TopFD

TopFD detects proteoform features from top-down liquid chromatography-mass spectrometry (LC-MS) data by grouping mass spectral peaks into coherent sets that represent intact proteoforms across isotopic compositions, charge states, and retention times for downstream identification and quantification.

Key Features:

• Proteoform Feature Detection: Clusters related mass spectral peaks into features representing intact proteoforms across isotopic compositions, charge states, and retention times.
• Feature Boundary Refinement: Applies algorithms to refine feature boundaries and delineate overlapping proteoform signals within complex spectra.
• Machine Learning Integration: Incorporates machine learning models to evaluate and score detected features to improve accuracy and reliability.

Scientific Applications:

• Proteoform Identification: Provides accurate feature groupings to support top-down proteomics workflows for intact proteoform characterization.
• Quantification: Enables reproducible abundance measurements by producing consistent feature detection across LC-MS runs.

Methodology:

Integrates multiple algorithms for proteoform feature detection and feature boundary refinement, coupled with machine learning models to evaluate and score detected features.