extPep-identifier-blackjack 0.0.9

Extended peptides identification given mass-spec search result and custom proteomic database

ExtPep_identifier

Xinhao Shao @Collage of Pharmacy, University of Illinois at Chicago

Purpose of the script

ExtPep_identifier allows researchers to efficiently identify potential extended peptides given mass-spec search results and custom database. The extended peptides can be identified after mapping all of the identified peptides to a custom extended database, followed by a standard non-extended database.

Usage

1. Package installation
Install the package by running:
pip install extPep-identifier-blackjack==0.0.9(or current version)

2. Import the package
import ExtPep_identifier

3. Prepare for a few parameters before calling main function
# a list of identified peptides strings, ex. ['PEPTIDE','TIDEPEP']
peptide_list=your_peptide_getter_function(search_result_file)

# a dictionary structure with identified peptide with key, the number of times such peptide being identified as value, ex. {'PEPTIDE':4,'TIDEPEP':5}
psm_dictionary = your_psm_getter_function(search_result_file)

# a dictionary structure with protein ID as key, it's extended sequence as value, ex. {'P1':'PEPTIDEPEP'}
merged_protein_dictionary = your_fasta_reader(custom_ext_database_file_path)

# a dictionary structure with protein ID as key, it's original sequence as value, ex. {'P1':'PEPTIDEP'}
original_protein_dictionary = your_fasta_reader(original_db_file_path)

4. Calling main function
ext_pep_list, ext_psm_list, ext_protein_set = ExtPep_identifier.__main__(peptide_list,psm_dictionary,merged_protein_dictionary,original_protein_dictionary)

How to cite:

Kyle Mangano, Tanja Florin, Xinhao Shao, Dorota Klepacki, Irina Chelysheva, Zoya Ignatova, Yu Gao, Alexander Mankin, View ORCID ProfileNora Vázquez-Laslop "Genome-wide effects of the antimicrobial peptide apidaecin on translation termination", accepted by eLife