Comet parameters

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Anju Nagpal

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Jul 25, 2022, 10:40:20 AM7/25/22
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Hi,
Why is a default value of 57.021464 is added for cysteine in comet parameter?

Eric Deutsch

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Jul 25, 2022, 10:56:37 AM7/25/22
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Since Cys is almost always alkylated with iodoacetamide in most experiments:

 

http://www.unimod.org/modifications_view.php?editid1=4

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Anju Nagpal

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Jul 26, 2022, 1:12:11 AM7/26/22
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What if my experiment does not include any alkylation step?
Do I need to change it to 0?

Eric Deutsch

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Jul 26, 2022, 1:31:42 AM7/26/22
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Correct, if you did not use iodoacetamide, then change it to 0.0

Anju Nagpal

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Jul 26, 2022, 1:33:20 AM7/26/22
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Can i get the parameter list for Tandem search?

With regards
Anju Nagpal
PhD Scholar
Animal Biotechnology Centre
National Dairy Research Institute, Karnal
   

Eric Deutsch

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Jul 26, 2022, 12:30:42 PM7/26/22
to spctools...@googlegroups.com, Eric Deutsch

I’m not certain I understand your question. If you’re looking for a template X!Tandem params file, there should be one in your installation in the data/params folder. There should be a tandem_params.xml? In the same folder as the template comet.params? Do you have that?

 

Eric

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