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,M:15.9949 to localize phosphorylation and oxidation)

--minprob Use specified minimum probability to evaluate peptides

--autodirect use direct evidence when the lability is high, use in combination with LABILITY

--cions use specified C-term ions, separate multiple ions by commas (default: y for CID, z for ETD)

--direct use only direct evidence for evaluating PTM site probabilities

--em set EM models to 0 (no EM), 1 (Intensity EM Model Applied) or 2 (Intensity and Matched Peaks EM Models Applied) (default 2)

--excludemassdiffmax Maximum mass difference excluded for MASSDIFFFMODE analysis (default=0)

--excludemassdiffmin Minimum mass difference excluded for MASSDIFFFMODE analysis (default=0)

--fragppmtol when computing PSM-specific mass_offset and mass_tolerance, use specified default +/- MS2 mz tolerance on fragment ions (default 15)

--ifrags use internal fragments for localization

--keepold Retain old PTMProphet results in the pepXML file

--lability compute Lability of PTMs

--massdiffmode Use the Mass Difference and localize

--massoffset adjust the massdiff by offset

--maxfragz limit maximum fragment charge (default: 0=precursor charge, negative values subtract from precursor charge)

--nions use specified N-term ions, separate multiple ions by commas (default: a,b for CID, c for ETD)

--output Output prefix file name (default "interact")

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

--static use static fragppmtol for all PSMs instead of dynamically estimated offsets and tolerances

--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,M:15.9949 sample.pep.xml

FAQ

Do I need TPP installed for running this ?

No