PIGSPRED1.0

PROPRIETARY NOTICE: This code is copyright 2025 Regeneron Pharmaceuticals, Inc. Use of this code is governed by the license stored within Regeneron Pharmaceutical’s “PIGSPRED1.0” directory at zenodo.org. Unauthorized use, modification, reproduction or distribution of this code will be considered a severe infringement of Regeneron's intellectual property rights, including (but not limited to) patent protections, which include (but are not limited to) PCT Publication No. WO/2023/122621 and U.S. Patent Publication No. 2023/0282304, as well as all patent applications based thereon and all patents granted therefrom.

LICENSE: License for Non-Commercial Academic Use of PIGSPRED1.0 code
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PIGSPRED1.0 is computational method to identify off-target peptides for TCR/Ab.

Code Dependencies:

1. Need netMHCPan Linux compiled code. The code can be put in the resource folder
2. Need Immunopeptidomics data (can be internal or external) and fill in the data in the format mentioned in the resources/MS/Complete_MS_Dataset_6_21_2021.csv file
3. Need GTEX expression data and formated as per the resources/gtex.ess.tpm.stats.max.oncoland.2020Q1.csv and gtex.ess.tpm.stats.max.oncoland.2020Q1.csv files.

Running the tool:

• Compile the RData

Rscript pigspred.R /home/dirname/

• Create the PIGSPRED input file

echo "Target,MHC,Gene,Beg,End" > pigtargets.csv

cp pigtargets.csv /home/dirname

Target: peptide sequence, MHC: HLA allele name, Gene: Gene name, Beg: peptide start position in the protein seq, End: peptide end position in the protein seq

• Run PIGSPRED

Rscript run-pigspred.R /home/dirname/

Auxillary Scripts

Three auxillary scripts are included in this repo to process MS data: preProcessPeaksExports.py, processPeaksExports_1_3.R, searchPeaksExports_4.4.py