MSModDetector

MSModDetector detects and quantifies mass shifts and infers potential post-translational modification patterns from individual ion mass spectrometry data using linear programming.

Key Features:

• Mass Shift Detection: The algorithm detects and quantifies mass shifts for a protein of interest from I2MS data.
• PTM Pattern Inference: The algorithm infers potential PTM patterns using linear programming.
• Condition Comparison: MSModDetector enables comparison of a protein's PTM pattern landscape across different conditions.
• Charge-State-Free Analysis: I2MS generates true mass spectra without the need to infer charge states.

Scientific Applications:

• Intact Protein PTM Analysis: MSModDetector studies PTM patterns from individual ion mass spectrometry data for intact proteins.
• Multi-PTM Pattern Characterization: The tool facilitates determination of how many PTMs are attached to a single protein molecule and assignment of PTMs at distant sites to the same protein molecule.
• PTM-Regulated Process Investigation: Improved analysis of PTM patterns enables deeper understanding of PTM-regulated cellular processes.
• Tumor Suppressor Protein Analysis: The algorithm was evaluated on experimental I2MS data for the tumor suppressor protein p53.

Methodology:

The algorithm first detects and quantifies mass shifts for a protein of interest and subsequently infers potential PTM patterns using linear programming. The method was evaluated on simulated I2MS data and experimental I2MS data for p53.