varpepdb 1.0.2

Generate reference database of variant peptides for peptide spectrum matching

Overview

varpepdb is a python package for generating a fasta database of genetically variant peptides for peptide spectrum matching after data acquisition by LC/MS. It takes in a list of amino acid substitutions for a protein sequence and generates all possible variant peptides after enzymatic cleaving. It allows for multiple digestion enzymes and up to 1 miscleavage. It also takes into account the effect of amino acid substitutions on enzyme cleavage.

Installation

Requires:

• Python version: >= 3.8
• rpg

You can install varpepdb from PyPI:

pip install varpepdb

Usage

import varpepdb
import rpg

# Set enzymes to Asp-N and trypsin from the rpg package
varpepdb.setenzyme([rpg.RapidPeptidesGenerator.ALL_ENZYMES[1], 
                    rpg.RapidPeptidesGenerator.ALL_ENZYMES[41]])
# Allow 1 miscleave
varpepdb.miscleave = True
# Set peptide length limits. Default values are 6 and 30. 
varpepdb.setpeptidelengths(min_length: 6, max_length: 30)

# Demo inputs. In practice, these will be generated programmatically.
variants = ['O75844:p.Trp11Trp', 
            'O75844:p.Ala22Lys', 
            'O75844:p.Glu34Thr', 
            'O75844:p.Gln41His']
sequence = 'MGMWASLDALWEMPAEKRIFGAVLLFSWTVYLWETFLAQRQRRIYKTTTH'
gene = 'ZMPSTE24'

# Generate variant peptides
peptides = generate_single(variants=variants, 
                           sequence=sequence, 
                           gene=gene)

# Removes variant peptides that do not contain at least 1 amino acid substitution
var_peptides=varpepdb.variant_containing_peptides(peptides)

# Write variant peptides into fasta file
varpepdb.write(path='path/to/output.fasta', 
                     peptides=var_peptides,
                     include_non_unique=True)

Multiple proteins can be processed in parallel using varpepdb.generate.

peptides = generate(input_list=[(variants1, sequence1, gene1),
                                (variants2, sequence2, gene3),
                                (variants3, sequence2, gene3)])

var_peptides=varpepdb.variant_containing_peptides(peptides)

varpepdb.write(path='path/to/output.fasta', 
                     peptides=var_peptides,
                     include_non_unique=True)

Enzymes

In-silico digestion is performed using the rpg package. Refer to rpg's documentation on which enzymes are available and how to create your own enzyme.

Fasta output

Example of an entry written into the fasta file:

>A0A8I5KQE6-v1 RPSA2 129-143 (p.Pro143Arg),p.Thr135Met 0
ADHQPLMEASYVNLR

A0A8I5KQE6-v1 is the sequence identifier of the parent protein (in this case the Uniprot ascension number) with
'v{number}' appended to identify it as a peptide of the parent protein.
RPSA2 is the name of the gene for this protein.
129-143 is the position of the parent protein sequence from which this peptide is dervied. (p.Pro143Arg) is an amino acid substitution that affected the enzyme cleavage site. Amino acid substitutions that introduce or remove cleavage sites are marked by parenthesis.
p.Thr135Met is an amino acid subtstitution that didn't affect enzyne cleavage site.
0 refers to the number of miscleavages

Contact

For further information please contact [e-mail]