffling or mass difference issues

Example

Execute a standard analysis on a pepXML file called sample.pep.xml, localizing phosphorylation and oxidation.

philosopher ptmprophet --mods STY:79.9663,MW:15.9949 sample.pep.xml

FAQ

Do I need TPP installed for running this ?

No