12.01.2026
Mass Spectrometry vs. NGS for HLA Peptide Analysis:Pros and Cons
While Next-Generation Sequencing (NGS) is excellent for identifying mutations, it cannot account for the complex rules of cellular processing and HLA binding. In contrast, mass spectrometry–based HLA peptide analysis provides a direct readout of the peptides physically presented on the cell surface.
| Feature | NGS Prediction | Alithea Bio Mass Spectrometry |
|---|---|---|
| Evidence | Theoretical | Physical / Direct |
| Accuracy | High False-Positive Rate | Validated HLA Presentation |
| PTMs | Cannot Detect | Detects Phosphorylation/Glycosylation |
| Speed | Fast for Sequencing | Deep Insight into Presentation |
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Advanced Immunopeptidomics for Validated Target Discovery
Alithea Bio’s proprietary MS technology captures low-abundance targets that traditional MS workflows miss, providing a “verified” list of targets that NGS-only approaches simply cannot provide. This direct readout ensures high-confidence data for neoantigen discovery and immunotherapy development.
