REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-VLDLr mAb	ATCC	ATCC CRL-2197
Polyclonal Rabbit Anti-Human Beta-2-Microglobulin	Dako	A0072
Experimental Models: Cell Lines
HeLa	ATCC	ATCC CCL-2
A375	ATCC	ATCC CRL1619
SKOV3	ATCC	ATCC HTB-77
A2780	Sigma-Aldrich	93112519 Sigma
OV90	ATCC	ATCC CRL11732
Software and Algorithms
PEAKS Studio	Zhang et al., 2012	http://www.bioinfor.com/peaks-studio/
PolySolver	Shukla et al., 2015	http://archive.broadinstitute.org/cancer/cga/polysolver
Optitype	Szolek et al., 2014	https://github.com/FRED-2/OptiType
Snp2HLA	Jia et al., 2013	http://software.broadinstitute.org/mpg/snp2hla/
NetMHCPan-3.0	Nielsen and Andreatta, 2016	http://www.cbs.dtu.dk/services/NetMHCpan/
Data analysis was done using Python 2.7	Python
Seaborn	Python library	https://seaborn.pydata.org/
Pandas	Python library	http://pandas.pydata.org/
Biopython	Python library	http://biopython.org/wiki/Seq
Other
Multi-allelic MS data	Bassani-Sternberg et al., 2015
MS MHC-I data	Abelin et al., 2017
MS MHC-I data (HLA alleles: HLA-A*01:01, HLA-A*02:01, HLA-A*24:02, HLA-B*07:02, and HLAB*51:01, eluted from HeLa cell line)	Trolle et al., 2016	http://www.iedb.org/subID/1000685 accession # 1000685.
Ensembl data	Yates et al., 2016	http://www.ensembl.org/index.html
GDC TCGA data	N/A	https://portal.gdc.cancer.gov/
Exome Variant Server	N/A	http://evs.gs.washington.edu/EVS/
UniProt	N/A	http://www.uniprot.org/
HLA frequency net	N/A	http://www.allelefrequencies.net/
National Center for Biotechnology Information (NCBI) Homo sapiens taxonomy	https://www.ncbi.nlm.nih.gov/	Taxonomy ID: 9606