ClipsMS

ClipsMS assigns terminal and internal fragments from top-down mass spectrometry (TD-MS) product ions to enable peptide and protein sequence characterization and precise localization of post-translational modifications.

Key Features:

• Comprehensive Fragment Assignment: Assigns both terminal fragments (containing the N- or C-terminus) and internal fragments that lack termini to expand identifiable sequence information.
• Enhanced Sequence Coverage: Incorporation of internal fragments increases sequence coverage, for example raising apo-myoglobin coverage to 78%.
• Modification Localization: Identifies and localizes post-translational modifications, demonstrated by confirming oxidation sites on methionine residues in oxidized apo-myoglobin.
• Complementary Data Extraction: Uses internal fragments that cover regions complementary to terminal fragments to extract additional information from a single top-down mass spectrum.

Scientific Applications:

• Proteomics: High-coverage protein characterization in proteomics studies requiring extensive sequence information.
• Post-translational modification mapping: Precise localization of PTMs, including oxidation events on methionine residues.
• Complex protein analysis: Improved characterization of complex proteins where internal fragments increase coverage beyond terminal-only analyses.

Methodology:

ClipsMS correlates product ions generated during TD-MS fragmentation to polypeptide sequences by systematically assigning both terminal and internal fragments.