calculateFragments() bug on mz calculation for charge 2 ions when Nterm is modified

[adder]

Hey all,

I think I found a bug in calculateFragments() for the mz calculation for the charge 2 peaks when Nterm is modified.

When I add a Nterm modfication of mass 10 I expect and extra mass of 10 for charge 1 b ions and and an extra mass of 5 for charge 2 b ions. Instead there is also a mass of 10 added to charge 2 b ions.

See example below:

> calculateFragments('A',z = 1:2,modifications = c(),type = 'b')
Modifications used: None
        mz ion type pos z seq
1 72.04439  b1    b   1 1   A
2 36.52583  b1    b   1 2   A
> calculateFragments('A',z = 1:2,modifications = c(Nterm = 10), type = 'b')
Modifications used: Nterm=10
        mz ion type pos z seq
1 82.04439  b1    b   1 1   A
2 46.52583  b1    b   1 2   A

[lgatto]

Thanks for this, @adder. I'll let @sgibb rely, as he's the author of this code and will be able to address it more appropriately.

[sgibb]

@adder you are right. Thanks for reporting. It is fixed in MSnbase 2.1.14.