Patterns of Fragmentation.

Patterns used in FragIt for different types of chemical systems. The patterns for proteins include protection patterns to increase accuracy by eliminating very small fragments and the default fragmentation pattern makes sure to keep the quasi-conjugated nature of the peptide bond intact. For polysaccharides a single pattern to match -D-galactopyranose units, the subunits of cyclodextrins, is included. We also include a pattern to fragment the backbone of DNA.