Noncanonical MAP atlas
downstream-application
Noncanonical MAP atlas: downstream-application. A proteogenomic pipeline based on deep-learning de novo sequencing plus open search mapped 8,601 noncanonical MHC class I peptides from noncoding regions across 11…
A proteogenomic pipeline based on deep-learning de novo sequencing plus open search mapped 8,601 noncanonical MHC class I peptides from noncoding regions across 11 cancer types.
| Kind | downstream-application |
| Deep learning | yes |
| Acquisition | DDA |
| Application area | Immunopeptidomics / neoantigen |
Data
What the papers describing this method trained it on and reported its results on, as each paper states it. A version is named only where the paper names one.
Also used, purpose not recorded
- Fully unsupervised identification of HLA-I motifs (as deposited)
- Global proteogenomic analysis of human MHC I peptides derived from noncanonical reading frames (as deposited)
- High-throughput MS-based immunopeptidomics (as deposited)
- Immunopeptidomics of colorectal cancer organoids (as deposited)
- MS-rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments (as deposited)
- Mass spectrometry profiling of HLA-associated peptidomes in mono-allelic cells enables more accurate epitope prediction (as deposited)
- The HLA-Ligand-Atlas. A resource of natural HLA ligands presented on benign tissues (as deposited)
Paper describing it
- The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides (2023, Cancer Immunology Research, peer-reviewed)