Enzymatic digestion scheme

General principle

Several PAMPA modules use in silico digestion to produce peptides from protein sequences:

• Classify, when using FASTA sequences insetad of a peptide table to achieve species identification
• Homology, to check wether the peptides found by sequence alignment are correctly cleaved
• Allpeptides, to generate all possible peptides and use them in a peptide table
• Fillin, to add the digestion status in the peptide table.

By default, PAMPA generates all tryptic peptides between 12 and 33 amino acids in length, allowing up to one missed cleavage site.

Modification of the digestion scheme

Web interface: all values can be changed in the Parameters for in silico digestion panel.

Command-line: You can copy the config.json file and create your own configuration file with your customized values.

"enzyme": "trypsin",
"number_of_missed_cleavages": 1,
"min_peptide_length":12,
"max_peptide_length":33,

The list of available enzymes is

• "arg-c"
• "asp-n"
• "chymotrypsin high specificity"
• "chymotrypsin low specificity"
• "glutamyl endopeptidase"
• "pepsin ph1.3"
• "pepsin ph2.0"
• "proline endopeptidase"
• "trypsin"
• "trypsin_exception"

Make sure to match the exact wording, including all special characters (such as spaces, '-', and '_').

To use your edited config file when launching PAMPA, use the -c option.