Help in geneting Sequest and X!Tandem parameter files

[JAVAN OKENDO]

Dear all,

It is my first time to run the SEQUEST and I am wodering how to generate this on TPP? Can someone share a sample parameter file?

[Jimmy Eng]

Javan,

Note that SEQUEST is a commercial product distributed by Thermo and does not come with the TPP.  I'm not even sure if current versions of SEQUEST through Thermo are compatible with the TPP pipeline.  Have you acquired  SEQUEST from Thermo?

On Mon, Apr 13, 2020 at 10:16 AM JAVAN OKENDO <javan...@gmail.com> wrote:

Dear all,

It is my first time to run the SEQUEST and I am wodering how to generate this on TPP? Can someone share a sample parameter file?

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[Javan Okendo]

Jimmy,

I thought I can run it within TPP? I can see it is listed as one of the sequence search engines within the TPP.  I have not contacted the Thermo guys yet.

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[Jimmy Eng]

SEQUEST can run within the TPP (at least that was the case in the early 2000s) but it is not provided with the TPP.  In the old days, you would acquire it as part of Thermo's BioWorks package ($10K+ price for that software suite).  I wouldn't be surprised if new/current versions of this software would not work with the TPP.

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