The analysis of LC-MS/MS data via search engine and TPP validation tools of PeptideProphet and iProphet produces high quality PSM matches. However, the position of PTMs assigned by the search engine is not always correct and few search engines currently generate PTM localization confidence measures.

PTMProphet is a software tools to compute PTM localization metrics. The input to PTMProphet is a pepXML file, the output is also a pepXML file but containing PTM site probabilities and other statistics described below.


Journal of Proteome Research : Shteynberg D. J. Proteome Res. DOI: 10.1021/acs.jproteome.9b00205


PTMProphet software is written in C++ and is compiled and tested on Windows and Linux. The code is distributed under an open-source LGPL license and is freely available on Sourceforge.


PTMProphet is a standard component of the Trans-Proteomic Pipeline (TPP).


The full usage statement and options can be viewed by simply typing the name of the command on the command-line PTMProphetParser and pressing [Enter].

USAGE: PTMProphetParser <OPTIONS> <input_file.pep.xml> [<output_file>]

        NOUPDATE        Don't update modification_info tags in pepXML
        EM=<number>	Set EM models to <number> which can be 0, 1 or 2:
                        0 -> no EM,
                        1 -> Intensity EM Model Applied Only (default),
                        2 -> Intensity and Matched Peaks EM Models Applied,
			3 -> Matched Peaks EM Model Applied Only
        KEEPOLD  	Option to retain old PTMProphet results in the pepXML file (default: off, old results are overwritten)
        VERBOSE  	Option to produce WARNINGS to help troubleshoot potential PTM shuffling or mass difference issues (default: off)
        MINO=<integer>   	Use specified number of pseudo-counts when computing Oscore (default=1)
	FRAGPPMTOL=<number>	Use specified +/- MS2 mz tolerance on fragment ions (default: estimate from the data)
        PPMTOL=<number>		Use specified +/- MS1 ppm tolerance on peptides which may have a slight offset depending on search parameters (e.g. iTRAQ4plex) (default=1)
        MINPROB=<number>      Use specified minimum probability to evaluate peptides (default=0)
        MAXTHREADS=<number>   Use specified number of threads for processing (0 uses all available processors, negative values are ok, default=1)
        MASSDIFFMODE     Use the Mass Difference and localize
        LABILITY         Compute Lability of PTMs
        DIRECT		Use only direct evidence for evaluating PTM site probabilities
        AUTODIRECT	Use direct evidence when the lability is high, use in combination with LABILITY
        NORMAL	Use Normal distribution to compute P-values (default: use Poisson)
        NIONS=	Use specified N-term ions, separate multiple ions by commas (default: b for CID, c for ETD)
        CIONS=	Use specified C-term ions, separate multiple ions by commas (default: y for CID, z for ETD)
        MASSOFFSET=<number>	Adjust the massdiff by offset <number> (default: 0)
        <amino acids, n, or c>:<mass_shift>:<neut_loss1>:...:<neut_lossN>,<amino acids, n, or c>:<mass_shift>:<neut_loss1>:...:<neut_lossN>
			Specify modifications (default: STY:79.9663,MW:15.9949 )

Note: depending on your local system set-up, you may need to adjust environment variable $PATH to include the directory where PTMProphetParser is installed on your system.


Last update: 18 October 2018, David Shteynberg