Hi David,

Thanks for posting the path to the PTMProphet documentation--was just 
looking for it last night.

After analyzing some data, and when viewing it in the PepXML viewer, what 
is the significance of the colored boxes above the individual residues in 
the PTMPeptide column? Despite the documentation, I've still not figured 
out what they mean.

Best,
-Zack 

On Friday, January 5, 2018 at 9:39:03 AM UTC-8, David Shteynberg wrote:
>
> Hello Paul,
>
> You can get the instructions on using PTMProphet by running the tool on 
> the commandline without any options.  This applies to most of the 
> commandline tools in the TPP.
>
> When you type "*PTMProphetParser" *into the commandline, you'll get the 
> following usage statement:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *PTMProphetParser <OPTIONS> <input_file.pep.xml> 
> [<output_file>]OPTIONS        NOUPDATE        Don't update 
> modification_info tags in pepXML        EM=<number>:    Set EM models to 
> <number> which can be 0, 1 or 2:                        0 -> no 
> EM,                        1 -> Intensity EM Model 
> Applied,                        2 -> Intensity and Matched Peaks EM Models 
> Applied (default=1)        KEEPOLD  Option to retain old PTMProphet results 
> in the pepXML file (off by default).        VERBOSE  Option to produce 
> WARNINGS to help troubleshoot potential PTM shuffling or mass difference 
> issues (off by default).        MZTOL=<number>   Use specified +/- MS2 mz 
> tolerance on site specific ions (default=0.1 dalton).        
> PPMTOL=<number>  Use specified +/- MS1 ppm tolerance on peptides which may 
> have a slight offset depending on search parameters (e.g. iTRAQ4plex) 
> (default=1 ppm).        MINPROB=<number>         Use specified minimum 
> probability to evaluate peptides (default=0).        MASSDIFFMODE     Use 
> the Mass Difference and localize        MASSOFFSET=<number>      Adjust the 
> massdiff by offset <number> (default: 0)        <amino acids, n, or 
> c>:<mass_shift>:<neut_loss1>:...:<neut_lossN>,<amino acids, n, or 
> c>:<mass_shift>:<neut_loss1>:...:<neut_lossN>     Specify modifications 
> (default: 
> STY:79.9663:-97.97690:-115.9880,M:15.9949:-63.998286:-81.024835:-82.008850 
> )*
>
> If you have any issues running the software I would can help you 
> understand them.  Currently we are putting together a publication on 
> PTMProphet, and more documentation will become available when that is 
> accepted.  There is still much to be done in understanding the optimal ways 
> of localizing PTMs.
>
> Thanks for considering the TPP for your proteomics analysis needs.
>
> -David
>
> On Fri, Jan 5, 2018 at 7:29 AM, Paul Abraham <pabrah...@gmail.com 
> <javascript:>> wrote:
>
>> Hello,
>>
>> I am having a difficult time locating documentation for several of the 
>> TPP tools. For example, the PTMProphet tool referenced on the wiki page 
>> does not have any supporting documentation. Am I missing some obscure 
>> landing page somewhere? The only information I find for how to efficiently 
>> utilize this tool is by scouring this forum and this is by no means a good 
>> use of time, considering most posts highlight the issues.
>>
>> Can anyone point to documentation for this tool particularly, but other 
>> TPP tools as well?
>>
>> Regards,
>> Paul
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>

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