Are the different Searches you draw different search engines or
different msms runs searched with you search engine?
The general workflow is to combine the runs belonging to each
experiment and searched with one search engine (e.g. X!Tandem)
together with PeptideProphet.
Do this for each search engine you are running and combine the
PeptideProphet files with iProphet. Here is the approach in a
diagram:
Runs 1, 2, ..., n ----> Search 1 -----> PeptideProphet \
|
------> iProphet -----> PTMProphet
----->ProteinProphet
-----> Search 2 -----> PeptideProphet /
...
-----> Search m -----> PeptideProphet /
Cheers,
-David
On Wed, Jun 4, 2014 at 6:46 AM, Chris <[email protected]> wrote:
> Hi everyone,
>
> I'm currently working on about 20 different mass spec runs and am new to
> using the TPP. I saw there are two approaches to using InterProphet. One is:
>
> Search 1->...->InterProphet->downstream analysis
> Search 2->...->InterProphet->downstream analysis
> Search 3->...->InterProphet->downstream analysis
> Search 4->...->InterProphet->downstream analysis
>
> The other is:
>
> Search 1----------
> \
> Search 2----------- InterProphet->downstream analysis
> /
> Search N-----------
>
> Hopefully that little ansi diagram renders in however you are viewing this.
> If not, it's basically showing the different of combining all your analyses
> in a single interprophet run versus interprophet after every analysis. Is
> there any difference to the 2 approaches?
>
> Chris
>
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