Water loss for b-fragments?

[sgibb]

This is a follow-up issue to #462.

MSnbase::calculateFragments(sequence = "GSDA")

             mz ion type pos z seq
1   58.02874  b1    b   1 1   G
2  145.06077  b2    b   2 1  GS
3  260.08771  b3    b   3 1 GSD
4   90.05495  y1    y   1 1   A
5  205.08189  y2    y   2 1  DA
6  292.11392  y3    y   3 1 SDA
7  227.09005 b3_   b_   3 1 GSD
8  172.08424 y2_   y_   2 1  DA
9   57.05730 y1_   y_   1 1   A
10 259.11627 y3_   y_   3 1 SDA

@mjhelf:

I'm also not sure if it is intentional to not allow losses of water at the C-terminus of b-ions (see b2 ion in the example)?

Based on #47 (comment) we just remove water from Cterm in x, y, z fragments. I am not a (bio)chemist but from the image below I am not sure that C≡O⁺ could lose any water?

@adder @mjhelf @pavel-shliaha: Should we allow water removal on b-fragments?

[mjhelf]

Hi @sgibb ,

looking back I see how my comment is not clear at all.
The loss of water of course comes from the side chains, like that of serine in the example.

What I meant was that in the example, I would expect a b2_ ion, because b2 contains a serine. Generally, it looks like residues that can undergo a loss of water are ignored (for neutral loss calculation) if they are at the C-terminus of a fragment.

Thanks for looking into this!

[sgibb]

Based on this flow chart water loss happens just on internal S:

In my interpretation an internal S means XSX (that's why I used the regular expression .S.). So any fragment with XS is no internal but a Cterm S, or am I wrong (in contrast to Nterm D/E)?

E.g. for ammonia loss there is Nterm K and internal K. So I assumed there are three possible positions: Nterm, internal, Cterm.