Peptide Fragmentation Tool

Different types of fragmentation techniques can be used for the validation of a peptide sequence, as well as for the detection, localization and characterization of post-translational modifications. For these types of experiments, the common fragments of a peptide sequence previously defined using the Sequence Editor can be generated in silico using the Peptide Fragmentation module [Tools → Peptide Fragmentation] icon. Depending on the fragmentation technique used, different fragments can be selected and generated. The currently available fragments are immonuim, a, a-NH3, a-H2O, b, b-NH3, b-H2O, c, x, y, y-NH3, y-H2O, and z (charge 1+ and 2+), as well as the internal fragments int., int.-CO, int.-NH3, and int.-H2O. The masses of the generated fragments can then be compared with the current peaklist within a specified tolerance.

peptide fragmentation tool

Peptide fragmentation tool.

Generate fragments

To generate the tables of fragment masses press Fragment button located in module control panel. All the checked fragment types will be generated. You can manually set which fragments you want to generate or Instrument Presets can be used. Default settings can be specified in application preferences.

Mass type settings

It is important to set proper mass type for masses calculations - Monoisotopic Mass [Config → Monoisotopic Mass] icon or Average Mass [Config → Average Mass] icon. Current mass type is shown in application statusbar.

Data matching

See the separate chapter.

Panel view

List of all generated fragment can also be viewed in separate panel. To show the panel press Show in panel button. Fragments can be filtered to show missed or matched only or sorted by mass or fragment type. The main purpose of this panel, however, is the ability to highlight selected mass in the current spectrum within specified Zoom. Using this feature you can easily find some missed peaks etc.

fragments list

Fragments list.