NetMHCIIphosPan: HLA Class II Phosphorylated Peptide Antigen Presentation Predictions

A machine learning tool for predicting human leukocyte antigen (HLA) class II presentation of phosphorylated peptides, developed by Heli M. Garcia Alvarez and last updated in April 2026. The model was trained on reanalyzed mass spectrometry-based immunopeptidomics datasets and incorporates data on unmodified ligands. It is presented as a state-of-the-art tool with potential applications in immunotherapy and vaccine design.

Use Cases

• Predicting HLA class II antigen presentation of phosphorylated peptides based on mass spectrometry immunopeptidomics data.
• Analyzing HLA-specific binding motifs for phospholigands compared to unmodified ligands as described.
• Benchmarking new prediction tools against NetMHCIIphosPan, NetMHCIIpan-4.3, and MixMHC2pred-1.3 for phosphorylated peptide presentation.
• Informing immunotherapy and vaccine design strategies by understanding the HLA-II phospholigandome.

Strengths

• Model demonstrates superior performance and robustness compared to existing tools NetMHCIIpan-4.3 and MixMHC2pred-1.3, as stated in the description.
• Predictive accuracy was enhanced by incorporating unmodified ligand data, particularly for HLA-DP and HLA-DQ molecules.
• Data is derived from a refined peptide identification workflow applied to mass spectrometry-based immunopeptidomics datasets.

Limitations

• Row count and column-level documentation are unknown, which may limit suitability assessment.
• The dataset is very small at 10.8 KB, suggesting it likely contains model parameters or summary results rather than raw training data.
• Description metadata is limited; actual data structure and content require manual inspection after download.

Provenance

Source

Heli M. Garcia Alvarez via figshare.

Collection Method

Developed using reanalyzed mass spectrometry (MS)-based immunopeptidomics datasets.

Time Range

Publication date suggests model development circa 2026.

Freshness

Last updated 2026-04-17 09:29:48.

Geography

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