REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Human Plasma	Healthy participants were recruited from a local research institution and the surrounding community prior to vaccination.	WIRB#1299650
Human Plasma	Unvaccinated COVID-19 convalescent individuals were recruited from participating clinical sites.	IRB#20204
Chemicals, peptides, and recombinant proteins
4 NTPs (ATP, CTP, GTP, UTP)	Lucigen	Cat# RN02825
Protease Inhibitor Cocktail	VWR	Cat# G6521
DYNAL MyOne Dynabeads Streptavidin T1	Thermo Fisher Scientific	Cat# 65604D
AcTEV Protease	Thermo Fisher Scientific	Cat# 12575015
RNase Inhibitor, Murine	New England Biolabs	Cat# M0314L
ProtoScript II Reverse Transcriptase	New England Biolabs	Cat# M0368X
RNase H	New England Biolabs	Cat# M02971
Q5 High-Fidelity DNA Polymerase	New England Biolabs	Cat# M0491L
T4 RNA Ligase 2	New England Biolabs	Cat# M0239L
Dynabeads Protein G for Immunoprecipitation	Thermo Fisher Scientific	Cat# 10004D
Critical commercial assays
Ampliscribe T7-Flash Transcription Kit	Lucigen	Cat# ASF3507
PURExpress In Vitro Protein Synthesis Kit	New England Biolabs	Cat# E6800L
SCoV-2 Detect™ IgG	InBios	Cat# COVE-G
SARS-CoV-2 Surrogate Virus Neutralization Test	GenScript	Cat# L00847-A
Deposited data
PepSeq read count data	Open Science Framework	https://osf.io/67r3d/
Oligonucleotides
Custom 15,000 oligo library CCTATACTTCCAAGGCGCAxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx xxxxxxGGTGACTCTCTGTCTTGGC	Agilent Technologies	G7225A
DNA amplification primer (Forward): GCG AATTAATACGACTCACTATAGGGCTTAA GTATAAGGAGGAAAAAATATGGGAGAA AACCTATACTTCCAAGGCGCA	Integrated DNA Technologies	N/A
DNA amplification primer (Reverse): GCT CCTGCTGCATTTCCGTTCAGCAGACGC AGCAGCCAAGACAGAGAGTCACC	Integrated DNA Technologies	N/A
Biotinylated oligo for bead purification: TT TTTCATATTTTTTCCTCCTTATACTTAAGCCC	Integrated DNA Technologies	N/A
Software and algorithms
Peptide design algorithm	Zenodo	https://doi.org/10.5281/zenodo.6613749
PepSIRF (version 1.3.2)	Zenodo	https://doi.org/10.5281/zenodo.6609194
Custom Python scripts (PepSIRF/extensions)	Zenodo	https://doi.org/10.5281/zenodo.6613749
R version 4.0.2	R project	https://www.r-project.org/
PyMol 2.3.2	Schrodinger LLC	https://pymol.org
Other
NextSeq 500/500 Mid Output Kit v2.5 (150 Cycle)	Illumina	Cat# 20024904
NextSeq 500/500 Mid Output Kit v2.5 (75 Cycle)	Illumina	Cat# 20024906