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PTMProphet
Felipe da Veiga Leprevost edited this page Feb 25, 2019
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PTM site localization
PTMProphet v5.01
philosopher ptmprophet [flags] [file]
--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
Execute a standard analysis on a pepXML file called sample.pepxml.
philosopher proteinprophet sample.pepxml
Do I need TPP installed for running this ?
No