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The comprehensive benchmarking platform for antibody de novo sequencing.
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Our platform provides the largest high-quality dataset to date, comprising 1,638,248 peptide-spectrum matches (PSMs) from 131 monoclonal antibodies (mAbs) across six species and 11 proteases, as well as eight mAbs with known sequences for evaluating full-length reconstruction. In addition, it offers an unbiased evaluation infrastructure that ensures fair comparisons. Through a unified training dataset, we benchmarked leading sequencing and assembly tools across six metric categories, spanning peptide sequencing (accuracy, robustness, efficiency, error types) and assembly (coverage depth, assembly score).
Antibody-specific Dataset
High-Quality PSM Dataset
Comprehensive dataset comprising 1,638,248 high-quality peptide-spectrum matches from 131 monoclonal antibodies across multiple species and proteases
Full-Length Validation Set
Eight monoclonal antibodies with known sequences for evaluating full-length sequence reconstruction and assembly performance
Comprehensive Benchmarking Features
Accuracy
Comprehensive accuracy metrics including amino acid and peptide precision/recall, PTM identification accuracy, and AUC performance
Efficiency
Performance evaluation focusing on computational efficiency and resource utilization for practical deployment
Robustness
Stability assessment across different experimental conditions including varying peptide lengths and spectral quality
Coverage Depth
Sequence coverage analysis evaluating the depth and completeness of peptide identification
Error Types
Detailed error analysis categorizing different types of prediction mistakes and their patterns
Assembly
Full-length sequence reconstruction evaluation including assembly quality and structural integrity
Research Applications
De Novo Sequencing
Advanced algorithms for peptide sequence prediction from tandem mass spectrometry data
Benchmarking
Comprehensive evaluation metrics and standardized datasets for model comparison
Ready to Benchmark Your Model?
Join researchers worldwide in advancing antibody de novo sequencing