/pep2prot

Primary LanguagePython

pep2prot

pep2prot (DIA-NN edition) maps peptide sequences to proteins when annotation was not provided by the used proteomics software (here DIA-NN) and returns info about the tryptic state of each peptide.

Requirements

  • Input: path to a DIA-NN output csv file, semi-colon separated, with unique peptide sequences in a "Peptide" column

  • Input: path to the proteome database in FASTA format which was used for the DIA-NN search

  • path to the output folder

Setup

Create a conda environment (use Miniconda):

conda create -n pep2prot

conda activate pep2prot

Install NumPy, Pandas, PyYAML, BioPython and termcolor:

conda install -c conda-forge -c bioconda numpy pandas pyyaml biopython termcolor

Clone this repo:

git clone https://github.com/npinter/pep2prot.git

How To Use

  1. Open the /config folder, copy and paste the YAML file ending with .diann.yaml.
  2. Edit the copied YAML file with any editor and change paths.
num_jobs: number of parallel jobs, 0=all availiable threads
protein_expression_csv: output csv from DIA-NN
fasta_db_path: FASTA database used in the DIA-NN search
output_folder: output folder for pep2prot result
  1. Save the YAML file and start pep2prot_diann.bat (Windows, modify the batch file first) or pep2prot_diann.py.
  2. Select your YAML file in the prompt.
  3. Press Enter to start the mapping.