I'll show you my logic then just in case it is in an actual functioning bit
of code:
>From xinteract (which TPP launches to handle everything it seems):
-i[iProphet options] [run iProphet on the PeptideProphet
result]
iProphet options [following the 'i']:
....
-M[PTMProphet options] [run PTMProphet on the iProphet
result]
PTMProphet options [following the 'M' (e.g. -M-STY,79.9663-MZTOL=0.4)]:
-{<amino acids, n, or c>,<mass_shift>,...} [specify mod
masses (e.g. -STY,79.9663,K,114.0429,M,15.9949)]
-MZTOL=<number> [Use specified
+/- mz tolerance on site specific ions (default=0.1 dalton)]
-NOUPDATE [Don't
update modification_info tags in pepXML]
which indicated to me the workflow is:
Pep Proph->iProph->PTMProphet
The code from PTMProphet which makes me believe it needs incorrect hits:
PTMProphet.cxx - line 216 comments on using decoys for the null
distribution, and is referenced in the for loop for line 391 and onward.
As a reference I'm using Polar Vortex
On Wednesday, June 4, 2014 1:30:18 PM UTC-4, David Shteynberg wrote:
>
> Chris,
>
> You must be looking at a non-functioning section of the code. PTMProphet
> relies only on the MS/MS spectrum information to determine the PTM site
> scores. PTMProphet assumes the identification is the correct peptide and
> attempts to find the most likely sites for the PTMs. It will work on any
> pepXML input file if run on the commandline, so either way of using the
> tool is fine.
>
> Cheers,
> -David
>
>
> On Wed, Jun 4, 2014 at 6:42 AM, Chris <[email protected] <javascript:>>
> wrote:
>
>> Hi everyone,
>>
>> I'm a bit confused about the workflow for finding PTMs. At first glance
>> and seeing the code for xinteract, it seems it should be:
>>
>> Search->PeptideProphet->InterProphet (apply 1% FDR)->PTMProphet
>>
>> However, looking at the code for PTMProphet, it uses the decoy hits to
>> build its null distribution. So my intuition says the following workflow
>> would be correct:
>>
>> Search->PeptideProphet->PTMProphet->InterProphet (apply 1% FDR)
>>
>> Because we want to have the false hits to build the null distribution in
>> PTMProphet.
>>
>> Can anyone clarify these points?
>>
>> Thank you,
>> Chris
>>
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