#189 Add support for ECD/ETD spectra to Tide

[William S Noble]

Please see the thread on crux-users@googlegroups.com with subject "Searching ETD spectra with Crux." I think this requires adding to Tide parameters analogous to Comet's use_*_ions parameters. However, it sounds like we need these:

z+H: [M] + OH - NH2 + H + Proton (m/z of singly charged ion, [M]=sum of all neutral residues)
z+2H: [M] + OH - NH2 + H + H + Proton
c: [M] + H + NH2 + Proton
c-H: [M] + NH2 + Proton

The thread contains a pointer to data to test this on.

We might consider also including meta-options (e.g., "use-ecd-ions") that turn on all the necessary ions for a given fragmentation method.

Bill