[spctools-discuss] Spectral library generation

[Srinivas Srikanth]

Hi Phil,

I have a 15 hek files searched with Mascot, X!Tandem and MSGF+ separately. 
I am trying to create a library using TPP pipeline and SpectraST.
I have convert the results individually to pepxml using Mascot2XML, 
Tandem2XML and Idconvert and then apply peptideprophet on each file. My 
question is about the next step,
Should I be merging individual search engine results using iprophet and to 
make three combined files and then merge them again using iprophet?
Or I merge each run from three searches together using iprophet and then 
merge the resulting 15 files together to apply ProteinProphet or Mayu ?


Srikanth

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[spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command

[Phillip Wilmarth]

Hi Javan,
Many (many) years ago Thermo had a command line executable SEQUEST that 
BioWorks called to run SEQUEST. Thermo put it inside hidden folders and 
there were license key issues. You could not copy the EXE to another 
machine and have it run. That scheme may have persisted for some of the 
earliest Proteome Discoverer releases.

I do not think that there is still a SEQUEST.EXE associated with Proteome 
Discoverer. Something made running SEQUEST from the command line break 
(ancient memory cells are recalling something more...). Maybe it was a 
transition to C# from C++ and command line parsing issues. I never could 
get it to work. I gave up trying to run SEQUEST when Comet came out. 

You can get a 60-day demo version of Proteome Discoverer from Thermo. I do 
not know if you can create things like pepxml files from PD so that you 
could post-process the SEQUEST searches with TPP. PD is internally all 
SQLite3 relational database tables (something like 80 of them). It is 
either not a very good design for the database tables or just really hard 
to try and figure out (or both). You can snoop on the SQLite DB with 
various tools, but a proper schema description would be helpful. Table 
names and field names are not real transparent.
Cheers,
Phil


On Monday, June 8, 2020 at 3:51:50 PM UTC-7, Jimmy Eng wrote:
>
> Javan,
>
> You're not going to be able to run SEQUEST through the TPP unless you've 
> purchased the software from Thermo and have it installed on the same 
> computer that's running the TPP.  It doesn't come with the TPP itself.  And 
> support for the SEQUEST pipeline option should probably be removed from the 
> UI unless anyone can confirm that it actually still works.
>
> On Monday, June 8, 2020 at 1:56:45 PM UTC-7, JAVAN OKENDO wrote:
>>
>>
>> I am getting the above mentioned error when running SEQUEST on TPP. I did 
>> install the TPP correctly and when I try to run the program it gives an 
>> error. See the screenshot with the error details
>>
>>
>>
>>
>>
>> [image: Screenshot from 2020-06-08 22-50-26.png]
>>
>>

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[spctools-discuss] Re: C:/TPP/bin/runsearch' is not recognized as an internal or external command

[Jimmy Eng]

Javan,

You're not going to be able to run SEQUEST through the TPP unless you've 
purchased the software from Thermo and have it installed on the same 
computer that's running the TPP.  It doesn't come with the TPP itself.  And 
support for the SEQUEST pipeline option should probably be removed from the 
UI unless anyone can confirm that it actually still works.

On Monday, June 8, 2020 at 1:56:45 PM UTC-7, JAVAN OKENDO wrote:
>
>
> I am getting the above mentioned error when running SEQUEST on TPP. I did 
> install the TPP correctly and when I try to run the program it gives an 
> error. See the screenshot with the error details
>
>
>
>
>
> [image: Screenshot from 2020-06-08 22-50-26.png]
>
>

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[spctools-discuss] Re: Percolator Error in TPP

[Jimmy Eng]

Confirm that you are using Comet's Percolator output which you can generate 
by setting "output_percolatorfile = 1" in the search parameters.  This will 
create a tab-delimited text file with a ".pin" file extension.  Note that 
this is different than Comet's ".txt" output file which is a different 
tab-delimited output file that's not meant for Percolator.

On Monday, June 8, 2020 at 3:22:31 PM UTC-7, Gabrielle H wrote:
>
> Hello, 
>
> I exported a Comet search as a txt file to search with percolator and the 
> percolator has now been "running" for three days. When I try to kill the 
> job, it gives me "Unable to kill command 8760! ()." I'm guessing it's 
> stuck in a loop, but I was wondering what the best way of ending job/fixing 
> the program would be. Thank you for your help. 
>

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Re: [spctools-discuss] Percolator Error in TPP

['Luis Mendoza' via spctools-discuss]

Hello,

Is this running on your local machine?  If so, you can see if Percolator is
still running by either opening the Task Manager (if on Windows) or
executing the "ps" command (in Linux).

Most likely, the command might have timed out due a very long running time,
and the interface (Petunia) is not aware of this.  On the command output
page, you can find a button that overrides the status and marks it as
"finished".

Hope this helps,
--Luis



On Mon, Jun 8, 2020 at 3:22 PM Gabrielle H  wrote:

> Hello,
>
> I exported a Comet search as a txt file to search with percolator and the
> percolator has now been "running" for three days. When I try to kill the
> job, it gives me "Unable to kill command 8760! ()." I'm guessing it's
> stuck in a loop, but I was wondering what the best way of ending job/fixing
> the program would be. Thank you for your help.
>
> --
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> 
> .
>

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[spctools-discuss] Percolator Error in TPP

[Gabrielle H]

Hello, 

I exported a Comet search as a txt file to search with percolator and the 
percolator has now been "running" for three days. When I try to kill the 
job, it gives me "Unable to kill command 8760! ()." I'm guessing it's stuck 
in a loop, but I was wondering what the best way of ending job/fixing the 
program would be. Thank you for your help. 

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