#108 Include fragment ions > +2 in theoretical spectra

[William S Noble]

For a peptide ion of charge n+, the theoretical spectrum should contain peaks of charge 1 through (n-1)+.

[Jeff Howbert]

For this change to have the full desired benefit on performance, it will be necessary to also address the fixed binOffset in Tide. Currently Tide binOffset = 0.5, which is definitely not optimal for charge > 2+ precursors.

[William S Noble]

This is the same as Issue #69