topdownr

topdownr automates and optimizes intact protein sequencing using multimodal tandem mass spectrometry (MS/MS) to maximize amino acid sequence coverage of whole proteins.

Key Features:

• R package: Implemented as an R package for construction and analysis of top-down MS/MS workflows.
• Orbitrap method automation: Automates the construction of MS/MS acquisition methods on Orbitrap instruments.
• Multimodal fragmentation: Supports CID, HCD, ETD, ETciD, EThcD, and UVPD fragmentation techniques.
• Data workflows: Provides workflows for systematic processing, visualization, and statistical modeling of MS/MS spectra.
• Target mass range: Applied to intact proteins in the 10–30 kDa range.
• Sequence coverage: Demonstrated analysis achieving 90–100% amino acid sequence coverage in tested datasets.
• Fragmentation optimization: Enables derivation of principles for optimal fragmentation strategies.

Scientific Applications:

• Protein pharmaceutical characterization: Characterizes intact protein pharmaceuticals through high-coverage MS/MS sequencing.
• De novo sequencing: Enables de novo sequencing of intact proteins using multimodal fragmentation data.
• Structural analysis: Facilitates detailed structural analysis by improving sequence coverage and fragmentation mapping.
• MS/MS method development: Supports development and optimization of MS/MS fragmentation strategies for intact proteins.

Methodology:

Automated construction of MS/MS acquisition methods on Orbitrap instruments; use of CID, HCD, ETD, ETciD, EThcD, and UVPD fragmentation; systematic processing, visualization, and statistical modeling of resulting spectra; analysis of thousands of MS/MS spectra from intact proteins in the 10–30 kDa range.