MassShiftFinder

MassShiftFinder detects and localizes post-translational modifications and amino acid substitutions by identifying equal mass shifts in overlapping peptide mass fingerprints generated using two proteases, supporting MALDI-TOF and TOF-TOF analyses.

Key Features:

• Blind Search Capability: Performs blind searches that detect known and unknown post-translational modifications and amino acid substitutions without predefined modification lists.
• Dual Protease Utilization: Combines peptide mass fingerprints from two proteases with different cleavage specificities to produce overlapping sequence coverage.
• Equal Mass Shift Algorithm: Identifies equal mass shifts in overlapping peptides to indicate potential modifications or substitutions and to restrict candidate regions.
• MALDI-TOF/TOF Integration: Directs proteins identified in MALDI-TOF experiments toward subsequent TOF-TOF analysis for detailed investigation of modifications and substitutions.
• Low-Throughput Characterization: Targets meticulous, single-protein characterization workflows rather than high-throughput discovery pipelines.

Scientific Applications:

• Discovery of Novel PTMs and Substitutions: Enables detection of unexpected or novel post-translational modifications and amino acid substitutions in proteomics studies.
• Protein Characterization in MALDI-TOF Workflows: Guides selection of MALDI-TOF-identified proteins for TOF-TOF follow-up to validate and localize modifications.
• Localization of Modification Sites: Narrows candidate regions within proteins by using overlapping peptide information and equal mass shifts.

Methodology:

Analyzes peptide mass fingerprints from two proteases with different cleavage specificities, focuses on overlapping peptides, and identifies equal mass shifts that indicate potential post-translational modifications or amino acid substitutions.