Peptide Landscape Antigenic Epitope Alignment Utility (PLAtEAU)
A Python script for identifying, aligning, and quantifying antigenic epitopes displayed by MHCII molecules.
Authors: Miguel Alvaro-Benito, Eliot Morrison, Esam Abualrous, Benno Kuropka, and Christian Freund (FU Berlin)
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*** PLAtEAU is now available as a free web tool! It can be accessed at https://plateau.bcp.fu-berlin.de/
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Instructions
This script requires the following libraries: numpy, scipy, itertools, pyteomics
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Perform identification of immunopeptidome mass spectrometric data using the MaxQuant software with the parameters of your choice.
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(optional) Filter the evidence.txt file to your specifications. Examples include removing potential contaminants, peptides identified with low confidence, or background peptides from IP controls.
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Copy the .fasta file used in (1) to your working folder with the filtered evidence.txt file.
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In this folder, run the script: python plateau-1.0.py -exp="experiment name" -evidence="evidence.txt" -fasta="fasta_file.fasta"
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The final output file is called "experiment name"_core_epitopes_final_renorm.txt The "Core Epitope" column represents the conserved antigenic epitopes. Core epitopes marked with * represent potential frame shifts and should be investigated closely. The "Whole Epitope" column represents the entire primary sequence covered by the identified peptides.