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Documentation of the <pipeline prophet> options

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Documentation of the <pipeline prophet> options edwin.lowe  2010-10-14 21:25
Status: Closed
 
I've been trying to find some documentation on setting the different peptide prophet options. Unfortunately the help section on the web site only shows up setting the min probability value. However in the forum a reply noted thaty accurate mass binning is also supported.

Is there somewhere where all the pipeline prophet commands are documented? I'm particularly interested in doing decoy database searchs and would like to define what the decoy is annotaed as.

Edwin
 
 
jeckels responded:  2010-10-18 18:08
Hi Edwin,

I just added a number of additional parameters to the documentation page:

https://www.labkey.org/wiki/home/Documentation/page.view?name=pipelineParams

You're most likely interested in the "pipeline prophet, decoy tag" option.

Thanks,
Josh
 
edwin.lowe responded:  2010-10-18 19:15
Thank you very much. Yes it's exactly what i was after!
 
markeys responded:  2011-01-05 09:03
Where within CPAS do we access and modify these settings? We are having difficulty locating 'pipeline prophet'.
 
Brian Connolly responded:  2011-01-05 09:38
You can specify these options when select/create the search protocol for your search. See https://www.labkey.org/wiki/home/Documentation/page.view?name=pipelineSearch for more information.

See "Search Engine Parameter Format" to understand the format you will need to use when specifying these paramters.

-Brian
 
markeys responded:  2011-01-05 13:29
Thank you - adding the lines:
  <note label="pipeline prophet, decoy tag" type="input">###REV###</note>
    <note label="pipeline prophet, accurate mass" type="input">yes</note>

resolved our problems with some Orbitrap runs being identified as Errors when they contain valid peptides. They now are processed smoothly through the TPP when we are using a reverse concatenated database.