Digestion Conditions Window

How To Setup Your In Silico Digestion

The Digestion Conditions Window is where you will specify the digestion criteria for your in silico digestion.

Proteases:

• All proteases present in the programs protease.tsv file are loaded, and are available as an option for in silico digestion.
• You can select as many proteases as you want for digestion. All proteases are treated as separate digestions.
• There are 12 combined enzyme options provided as default (Trypsin + alt protease).
• If you want to use a protease, or combination of proteases not provided by default, you can create a custom protease by selecting the "Add Custom Protease" button.

Parameters:

• Max Missed Cleavages: The number of missed cleavages allowed during digestion by the protease(s).
• Min Peptide Length: The minimum allowed peptide length.
• Max Peptide Length: The maximum allowed peptide length.
• Min Peptide Mass (optional): The minimum allowed peptide monoisotopic mass.
• Max Peptide Mass (optional): The maximum allowed peptide monoisotopic mass.
• Treat modified peptides as different peptides: When this box is checked, modified peptides that are not unique based upon the amino acid sequence may be labeled as unique peptides if they are distinguishable by PTMs.
• Apply Fixed Carbamidomethylation of C: When this box is checked, carbamidomethylation of cysteine, which is common for digested protein samples that have been reduced and alkylated with iodoacetamide, is applied during in silico digestion. The modified residues are annotated in the peptide's full sequence and affect the molecular weight reported.
• Apply Variable Oxidation of M: When this box is checked, oxidation of methionine is applied as a variable modification during in silico digestion. This means that two versions of each Methionine containing peptide with be generated, one with and one without oxidation. The modified residues are annotated in the peptide's full sequence and affect the molecular weight reported.