Re: [spctools-discuss] Navigating peptideSieve Tips/Tricks?

['David Shteynberg' via spctools-discuss]

Sure!  This was my command:

[image: image.png]


On Tue, Aug 1, 2023 at 10:48 AM sophie culos  wrote:

> David, would you be at all willing to post the code that you were using?
> I'll give "/" a shot in my path definitions.
>
>
>
> On Tuesday, August 1, 2023 at 10:35:06 AM UTC-7 David Shteynberg wrote:
>
>> For what it is worth, yesterday I downloaded the PeptideSieve and ran it
>> on my system commandline to generate non-empty output files successfully.
>> I used '/' in my path definitions, but I am not sure it that makes a
>> difference.  Good luck!
>>
>> On Tue, Aug 1, 2023 at 1:21 AM 'Luis Mendoza' via spctools-discuss <
>> spctools...@googlegroups.com> wrote:
>>
>>> Hello Sophie,
>>> I don't have much help to offer at this point, since we have not used
>>> that software in a very long time.  But one thing I notice from your
>>> screenshots is that the folder/directory name appears to have a space in
>>> "MS User", which is not present in the commands, e.g.
>>> "C:\Users\msuser\TPP\...".  Perhaps this is causing the errors you observe?
>>> Cheers,
>>> --Luis
>>>
>>> On Mon, Jul 31, 2023 at 4:54 PM sophie culos  wrote:
>>>
 Hello,

 I am trying to use peptideSieve for an in silico digestion to identify
 proteotypic peptides for MALDI.

 I've attached a screenshot of what I've been inputting into the command
 line and the error I've been consistently getting. The output file is
 always blank,  and I'm not sure how to proceed.

 Any help would be very much appreciated!

 Cheers,
 Sophie
 [image: peptideSieve error.PNG]



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Re: [spctools-discuss] Navigating peptideSieve Tips/Tricks?

[sophie culos]

David, would you be at all willing to post the code that you were using? 
I'll give "/" a shot in my path definitions. 



On Tuesday, August 1, 2023 at 10:35:06 AM UTC-7 David Shteynberg wrote:

> For what it is worth, yesterday I downloaded the PeptideSieve and ran it 
> on my system commandline to generate non-empty output files successfully.  
> I used '/' in my path definitions, but I am not sure it that makes a 
> difference.  Good luck!
>
> On Tue, Aug 1, 2023 at 1:21 AM 'Luis Mendoza' via spctools-discuss <
> spctools...@googlegroups.com> wrote:
>
>> Hello Sophie,
>> I don't have much help to offer at this point, since we have not used 
>> that software in a very long time.  But one thing I notice from your 
>> screenshots is that the folder/directory name appears to have a space in 
>> "MS User", which is not present in the commands, e.g. 
>> "C:\Users\msuser\TPP\...".  Perhaps this is causing the errors you observe?
>> Cheers,
>> --Luis
>>
>> On Mon, Jul 31, 2023 at 4:54 PM sophie culos  wrote:
>>
>>> Hello,
>>>
>>> I am trying to use peptideSieve for an in silico digestion to identify 
>>> proteotypic peptides for MALDI. 
>>>
>>> I've attached a screenshot of what I've been inputting into the command 
>>> line and the error I've been consistently getting. The output file is 
>>> always blank,  and I'm not sure how to proceed. 
>>>
>>> Any help would be very much appreciated! 
>>>
>>> Cheers,
>>> Sophie 
>>> [image: peptideSieve error.PNG]
>>>
>>>
>>>
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>>>  
>>> 
>>> .
>>>
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>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Problem with PeptideProphet

['Luis Mendoza' via spctools-discuss]

Hello Tanmay,
How did you generate the input pepXML files?  Which search engine did you
use?  Are you able to open both of those files and verify that they have
results?
Can you process results from another search engine (e.g. Comet or X!Tandem)
of the same mzML data?
Cheers,
--Luis

On Wed, Jul 26, 2023 at 8:01 AM Tanmay Singh  wrote:

> Dear all
> I keep trying to run PeptideProphet on two * pep.xml files but keep
> getting this error. What could the issue be and how can I solve it?
>
> Error
> C:/TPP/bin/xinteract (TPP v6.3.2 Arcus, Build 202305092202-8951
> (Windows_NT-x86_64)) using MAXTHREADS=1 for PeptideProphet... running:
> "C:/TPP/bin/InteractParser "interact.pep.xml"
> "OR20080317_S_SILAC-LH_1-1_01.pep.xml"
> "OR20080320_S_SILAC-LH_1-1_11.pep.xml" -L"7"" file 1:
> OR20080317_S_SILAC-LH_1-1_01.pep.xml file 2:
> OR20080320_S_SILAC-LH_1-1_11.pep.xml processed altogether 17620 results
> command "C:/TPP/bin/InteractParser "interact.pep.xml"
> "OR20080317_S_SILAC-LH_1-1_01.pep.xml"
> "OR20080320_S_SILAC-LH_1-1_11.pep.xml" -L"7"" failed: Unknown error
> command "C:/TPP/bin/InteractParser "interact.pep.xml"
> "OR20080317_S_SILAC-LH_1-1_01.pep.xml"
> "OR20080320_S_SILAC-LH_1-1_11.pep.xml" -L"7"" exited with non-zero exit
> code: -1073741819 QUIT - the job is incomplete
>
> Any help would be appreciated
>
> Many thanks
> Tanmay
>
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Re: [spctools-discuss] converting prot.xml to tsv/something else

['Luis Mendoza' via spctools-discuss]

Hi Emma,
The ProtXMLViewer is under the cgi-bin/ directory of the image.  However,
the version in 6.2.0 does not have the command-line capability of exporting
protXML to TSV.  We introduced this feature in 6.3.0, and will be available
once we produce the related image.  (well, after fixing some bugs and
releasing 6.3.3, soon).

Do note that if using the viewer interactively, you can export to TSV via
the File & Info tab of ProtXMLViewer.

We can gladly help convert a few files for you if you are able to share
those; just contact me directly if so.

Thanks,
--Luis


On Wed, Jul 26, 2023 at 2:52 AM Emma Whittington  wrote:

> Hi,
>
> I am running TPP 6.2.0 via a singularity image. I have been using the
> EXCELXX option in ProteinProphet to a tab-separated file. However, that is
> for some reason not working at the moment (tried today and yesterday). I
> tried to also use ProtXMLViewer.pl but it doesn't seem to exist in the
> singularity image. How else can I convert the prot.xml files?
>
> Thank you!
>
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