REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
HLA Class I antibody W6/32 for HLA-IP	Santa Cruz Biotechnology	Cat # sc-32235; RRID:AB_627934
HLA Class I antibody W6/32 for in-vitro binding assay	ATCC	Cat # HB-95; RRID_CVCL_7872
SARS-CoV Nucleocapsid (N) Protein (RABBIT) polyclonal antibody	Rockland	Cat # 200-401-A50; RRID:AB_828403
Alexa Fluor 568 goat anti rabbit antibody	Invitrogen	Cat # A11011; RRID:AB_143187
anti mouse IFNy mAB AN18 purified 250 ug (1mg/mL)	Mabtech	Cat # 3321-3-250; RRID:AB_907279
anti-mouse IFNy mAb R4-6A2, biotinylated 250ug (1mg/mL)	Mabtech	Cat # 3321-6-250; RRID:AB_907271
MS CD3E pure mAB 0.5 mg/mL	BD Biosciences	Cat # 553058, RRID:AB_394591
Bacterial and virus strains
SARS-CoV-2	Centers for Disease Control and Prevention and BEI Resources	2019-nCoV/USA-WA1/2020 isolate (NCBI accession number: MN985325.1)
Biological samples
Convalescent donor blood sample	Precision for Medicine (USA)	https://www.precisionformedicine.com/
Convalescent donor blood sample	Sanguine (USA)	https://sanguinebio.com/
Convalescent donor blood sample	CTL (USA)	http://www.immunospot.com/ImmunoSpot-ePBMC
Convalescent donor blood sample	The Immune Monitoring Laboratory, MGH	https://www.massgeneral.org/cancer-center/clinical-trials-and-research/immunotherapy/cellular-immunotherapy-program/immune-monitoring-laboratory
Chemicals, peptides, and recombinant proteins
1 M Tris, pH 8.0	Invitrogen	Cat # AM9855G
EDTA	Sigma Aldrich	Cat #7789
Sodium chloride	Sigma Aldrich	Cat #71376
Triton-X	Sigma Aldrich	Cat #T9284
Octyl β-d-glucopyranoside	Sigma Aldrich	Cat # 08001
Phenylmethanesulfonyl fluoride	Sigma Aldrich	Cat # 78830
C0mplete Protease Inhibitor Tablet-EDTA free	Sigma Aldrich	Cat # 5056489001
Aprotinin	Sigma Aldrich	Cat: # A6103
Leupeptin	Roche	Cat: # 11017101001
Sodium fluoride	Sigma Aldrich	Cat: #S7920
Phosphatase inhibitor cocktail 2	Sigma Aldrich	Cat: #P5726
Phosphatase inhibitor cocktail 3	Sigma Aldrich	Cat: #P0044
DNase I	Sigma Aldrich	Cat # 4716728001
Gammabind Plus Sepharose beads	Millipore Sigma	Cat #17-0886-01
Dithiothretiol, No-Weigh Format	Fisher Scientific	Cat # 20291
Iodoacetamide	Sigma Aldrich	Cat: # A3221
Lysyl endopeptidase (LysC),	Wako Chemicals	Cat # 129-02541
Trypsin, Mass Spec Grade	Promega	Cat # V511X
Formic Acid	Sigma Aldrich	Cat # F0507
Acetonitrile	Honeywell	Cat # 34967
Trifluoretic acid	Sigma Aldrich	Cat # 302031
TMT sixplex Isobaric Label Reagent Set	ThermoFisher	Cat # 90061
0.5M HEPES, pH 8.5	Alfa Aesar	Cat # J63218
Hydroxylamine solution, 50% (vol/vol) in H2O	Sigma Aldrich	Cat #467804
Methanol	Honeywell	Cat # 34966
Ammonium hydroxide solution, 28% (wt/vol) in H2O	Sigma Aldrich	Cat # 338818
Acetic acid, glacial	Sigma Aldrich	Cat # AX0073
Avicel	DuPont	Cat # RC-581
Benzonase	Thomas Scientific	Cat # E1014-25KU
Synthetic peptides, 5mg > 90% purity	Genscript	Customized quote
SARS-CoV-2 Nucleocapsid peptides pool	JPT	PM-WCPV-NCAP
Human IFNγ ELISpot	CTL	Cat #hIFNgp-2M/2
Illumina TruSeq Stranded mRNA (LT)	Illumina	Cat # FC-122-2101
Agilent 2200 TapeStation D1000 ScreenTape	Agilent	Cat # 5067-5582
NextSeq V2.5 High Output 75 cycle kit	Illumina	Cat # 20024906
NextSeq V2.5 High Output 150 cycles kit	Illumina	Cat # 20024907
PolyIC/LC, Hiltonol (2mg/ml)	Oncovir
Streptavidin HRP	Mabtech	Cat # 3310-9-1000
Substrate for Elispot: TMB	Mabtech	Cat # 3651-10
M. Tuberculosis H37 RA	DIFCO Laboratories	Cat # 231141
Adjuvant complete freund	Becton, Dickinson and Co	Cat # 263810
GIBCO Phytohemagglutinin, M form (PHA-M)	GIBCO	Cat #10576015
Multiscreen IP WHT STRL	Thermo Fisher Scientific	Cat #MSIPS4W10
SDB-XC disk, 47mm	Empore 3M	Cat # 2240
Critical commercial assays
HLA-A,B,C typing	Histogenetics	Customized quote
Deposited data
RNA sequencing data	GEO	GSE159191
original mass spectra, peptide spectrum matches and databases	MassIVE	MSV000087225
Experimental models: Cell lines
A549	ATCC	CCL-185
HEK293T	ATCC	CRL-3216
VERO E6	ATCC	CRL-1586
Experimental models: Organisms/strains
B6.Cg-Immp2lTg(HLA-A/H2-D)2Enge/J	The Jackson Laboratory	Stock # 004191
Software and algorithms
Spectrum Mill software package v7.1 pre-Release	Broad Institute	https://proteomics.broadinstitute.org/
Bowtie 1.1.2	(Langmead et al., 2009)	http://bowtie-bio.sourceforge.net/index.shtml
HLAthena binding prediction	Broad Institute	http://hlathena.tools/
Other
Easy-nLC 1200 System	Thermo Fisher Scientific	LC140
Orbitrap Exploris 480	Thermo Fisher Scientific	BRE725532
FAIMS Pro Interface	Thermo Fisher Scientific	FNS02-10001
Sequences, analyses, and barcoded tetramer pools used to determine peripheral T cell specificity	This paper	N/A