directLFQ

directLFQ performs label-free protein quantification from peptide or fragment-ion intensities to enable scalable normalization and intensity estimation in mass spectrometry-based proteomics.

Key Features:

• Scalability: Employs a ratio-based algorithm that scales linearly with the number of samples, enabling quantification of ~10,000 proteomes in ≈10 minutes and ~100,000 proteomes in under two hours, with up to 1,000-fold speed improvement versus MaxLFQ.
• Ratio-based normalization: Uses ratio-based sample normalization and protein intensity calculation for consistent quantitative estimates.
• Logarithmic-space alignment: Aligns samples and ion traces by shifting in logarithmic space to achieve precise normalization across samples.
• Normalization and performance: Shows normalization properties and benchmark performance comparable to MaxLFQ for both DDA and DIA datasets.
• Peptide-level intensity estimates: Provides normalized peptide intensity estimates for detailed peptide-level comparisons in addition to protein-level quantification.
• Integration with workflows: Compatible with the AlphaPept ecosystem and designed to operate downstream of common proteomics workflows.

Scientific Applications:

• Large-scale proteomics: Enables rapid protein quantification in large-scale, high-throughput proteomic studies.
• DDA and DIA analysis: Supports normalization and comparative quantification in both data-dependent acquisition (DDA) and data-independent acquisition (DIA) datasets.
• Peptide-level analyses: Facilitates peptide-level differential analysis using normalized peptide intensity estimates.

Methodology:

Implements a ratio-based sample normalization and protein intensity calculation, aligns samples and ion traces by logarithmic-space shifting, and outputs normalized peptide and protein intensity estimates with algorithms that scale linearly with sample number.