PAMPA CRAFT: Deamidation

The deamidation modules takes as input a peptide table, and adds deamidation modifications. It applies up to one deamidation to peptide markers containing at least one asparagine or glutamine and that have not yet undergone deamidation. This increases the peptide's mass by 0.984016 Da. By default, all markers are processed. The list of peptide markers to process can be adjusted with the -l option.

Usage

''' python3 pampa_craft.py --deamidation -p table_A -o table_B [-l limit_file] '''

This command generates a new peptide table, table_B, which includes all markers from the original peptide table, table_A, along with newly deamidated peptides. The set of markers affected by the modification can optionally be limited using the -l option.

Peptide table (-p)

This table contains the original peptide markers. The format of this table is described in Peptide tables.

Limiting file -l

This option allows to limit the set of markers to process, with the DEAMIDATION= tag. The full description of the syntax is given in section Limiting searches.

Output file (-o)

This is the name of the new peptide table created by the program, that contains deamidated peptides (with "1D" in the PTMs description).