REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
PE anti-human HLA-A,B,C (clone W6/32)	Biolegend	Cat#311406; RRID:AB_314875
FITC anti-human CD8a (clone RPA-T8)	Biolegend	Cat#301050; RRID:AB_2562055
BV785 anti-human CD19 (clone HIB19)	Biolegend	Cat# 302240; RRID:AB_2563442
BV785 anti-human CD56 (clone 5.1H11)	Biolegend	Cat# 362550; RRID:AB_2566059
BV785 anti-human CD14 (clone M5E2)	Biolegend	Cat# 301840; RRID:AB_2563425
BV785 anti-human CD4 (clone RPA-T4)	Biolegend	Cat# 300554; RRID:AB_2564382
PE anti-human-CD8 a (Clone RPA-T8)	Biolegend	Cat# 301008; RRID:AB_314126
FITC anti-human CD20 (clone 2H7)	Biolegend	Cat# 302304; RRID:AB_314252
Alexa Fluor 647 anti-human CD137 (clone 4B4-1)	Thermo Fisher Scientific	Cat# A51019; RRID:AB_2633303
PE-conjugated goat-anti-human IgG-Fc	Jackson ImmunoResearch	RRID: AB_2922837
Biological samples
COVID-19 convalescent donor serum and PBMC samples	This paper	N/A
Healthy pre-pandemic donor PBMC samples	This paper	N/A
Healthy pandemic control donor serum	This paper	N/A
Chemicals, peptides, and recombinant proteins
Custom made synthetic peptides	GenScript	N/A
PMSF	Sigma-Aldrich	Cat# P7626
Protease Inhibitors Cocktail	Sigma-Aldrich	Cat# P8340
n-Dodecyl-β-D-Maltopyranoside	Anatrace	Cat# D310S
Amino Link Plus Resin	Thermo Fisher Scientific	Cat# 20501
Bacterially expressed full-length Nucleocapsid from SARS-CoV-2	Prospec Bio	Cat # SARS-013
PE-Streptavidin	Invitrogen	Cat# S866
APC-Streptavidin	Invitrogen	Cat# S868
Brilliant Violet 421™ Streptavidin	Biolegend	Cat# 405225
Brilliant Violet 605-Streptavidin	Biolegend	Cat# 405229
PE-Cy™7 Streptavidin	Biolegend	Cat# 405206
PE-CF594 Streptavidin	BD Biosciences	Cat# 562284
PE-Cy5 Streptavidin	BD Biosciences	Cat# 554062
APC-R700 Streptavidin	BD Biosciences	Cat# 565144
BB790-P Streptavidin	BD Biosciences	prototype kindly provided by Bob Balderas
Live/Dead-NearInfraRed (LD-NIR)	Thermo Fisher Scientific	Cat# L10119
Recombinant human IL-2	R&D Systems	Cat# 202-IL-500
Recombinant human IL-15	Peprotech	Cat# 200-15
PHA (Remel)	Remel	Cat# 10082333
Amine-functionalized pmma microspheres 6 μm and 8 μm	Bangs Laboratories	custom-order
Sulfo-Biotin-LC-NHS	Proteochem	Cat # b2103
SARS-CoV-2 RBD domain antigen	Sino Biologicals	Cat # 40592-V08H115
D-Biotin	Sigma-Aldrich	Cat #2031-1GM
Neutravidin	Thermo Fisher Scientific	Cat# 31055
Sulfo-Cy5 NHS	Lumiprobe	Cat# 53320
BDP-FL	Lumiprobe	Cat# 51420
Sulfo-Cy7-NHS	Lumiprobe	Cat# 55320
Pacific Blue-NHS	Thermo Fisher Scientific	Cat# P10163
Fetal bovine serum (FBS)	Merck Life Science AS	Cat# F7524-500ML
Doxycycline hyclate	Sigma-Aldrich	Cat# D9891
X-Vivo-20	BioNordika	Cat # BE04-448Q
Normal Human Serum, off clot, male, pooled	Trina Bioreactives AG	Cat# SN0300
Human Fc Receptor binding inhibitor	AH Diagnostics	Cat# 14-9161-73
CountBright™ Absolute Counting Beads	Invitrogen	Cat# C36950
Critical commercial assays
DNeasy Blood & Tissue Kit	Qiagen	Cat 69506
NGSgo®-AmpX HLA GeneSuite (NGSgo®-AmpX HLA-A, B, C, DRB1, DQB1 & NGSgo®-AmpX HLA-DPA1, DPB1, DQA1, DRB3/4/5 kits)	GenDx	Cat # 2341602
Deposited data
RAW MS files	ProteomeXchange	PXD028862
Experimental models: Cell lines
HLA class I-deficient B721.221 cells	FRED HUTCH Research Cell bank	Cat# IHW00001
Expi293F cells	Thermo Fisher Scientific	Cat# A14528
Recombinant DNA
Plasmid: encoding the receptor-binding domain of Spike-1 protein (RBD)	Florian Krammer	PMID: 32398876
Plasmid: HLA-A∗03:01; HLA-A∗01:01, HLA-A∗02:01, HLA-B∗07:02, HLA-B∗08:01 cloned into pMP71 vector backbone	This paper	N/A
Plasmid: pRetroX-TetOne-Puro-SARS-CoV-2-Spike	This paper	N/A
Plasmid: pRetroX-TetOne-Puro-SARS-CoV-2-Spike 1_1-541aa	This paper	N/A
Plasmid: pRetroX-TetOne-Puro-SARS-CoV-2-Spike 2_490-975aa	This paper	N/A
Plasmid: pRetroX-TetOne-Puro-SARS-CoV-2-Spike 3_888-1273aa	This paper	N/A
Plasmid: pRetroX-TetOne-Puro-SARS-Cov-2-Nucleocapsid	This paper	N/A
Plasmid: pRetroX-TetOne-Puro-SARS-CoV-2 -Envelope_2A_Membrane	This paper	N/A
Plasmid: pRetroX-TetOne-Puro-SARS-CoV-2-ORF3a	This paper	N/A
Software and algorithms
FlowJo	FlowJo LLC	https://www.flowjo.com; RRID:SCR_008520
RStudio 2021.09.2 + 382 “Ghost Orchid” for macOS	Posit, PBC	https://www.rstudio.com/; RRID:SCR_000432
R version 4.0.4	R core team	https://www.r-project.org/
GraphPad Prism 8.3.0	Graphpad	https://www.graphpad.com; RRID:SCR_002798
PEAKS	Bioinformatics Solutions Inc	RRID:SCR_022841
OrgMassSpecR	CRAN	https://cran.r-project.org/web/packages/OrgMassSpecR/index.html
Adjusted population coverage	This paper	Github https://doi.org/10.5281/zenodo.7447391
NetMHCpan version 4.1	NetMHCpan 4.1 Server	dtu.dk; RRID:SCR_018182
NetMHC version 4.0	NetMHC 4.0 Server	dtu.dk; RRID:SCR_021651
ClustalOmega	Sievers et al. (2011)71 Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7:539 PMID: 21988835 https://doi.org/10.1038/msb.2011.75	https://www.ebi.ac.uk/Tools/msa/clustalo/; RRID:SCR_001591
Immune epitope database (IEDB)	Vita R et al. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 2018 Oct 24. https://doi.org/10.1093/nar/gky1006. PMID: 30357391; PMCID: PMC6324067	https://www.iedb.org/; RRID:SCR_006604