Protein Digest Tool

Many experiments, involving the detection of modifications, protein validation etc., apply the specific enzymatic digestion of a protein with a known sequence. The Protein Digest module [Tools → Protein Digest] icon can be used to generate a list of peptides resulting from in silico enzymatic digestion or in silico chemical digestion of a sequence previously defined using Sequence Editor. The masses of these peptides can then be compared with the current peaklist within a specified tolerance.

protein digest tool

Protein digest tool.

Digest settings

In the module control panel some digest options can be set. You can specify used Enzyme or number of missed cleavage sites - Partials. If there are any modifications in the sequence, all combinations of modifications can be calculated for each peptide - Optional modifications. A Charge state and Mass limits of resulted peptides can be also set.

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.

Generate peptides

To generate the list of peptide masses press Digest button located in module control panel.

Data matching

See the separate chapter.

Panel view

List of all generated peptides can also be viewed in separate panel. To show the panel press Show in panel button. Peptides can be filtered to show missed or matched only or sorted by the range, partials, mass or sequence. 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.

peptides list

Peptides list.