MASSPEC

MASSPEC reconstructs protein amino acid sequences directly from mass spectra of mixed peptide fragments produced by single-solution digestion, enabling sequence determination without chromatographic separation.

Key Features:

• Random fragmentation modeling: Models random fragmentation such as partial acid hydrolysis to represent mixed peptide fragment generation.
• Derivatization modeling: Models derivatization of resulting peptide fragments to produce volatile analytes suitable for mass spectrometric measurement without prior chromatographic separation.
• Idealized spectra input: Operates on idealized mass spectra of the fragment mixture as the basis for computational reconstruction.
• Fragment mass matching: Infers amino acid sequences by matching observed fragment masses against theoretical fragmentation patterns.
• Overlap redundancy exploitation: Exploits redundancy inherent in overlapping fragment coverage to resolve sequence ambiguity.
• Simulation-driven reconstruction: Implements a simulation-driven reconstruction pipeline enabling end-to-end sequence determination from minimal sample quantities (~1 mg).

Scientific Applications:

• Sequence reconstruction from mixed-fragment spectra: Reconstructing protein sequences directly from mixed-fragment mass spectra obtained without chromatographic separation.
• Low-input samples: Sequence determination from minimal sample quantities (~1 mg) and other scarce biological material.
• Single-organism analyses: Applications to single-organism analyses where sample quantity or purity is limited.

Methodology:

Given idealized mass spectra of the fragment mixture, the algorithm infers underlying amino acid sequences by matching observed fragment masses against theoretical fragmentation patterns and exploiting redundancy from overlapping fragment coverage in a simulation-driven reconstruction pipeline.