PeptideMass

PeptideMass generates theoretical peptide masses to support peptide mass fingerprinting and interpret mass spectrometry data by simulating enzymatic cleavage and incorporating sequence annotations and known modifications.

Key Features:

• Theoretical peptide mass generation: Produces theoretical peptide masses from protein sequences for comparison with experimental mass spectrometry data.
• Enzymatic cleavage simulation: Simulates enzymatic cleavage of protein sequences and accounts for missed cleavage sites to predict peptide masses.
• SWISS-PROT integration: Leverages the SWISS-PROT database and accepts user-specified sequences to generate theoretical peptide masses.
• Annotation-aware mass calculation: Incorporates annotations for signal sequences, propeptides, transit peptides, simple post-translational modifications, and disulfide bonds in mass calculations.
• Explanation of unexplained masses: Identifies potential causes of unexplained peptide masses including missed cleavages, lack of reduction and alkylation, methionine oxidation, post-translational modifications, database errors, unusual splicing events, protein variants, and artifactual modifications.
• Alerts for mass changes: Flags possible peptide mass changes arising from biological and technical factors.

Scientific Applications:

• Protein identification and characterization: Supports identification and characterization of proteins from mass spectrometry by providing theoretical peptide masses.
• Post-translational modification analysis: Facilitates analysis of post-translational modifications by accounting for known modifications in mass predictions.
• Database verification: Assists in verifying SWISS-PROT entries and detecting database conflicts or errors by comparing theoretical and experimental masses.

Methodology:

Takes a protein sequence (from SWISS-PROT or user-defined), simulates enzymatic cleavage to predict resulting peptide masses, and incorporates sequence annotations and known modifications to produce theoretical mass profiles for comparison with experimental data.