X!Tandem- Help please

[vipulb...@gmail.com]

Hello,

I am a novice using  TPP v5.2.0 Flammagenitus on  a workstation (Intel, Xeon, E5-2630 ver.5, 32Gb RAM, win 10). I have successfully run Comet, however, the X!Tandem search is still on , its been more than 56 hours. How much time does it take to complete the search?

What is the issue with the search? Please help.

 

The params file is: 

<?xml version="1.0" encoding="UTF-8"?>

-<bioml>

<note label="list path, default parameters" type="input">D:/TPP/data/params/isb_default_input_kscore.xml</note>

<note label="spectrum, path" type="input">full_mzXML_filepath</note>

<note label="output, path" type="input">full_tandem_output_path</note>

<note label="output, log path" type="input"/>

<note label="output, sequence path" type="input"/>

<note label="list path, taxonomy information" type="input">D:/TPP/data/params/taxonomy.xml</note>

<note label="protein, taxon" type="input">protein_database</note>

<note label="spectrum, parent monoisotopic mass error minus" type="input">2.0</note>

<note label="spectrum, parent monoisotopic mass error plus" type="input">4.0</note>

<note label="spectrum, parent monoisotopic mass error units" type="input">Daltons</note>

<note label="spectrum, parent monoisotopic mass isotope error" type="input">no</note>

<note label="residue, modification mass" type="input">57.021464@C</note>

<note label="residue, potential modification mass" type="input">15.994915@M</note>

<note label="residue, potential modification motif" type="input"/>

<note label="protein, N-terminal residue modification mass" type="input"/>

<note label="protein, C-terminal residue modification mass" type="input"/>

<note label="protein, cleavage semi" type="input">yes</note>

<note label="scoring, maximum missed cleavage sites" type="input">2</note>

<note label="refine" type="input">no</note>

<note label="refine, maximum valid expectation value" type="input">0.1</note>

<note label="refine, modification mass" type="input">57.012@C</note>

<note label="refine, potential modification mass" type="input">15.994915@M</note>

<note label="refine, potential modification motif" type="input"/>

<note label="refine, cleavage semi" type="input">yes</note>

<note label="refine, unanticipated cleavage" type="input">no</note>

<note label="refine, potential N-terminus modifications" type="input"/>

<note label="refine, potential C-terminus modifications" type="input"/>

<note label="refine, point mutations" type="input">no</note>

<note label="refine, use potential modifications for full refinement" type="input">no</note>

</bioml>

[Robert Winkler]

Hi, congratulations for using TPP!

From my experience, comet is much more performant, I only would use
X!Tandem if you need special features of it.

Best, Robert

Excerpts from vipulb...@gmail.com's message of 2020-09-29 22:43:24 -0700:

> Hello,
>
> I am a novice using TPP v5.2.0 Flammagenitus on a workstation (Intel,
> Xeon, E5-2630 ver.5, 32Gb RAM, win 10). I have successfully run Comet,
> however, the X!Tandem search is still on , its been more than 56 hours. How
> much time does it take to complete the search?
> What is the issue with the search? Please help.
>
>

> *The params file is: *
> *<?xml version="1.0" encoding="UTF-8"?>*
>
> *-<bioml>*
>
> *<note label="list path, default parameters"
> type="input">D:/TPP/data/params/isb_default_input_kscore.xml</note>*
>
> *<note label="spectrum, path" type="input">full_mzXML_filepath</note>*
>
> *<note label="output, path" type="input">full_tandem_output_path</note>*
>
> *<note label="output, log path" type="input"/>*
>
> *<note label="output, sequence path" type="input"/>*
>
> *<note label="list path, taxonomy information"
> type="input">D:/TPP/data/params/taxonomy.xml</note>*
>
> *<note label="protein, taxon" type="input">protein_database</note>*
>
> *<note label="spectrum, parent monoisotopic mass error minus"
> type="input">2.0</note>*
>
> *<note label="spectrum, parent monoisotopic mass error plus"
> type="input">4.0</note>*
>
> *<note label="spectrum, parent monoisotopic mass error units"
> type="input">Daltons</note>*
>
> *<note label="spectrum, parent monoisotopic mass isotope error"
> type="input">no</note>*
>
> *<note label="residue, modification mass" type="input">57.021464@C</note>*
>
> *<note label="residue, potential modification mass"
> type="input">15.994915@M</note>*
>
> *<note label="residue, potential modification motif" type="input"/>*
>
> *<note label="protein, N-terminal residue modification mass" type="input"/>*
>
> *<note label="protein, C-terminal residue modification mass" type="input"/>*
>
> *<note label="protein, cleavage semi" type="input">yes</note>*
>
> *<note label="scoring, maximum missed cleavage sites" type="input">2</note>*
>
> *<note label="refine" type="input">no</note>*
>
> *<note label="refine, maximum valid expectation value"
> type="input">0.1</note>*
>
> *<note label="refine, modification mass" type="input">57.012@C</note>*
>
> *<note label="refine, potential modification mass"
> type="input">15.994915@M</note>*
>
> *<note label="refine, potential modification motif" type="input"/>*
>
> *<note label="refine, cleavage semi" type="input">yes</note>*
>
> *<note label="refine, unanticipated cleavage" type="input">no</note>*
>
> *<note label="refine, potential N-terminus modifications" type="input"/>*
>
> *<note label="refine, potential C-terminus modifications" type="input"/>*
>
> *<note label="refine, point mutations" type="input">no</note>*
>
> *<note label="refine, use potential modifications for full refinement"
> type="input">no</note>*
>
> *</bioml>*
>

[Jimmy Eng]

Your Xeon has 6 physical cpu cores so make sure you set the number of X!Tandem threads ("spectrum, threads") to "6" to make use of all of them as it looks like the default is "1".

   <note label="spectrum, threads" type="input">6</note>

I'd also confirm that you are intending to perform a semi-tryptic search ("protein, semi cleavage" set to "yes"); if not, set that parameter to "no".  And on a semi-related note, the default parameter set you chose is the "isb_default_input_kscore.xml".   If you are looking for a more complementary search engine, you should use the native X!Tandem score function by specifying "isb_default_input_native.xml" for the default parameters as below.  The K-score is a pluggable score function that we implemented in X!Tandem that mimics (but is not exactly the same as) the cross-correlation score that is used in SEQUEST and Comet.

   <note label="list path, default parameters" type="input">D:/TPP/data/params/isb_default_input_native.xml</note>

Good luck.

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[vipulb...@gmail.com]

Hello Robert, 

Thanks for replying. Can you please clarify what you mean by special features of X!Tandem? I was using it hoping that I will be able to identify more proteins in my sample after combing the search from Comet and  X!Tandem . Am I correct? 

[vipulb...@gmail.com]

Hello Jimmy, 

Thanks for replying. Firstly, I am not sure about semi-tryptic search so I will set it to "no". Secondly, whenever I chose "tandem.params" file it automatically picks up the  "isb_default_input_kscore.xml" rather than "isb_default_input_native.xml"  as the default parameter. I do not know how I can change that. 

[Robert Winkler]

Hi, e.g. I used X!Tandem in the past when searching for point mutations
in proteins. For most tasks, I would use Comet, because it is easy to
set-up and extremely fast.

Excerpts from vipulb...@gmail.com's message of 2020-10-01 22:46:58 -0700: