REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited Data
IEDB MHC ligand data	Vita et al. (2019)	https://www.iedb.org/database_export_v3.php
IEDB-derived multi-allelic benchmark samples	This paper	Table S2; https://github.com/bravib/rbm-mhc/tree/master/data/Multiallelic_Synthetic_individuals
Software and Algorithms
RBM-MHC	This paper	https://github.com/bravib/rbm-mhc
NetMHCpan4.0	Jurtz et al. (2017)	http://www.cbs.dtu.dk/services/NetMHCpan-4.0
NetMHCpan4.1	Reynisson et al. (2020)	http://www.cbs.dtu.dk/services/NetMHCpan-4.1/
NetMHC4.0	Andreatta and Nielsen (2016)	http://www.cbs.dtu.dk/services/NetMHC
MixMHCp2.1	Bassani-Sternberg and GFeller (2016); Gfeller et al. (2018)	https://github.com/GfellerLab/MixMHCp
Other
MS-identified peptides in mono-allelic cell lines	Sarkizova et al. (2020)	https://github.com/bravib/rbm-mhc/tree/master/data/Allele-specific_models
MS-identified peptides carrying mutations in cancer cell lines SKOV3, A2780, OV90, HeLa, A375	Marty et al. (2017)	https://github.com/bravib/rbm-mhc/tree/master/data/Allele-specific_models
SARS-CoV-2 epitopes (tested in vitro)	Immunitrack and Intavis	https://www.immunitrack.com/free-coronavirus-report-for-download/
SARS-CoV and SARS-CoV-2 homolog epitopes	Grifoni et al. (2020)	N/A
Multi-allelic MS cancer sample 12T	Kalaora et al. (2016); Kalaora et al. (2018)	https://github.com/bravib/rbm-mhc/tree/master/data/Multiallelic_Cancer_samples
Multi-allelic MS cancer samples Mel8, Mel15, Mel5	Bassani-Sternberg et al. (2016)	https://github.com/bravib/rbm-mhc/tree/master/data/Multiallelic_Cancer_samples
Cosmic Cell Lines Project	Forbes et al. (2016)	https://cancer.sanger.ac.uk/cosmic
Genomics of Drug Sensitivity Center	Yang et al. (2013)	https://www.cancerrxgene.org/
Single Nucleotide Polymorphism Database (dbSNP)	Sherry et al. (2001)	http://www.ncbi.nlm.nih.gov/SNP/
GenBank	Benson et al. (2013)	https://www.ncbi.nlm.nih.gov/genbank/
UniProt	UnitProt Consortium, 2019	http://www.uniprot.org/
HLA frequency net	González-Galarza et al. (2015)	http://www.allelefrequencies.net/