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1. Features in dbPepNeo 2.0?

dbPepNeo 2.0 provides a systematic, quality-controlled catalog of validated neoantigen peptides, TCRs, and HLA peptidomes. we provide about 801 HC neoantigens and 864884 low LC peptidomes. Notably, 55 class Ⅱ HC neoantigens and 630 neoantigen-reactive T cell TCRβ sequences were included. Besides, four analytical tools were incorporated into dbPepNeo2.0 to provide useful tools for the immunogenicity of neoantigens. All of these data and tools are intended to support the development of neoantigen-based cancer vaccines and facilitate research in clinical cancer immunotherapy.

2. Pipeline to construct dbPepNeo 2.0 database?

3. How to use dbPepNeo 2.0?

LC: low confidence

MC: medium confidence

HC: high confidence

Cancer: cancer type

Gene: gene name

HLA allele: HLA allele

Mut peptide: mutated peptide sequence

Mut affinity (nM): mutated peptide affinity IC50 (nM), the predicted binding affinity between mutant peptide and HLA allele by NetMHCpan (v4.1)/NetMHCⅡpan (v4.0).

NetMHCpan (v4.1)

Mut binding level: binding level between mutant peptide and HLA allele. Scoring criteria: Rank% < 0.5 defined as strong binding, denoted as 'SB'; 0.5< Rank% <2 defined as weak binding, denoted as 'WB'; Rank% >2 defined as Nonbinding, denoted as 'NB'.

NetMHCⅡpan (v4.0)

Mut binding level: binding level between mutant peptide and HLA allele. Scoring criteria: Rank% < 1 defined as strong binding, denoted as 'SB'; 1< Rank% <5 defined as weak binding, denoted as 'WB'; Rank% >5 defined as nonbinding, denoted as 'NB'.

WT peptide: wild type peptide sequence

Peptide length: the number of amino acids contained in the peptide

Mutation: amino acid change

Verification: method of experimental verification

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