Re: [spctools-discuss] Index mzXML file error

[Luis Mendoza]

Hello Pavel,

This is happening because the index of file 1.mzXML is valid and thus a new
file is not created.  If the index is incorrect or missing, then a new file
is created.

We will update the user interface to make this more clear and avoid giving
the impression of an error.

Thanks for the report,
--Luis


On Sat, Mar 17, 2018 at 9:12 AM, Pavel  wrote:

> Hi,
> I try to re-index some mzXML files (SWATH wiff files converted to mzML
> with AB Sciex convertor and then using MSConvert for mzML to mzXML
> conversion) with TPP, but the new files are not created. The error below
> still occurs. Any idea? Thanks
>
> COMMAND 1 [SAT MAR 17 16:42:17 2018]
> EXECUTING: C:/TPP/bin/indexmzXML d:/TPP/data/1.mzXML
>  indexmzXML
>
>  Analyzing:  d:/TPP/data/1.mzXML
>  Validate index: d:/TPP/data/1.mzXML
>
> Command Successful
>
> RETURN CODE:0
>   COMMAND 2 [SAT MAR 17 16:42:22 2018]
> EXECUTING: mv -v d:/TPP/data/1.mzXML d:/TPP/data/1.old_index.mzXML
> d:/TPP/data/1.mzXML -> d:/TPP/data/1.old_index.mzXML
>
> Command Successful
>
> RETURN CODE:0
>   COMMAND 3 [SAT MAR 17 16:42:22 2018]
> EXECUTING: mv -v d:/TPP/data/1.mzXML.new d:/TPP/data/1.mzXML
> mv: d:/TPP/data/1.mzXML.new: No such file or directory
>
> Command FAILED
> RETURN CODE:256
>
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[spctools-discuss] TPP for large databases/ metaproteomics

[Andreas Otto]

Dear all,

We are currently trying to set up the TPP for large databases (>4GB) and
would like to know if there is anyone who could propose the best setup for
the software? Is there any way of allocating kernels/ memory to the TPP to
let it run faster?

I appreciate your help!

best

Andreas

 

 

Dr. Andreas Otto

Institute for Microbiology

Department of Microbial Proteomics

Ernst-Moritz-Arndt-University Greifswald

F.- Hausdorff-Str. 8

17489 Greifswald

 

phone: +49 3834 420 5920

fax:+49 3834 420 5902

 

 

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[spctools-discuss] TPP for large databases/ metaproteomics

[Dr. Andreas Otto]

Dear all,

We are currently trying to set up the TPP for large databases (>4GB) and
would like to know if there is anyone who could propose the best setup for
the software? Is there any way of allocating kernels/ memory to the TPP to
let it run faster?

I appreciate your help!

best

Andreas

 

 

Dr. Andreas Otto

Institute for Microbiology

Department of Microbial Proteomics

Ernst-Moritz-Arndt-University Greifswald

F.- Hausdorff-Str. 8

17489 Greifswald

 

phone: +49 3834 420 5920

fax:+49 3834 420 5902

 

 

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Re: [spctools-discuss] Exporting Proteome Discoverer 2.2 results to TPP

[David Shteynberg]

Hello Joseph,

There is no support for the ProteomeDiscoverer pepXML file in the TPP.  But
the TPP comes with the open-source and free comet search engine, which
should be comparable to sequest.  However, if you are able to post your
pepXML file I may be able to change the code to implement support in the
TPP.  If you are interested,  please post your  mzML (or raw) file,
database, sequest parameters and pepXML somewhere on the cloud so I can
grab them and use for a test case.

Cheers,
-David

On Mar 14, 2018 6:37 PM, "Joseph Gillen"  wrote:

> Hello,
>
> I recently discovered TPP and have been trying to analyze my recent data
> from Proteome Discoverer 2.2 with PeptideProphet and every time I try to
> analyze the .pep.xml file that Proteome Discoverer exports I get the error
> below.  I've downloaded the tutorial set and that worked fine and if I
> convert my RAW file to a mzXML and process it with Tandem then I can
> analyze the .tandem.pep.xml file with PeptideProphet.  Basically do I need
> to reanalyze all my RAW files with Tandem or is it possible to export my
> Sequest result to TPP?
>
> Thank you,
> Joseph Gillen
>
> C:/TPP/bin/xinteract (TPP v5.1.0 Syzygy, Build 201711031215-7670 
> (Windows_NT-x86_64))
>  PPM mode in Accurate Mass Model ...
> running: "C:/TPP/bin/InteractParser 
> "/tmp/a06048/demo/tandem/interact.pep.xml" "171120_JG_4B_1.pep.xml" -L"7"" 
> file 1: 171120_JG_4B_1.pep.xml
>
> command "C:/TPP/bin/InteractParser "/tmp/a06048/demo/tandem/interact.pep.xml" 
> "171120_JG_4B_1.pep.xml" -L"7"" failed: Unknown error
>
> command "C:/TPP/bin/InteractParser "/tmp/a06048/demo/tandem/interact.pep.xml" 
> "171120_JG_4B_1.pep.xml" -L"7"" exited with non-zero exit code: -1073741819
> QUIT - the job is incomplete
>
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