PTMProphet flags

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Pedro Cardoso

Oct 18, 2021, 11:12:22 AM10/18/21
to spctools-discuss

I am using PTMProphet (v4.0.0) but I can't really understand what some of the optional flags are supposed to do. 
I have went through the publication and its supplementary figures but still can't know for sure what changes when some of the flags are used.
The flags that seem interesting to me are:
--massdiffmode - this should be used with open database searches, correct??

Can you please provide more detailed information of these flags? Or maybe point me to some other documentation other than the published article and the basic description of each flag?

Thank you,

David Shteynberg

Nov 1, 2021, 4:01:24 PM11/1/21
to spctools-discuss
Dear Pedro,

Sorry about the delay in my response to your query.

I am not sure what version of PTMProphet you are using, we are currently on TPP 6.0.0 official release (6.1.0 available as a release candidate.)

Here is some more information about the options you are interested in:

LABILITY         Compute Lability of PTMs

  Compute the "lability" of the PTM, the likelihood that some number PTMs of a given type in the PSM have fallen off the peptide backbone, given the fragment spectrum information.

DIRECT   Use only direct evidence for evaluating PTM site probabilities
   This option forces PTMProphet to use only fragments that retain the PTM and thus constitute "direct" evidence of PTM for site localization
AUTODIRECT       Use direct evidence when the lability is high, use in combination with LABILITY

  This option is used in combination with the LABILITY option, which estimates how "labile" (likely to fall off) is the PTM in the given PSM.  When  the estimated lability is high and AUTODIRECT enabled, PTMProphet will use only direct evidence peaks for PTM site localization.

IFRAGS   Use internal fragments for localization (default: do not use internal fragments)

  This option enables the use of internal fragments for PTM site localization.

EXCLUDEMASSDIFFMIN=<number>      Minimum mass difference excluded for           MASSDIFFFMODE analysis (default=0).

EXCLUDEMASSDIFFMAX=<number>      Maximum mass difference excluded for  MASSDIFFFMODE analysis (default=0).

MASSDIFFMODE     Treat the mass difference between measured and theoretical mass as a modification and localize
  This option enables treatment of the observed mass difference like any other PTM and localizing the mass difference on the peptide backbone, this option is used with EXCLUDEMASSDIFFMIN= and EXCLUDEMASSDIFFMAX= to limit localization of mass differences as defined by the user.

Please write back if you have additional questions or problems with the TPP.  The usage statement for PTMProphetParser (part of the TPP is available when you run PTMProphetParser on the commandline without any inputs.  


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