Variable mod query in COMET

[Debojyoti Pal]

Hello everyone

I have a specific scenario where I want to search for peptide in which cysteine must either have +50 or +90 mod. Basically:

1) Cys can only have one of +50 or +90

2) Cys much have one of +50 or +90 (ie It cannot be unmodified)

Only way I can achieve this is to put a static mod of +50 and variable mod of +40 (40+50 = +90). Is there any better way to do this.

Regards

Debojyoti

[Jimmy Eng]

Hi  Debojyoti.

Another option for you is to use two variable mods as shown below.  With the addition of the "require_variable_mod = 1" parameter, that forces Comet to only analyze peptides that contain a variable modification.  Does this sound like what you're attempting to accomplish?

variable_mod01 = 50.0 M 0 3 -1 0 0 0.0

variable_mod02 = 90.0 M 0 3 -1 0 0 0.0

require_variable_mod = 1

However, I don't know that this is any better (or worse) than the search you proposed of a combination of static +50 and variable +40.  The search space for the two searches is slightly different but hopefully the confident identifications are similar.

[Debojyoti Pal]

Hi Jimmy

Yes, I had considered this option. However, this also forces any other variable modification I use, suppose for other amino acids. What if I don't want to force other variable modifications. 

Regards

Debojyoti

[Jimmy Eng]

I've implemented options to force the inclusion of any specific variable modification or force the analyzed peptide to contain at least one variable mod.  But there's no mechanism to force a peptide to include a modification from a subset of two or more mods from all variable mods specified.

If you let me know which binary (Windows, Linux?) and which version of Comet you prefer using, I'll add that functionality for you via some extension of the "require_variable_mod" parameter.  It might take me a day or two to get to it.

Jimmy

[Debojyoti Pal]

Hi Jimmy

That would be great. I am using the COMET that came with TPP 6.3.2.

Thank you

Debojyoti

[Debojyoti Pal]

I am on windows