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
www.tppms.org) is available when you run PTMProphetParser on the
commandline without any inputs.
Cheers,
-David
On Mon, Oct 18, 2021 at 8:12 AM Pedro Cardoso <pedro.e.m.card...@gmail.com>
wrote:
> Hi,
>
> 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:
> --direct
> --autodirect
> --ifrags
> --lability
> --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,
> Pedro
>
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