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.
On Wednesday, 30 September 2020 at 21:30:02 UTC+5:30 Jimmy Eng wrote:
> Your Xeon has 6 physical cpu cores so make sure you set the number of
> X!Tandem threads ("spectrum, threads
> <https://www.thegpm.org/TANDEM/api/st.html>") 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
> <https://academic.oup.com/bioinformatics/article/22/22/2830/196979> 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.
>
> On Tue, Sep 29, 2020 at 10:43 PM vipulb...@gmail.com <vipulb...@gmail.com>
> wrote:
>
>> 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>*
>>
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