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PAMPA CRAFT
The module PAMPA CRAFT is for the design of custom peptide tables, that can then be utilized by PAMPA CLASSIFY.
It offers five distinct approaches for constructing a new peptide table or enriching an existing peptide table.
This module takes as input a set of amino-acids sequences (typically COL1A1 and COL1A2), generates all tryptic peptides together with their theoretical mass and constructs a peptide table from these peptides.
This module takes as input a peptide table, and adds deamidation modifications.
This module allows to supplement an existing peptide table by filling in missing values. This option allows to compute theoretical masses of peptides, add PTMs, find the position of a peptide within a protein sequence, compute the positions within the helical region, find plausible peptides from their mass, verify wether a peptide is enzymatically digested.
This module takes as input a set of amino acid sequences (typically COL1A1 and COL1A2) along with a peptide table containing known markers from related species. It generates new peptide markers based on sequence similarity. It also verifies whether the newly generated markers are enzymatically digested.
This module takes as input a peptide table and a collection of MS spectra from the same species. It selects peptide markers from the table that correspond to peaks in the spectra.
The selection module can be used alone or combined with any of the four other modules. For example, selection used in conjunction with allpeptides will cause the program to generate all tryptic peptides, computes their masses, and then selecting only peptides whose theoretical mass matches peaks from the set of spectra. Similarly, selection used in conjunction with deamidation will systematically apply one deamidation to any legit peptide and then select those whose mass is visible in the set of spectra.