Additional var mods added?

[Roger Olivella]

Hello!

I've seen in the doc, here: 

https://comet-ms.sourceforge.net/parameters/parameters_202101/variable_mod01.php

That there're two mods that I dont' clearly see where they belong: 

variable_mod08 =  0.0 X 0 3 -1 0 0 0.0
variable_mod09 =  0.0 X 0 3 -1 0 0 0.0

I'm also using CometAdpater from OpenMS and the params file created on the fly also adds sysematically a number of variable modifications up to 9, like this example:

variable_mod01 = 15.9949 M 0 3 -1 0 0 0.0
variable_mod02 = 0.0 X 0 3 -1 0 0 0.0
variable_mod03 = 0.0 X 0 3 -1 0 0 0.0
variable_mod04 = 0.0 X 0 3 -1 0 0 0.0
variable_mod05 = 0.0 X 0 3 -1 0 0 0.0
variable_mod06 = 0.0 X 0 3 -1 0 0 0.0
variable_mod07 = 0.0 X 0 3 -1 0 0 0.0
variable_mod08 = 0.0 X 0 3 -1 0 0 0.0
variable_mod09 = 0.0 X 0 3 -1 0 0 0.0

So the variable_mod01 is defined by me, but from 02 to 09? Are this mods affecting the search performance? thanks!

Roger

[Jimmy Eng]

Roger,

The first parameter entry for the variable_mod0X parameters is the modification mass difference.  If that modification mass difference is set to "0.0" then that variable modification parameter is not used/applied.  So in your OpenMS example list of modifications, that search would only analyze oxidize methionine (15.9949 on M) as the sole variable modification.  The rest of the variable modification parameters in the list have a "0.0" modification mass and are ignored/unused.  If this doesn't answer your question, follow-up here.

Jimmy