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PAMPA CRAFT

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touzet edited this page Jan 8, 2025 · 18 revisions

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.

allpeptides

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.

deamidation

This module takes as input a peptide table, and adds deamidation modifications.

fillin

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.

See PAMPA CRAFT: Fillin

homology

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.

See PAMPA CRAFT: Homology

selection

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.

Usage

pampa_craft  [-h] 
   [--homology | --allpeptides | --fillin | --deamidation] 
   [-f FASTA | -d DIRECTORY] [-p PEPTIDE_TABLE] [-s SPECTRA PATH] [-t TAXONOMY] [-l LIMIT] -o OUTPUT

The description of each of these options is provided below.

Spectra filtering: -s and -e options

This pair of option enables filtering markers based on peaks identified within a set of mass spectra. It can be applied in conjunction with --homology, --allpeptides, --fillin or independently.

python3 pampa_craft.py --fillin -p table_A -s SPECTRA_DIR   -e 0.1 -o new_table.tsv

This command fills in missing information in table_A (like missing masses) and selects peptides whose masses are present in at least half of the mass spectra in SPECTRA_DIR. The chosen peptides are then compiled into a new table, new_table.tsv.

python3 pampa_craft.py -p table_A -s SPECTRA_DIR  -e 0.1 -o new_table.tsv

In contrast to the previous example, this command uses peptide markers from table_A as they are. So those with missing masses are ignored. The command selects peptides whose masses are present in at least half of the mass spectra in SPECTRA_DIR. The chosen peptides are then compiled into a new table, new_table.tsv.

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