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

[Luis Mendoza]

Hi Debojyoti,

Yes, I would say this is the most straightforward way of conducting this search.

Note that you may need to make further adjustments to the variable mod string settings if, say, a given peptide must have *all* of its Cysteines in one state (+50) or the other (+90).  The default is to allow for mixed Cysteines in the peptide, e.g. PEPC[50]TIDEC[90]R.

Hope this helps,

--Luis

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[Debojyoti Pal]

Thanks Luis. I have asked this on the COMET group as well. They will probably come up with an update or something to enable it.

[Luis Mendoza]

This should already be possible with, e.g.

variable_mod02 = 40.000 C 0 3 -1 0 0 0.0

add_C_cysteine = 50.000

(Of course using whatever masses are appropriate.)

Or does this not work?

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[Debojyoti Pal]

I meant that they would come up with something to get it done with only variable modifications. By updating the code. Not by the static + variable workaround we are doing.

Thanks

Debojyoti

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