[spctools-discuss] Re: Software documentation issue

[Paul Abraham]

I accidentally posted this twice. Topic has been addressed in earlier post.

On Friday, January 5, 2018 at 1:44:54 PM UTC-5, Paul Abraham wrote:
>
> Hello,
>
> It seems that the wiki page has very limited information on how to most 
> efficiently use the TPP tools. For example, the tool PTMProphet is listed 
> as a tool yet doesn't have any documentation. It is quite frustrating when 
> you have to mine google group forums to identify what didn't work for 
> people in order to identify would should be okay parameters. 
>
> Am I missing some obscure landing page?
>
> --
> Paul
>

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Re: [spctools-discuss] TPP documentation issue

[Hampton, Brian]

Hello Paul,

The quickest way to greater understanding on the use of the tools is to execute 
the binaries in question at the command line with no options specified.  The 
output will show information about their usage.  For example on my old Linux 
install of TPP 4.8, at the command line, I change directory to the …/tpp/bin 
directory and type in e.g. ./xinteract.  There is quite a bit of usage 
information output for xinteract since it is a wrapper for many of the binaries 
to execute them in succession to form the pipeline.  If you page down (in my 
version) after running the xinteract command there is this output which 
references PTMProphet:

PTMProphet options [run PTMProphet on the iProphet result with options that 
follow the '-M' (e.g. -M-STY,79.9663-MZTOL=0.4)]:
 -{,,...}  [specify mod 
masses (e.g. -STY,79.9663,K,114.0429,M,15.9949)]
 -MZTOL= [Use specified +/- 
mz tolerance on site specific ions (default=0.1 dalton)]
 -NOUPDATE   [Don't update 
modification_info tags in pepXML]



Also running the binaries at the command line can sometimes aid in 
troubleshooting since they tend to output more information about what is going 
on than is displayed via the GUI web interface.

Aside from this, you can also look up the published papers on many of the 
tools, attend the periodic TPP training courses, and ask questions to this 
forum.  I am personally not aware of any tutorials for PTMProphet or most of 
the other tools for that matter.

It would be a wonderful thing were the TPP developer team to provide tutorials 
(online not just the courses which you must attend in person) that cover the 
breadth and depth of the TPP toolset much like what the developers of Skyline 
and Maxquant have done. This would enable many more people to learn and use the 
TPP tools at their own pace, in their own environment.   I think that would 
markedly increase TPP usage around the world.

Cheers,

Brian


On Jan 5, 2018, at 10:29 AM, Paul Abraham 
> 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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Re: [spctools-discuss] TPP documentation issue

[David Shteynberg]

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  
[]OPTIONSNOUPDATEDon't update
modification_info tags in pepXMLEM=:Set EM models to
 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=   Use specified +/- MS2 mz
tolerance on site specific ions (default=0.1 dalton).
PPMTOL=  Use specified +/- MS1 ppm tolerance on peptides which may
have a slight offset depending on search parameters (e.g. iTRAQ4plex)
(default=1 ppm).MINPROB= Use specified minimum
probability to evaluate peptides (default=0).MASSDIFFMODE Use
the Mass Difference and localizeMASSOFFSET=  Adjust the
massdiff by offset  (default: 0):::...:,:::...: 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  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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> For more options, visit https://groups.google.com/d/optout.
>

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Re: [spctools-discuss] TPP documentation issue

[Paul Abraham]

Brian and David,

Thank you for chiming in. Yes, I am aware of the "--help" option that is 
available. I was hoping to get a better understanding of PTMprophet in 
particular, so thank you for highlighting the upcoming publication. In 
regards to PTMProphet, I'd like to use this in conjunction with MSFragger 
open-search specifically. Can localization be done for the collection of 
mods (mass shifts) identified by MSFragger or is PTMProphet limited to a 
pre-defined mass shift list, in which the modifications have to be 
specified upfront.

I should note that I am using the Philosopher software and using PTMProphet 
in between PeptideProphet and ProteinProphet.

Thanks,
Paul

On Friday, January 5, 2018 at 12:39:03 PM UTC-5, 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   
> []OPTIONSNOUPDATEDon't update 
> modification_info tags in pepXMLEM=:Set EM models to 
>  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=   Use specified +/- MS2 mz 
> tolerance on site specific ions (default=0.1 dalton).
> PPMTOL=  Use specified +/- MS1 ppm tolerance on peptides which may 
> have a slight offset depending on search parameters (e.g. iTRAQ4plex) 
> (default=1 ppm).MINPROB= Use specified minimum 
> probability to evaluate peptides (default=0).MASSDIFFMODE Use 
> the Mass Difference and localizeMASSOFFSET=  Adjust the 
> massdiff by offset  (default: 0) c>:::...:, c>:::...: 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  > 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
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to spctools-discu...@googlegroups.com .
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>> .
>> Visit this group at https://groups.google.com/group/spctools-discuss.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>

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Re: [spctools-discuss] TPP documentation issue

[David Shteynberg]

Hello Zack,

Each evaluated modification site gets a PTMProphet calculated probability
of the modification being at that site.  If you mouse over the bar you will
get the value of the probability.  You can export the results to xls file
and the ptm_peptide column will show the values next to the evaluated site
in parenthesis.

Cheers,
-David

On Fri, Jan 5, 2018 at 4:46 PM, Zack Potter  wrote:

> 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  
>> []OPTIONSNOUPDATEDon't update
>> modification_info tags in pepXMLEM=:Set EM models to
>>  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=   Use specified +/- MS2 mz
>> tolerance on site specific ions (default=0.1 dalton).
>> PPMTOL=  Use specified +/- MS1 ppm tolerance on peptides which may
>> have a slight offset depending on search parameters (e.g. iTRAQ4plex)
>> (default=1 ppm).MINPROB= Use specified minimum
>> probability to evaluate peptides (default=0).MASSDIFFMODE Use
>> the Mass Difference and localizeMASSOFFSET=  Adjust the
>> massdiff by offset  (default: 0)> c>:::...:,> c>:::...: 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  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
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "spctools-discuss" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to spctools-discu...@googlegroups.com.
>>> To post to this group, send email to spctools...@googlegroups.com.
>>> Visit this group at https://groups.google.com/group/spctools-discuss.
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
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Re: [spctools-discuss] TPP documentation issue

[Zack Potter]

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   
> []OPTIONSNOUPDATEDon't update 
> modification_info tags in pepXMLEM=:Set EM models to 
>  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=   Use specified +/- MS2 mz 
> tolerance on site specific ions (default=0.1 dalton).
> PPMTOL=  Use specified +/- MS1 ppm tolerance on peptides which may 
> have a slight offset depending on search parameters (e.g. iTRAQ4plex) 
> (default=1 ppm).MINPROB= Use specified minimum 
> probability to evaluate peptides (default=0).MASSDIFFMODE Use 
> the Mass Difference and localizeMASSOFFSET=  Adjust the 
> massdiff by offset  (default: 0) c>:::...:, c>:::...: 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  > 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
>> -- 
>> You received this message because you are subscribed to the Google Groups 
>> "spctools-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to spctools-discu...@googlegroups.com .
>> To post to this group, send email to spctools...@googlegroups.com 
>> .
>> Visit this group at https://groups.google.com/group/spctools-discuss.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>

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