MS-TAFI

MS-TAFI analyzes tandem mass spectrometry (MS/MS) spectra of intact proteins to deconvolute fragment ions, map charge sites using 193 nm ultraviolet photodissociation, and support top-down and native mass spectrometry studies.

Key Features:

• MS/MS deconvolution and visualization: Deconvolutes complex MS/MS spectra of intact proteins and visualizes fragment ion distributions and relative abundances.
• Native mass spectrometry and holo-ion search: Searches for fragment ions that retain ligands (holo ions) to characterize protein-ligand interactions in native MS experiments.
• Charge site visualization via 193 nm ultraviolet photodissociation: Uses 193 nm UVPD data to identify and visualize charge-site locations across protein molecules.
• Python implementation: Implemented as a Python-based application for computational analysis of top-down proteomics data.

Scientific Applications:

• Top-down proteomics: Enables analysis of intact proteins to resolve fragment ions and support proteoform-level characterization.
• Protein-ligand binding dynamics: Supports investigation of protein-ligand interactions by detecting holo ions in native MS datasets.
• Post-translational modification analysis: Facilitates mapping of modifications on intact proteins through interpretation of MS/MS fragment ions.
• Protein complex and conformational studies: Assists characterization of protein complexes and conformational changes by combining deconvolution with charge-site mapping.

Methodology:

Leverages algorithms to deconvolute complex MS/MS spectra and identify fragment ions with their corresponding charge states, and integrates 193 nm ultraviolet photodissociation (UVPD) data for localization of charge sites.