Peptide-PRISM
adjacent · Hybrid de novo + database search
Peptide-PRISM: adjacent · Hybrid de novo + database search. Identifies cryptic HLA-I peptides by matching the top de novo sequencing candidates for each spectrum against a six-frame translation of the genome and transcriptome…
Identifies cryptic HLA-I peptides by matching the top de novo sequencing candidates for each spectrum against a six-frame translation of the genome and transcriptome, then scoring them in a stratified FDR; showed cryptic peptides are a substantial part of the HLA-I immunopeptidome.
| Kind | adjacent |
| Deep learning | no |
| Acquisition | DDA |
| Family | Hybrid de novo + database search |
Paper describing it
- Identification of the Cryptic HLA-I Immunopeptidome (2020, Cancer Immunology Research, peer-reviewed)
Papers using it (3)
Applications and evaluations that ran this method. They are not counted among its authors below.
- SILAC-based quantification reveals modulation of the immunopeptidome in BRAF and MEK inhibitor sensitive and resistant melanoma cells (2025, Frontiers in Immunology, peer-reviewed)
- Exploring the Immunogenicity of Noncanonical HLA-I Tumor Ligands Identified through Proteogenomics (2023, Clinical Cancer Research, peer-reviewed)
- T cells of colorectal cancer patients’ stimulated by neoantigenic and cryptic peptides better recognize autologous tumor cells (2022, Journal for ImmunoTherapy of Cancer, peer-reviewed)