POTAMOS

POTAMOS calculates mass and charge properties of peptides and proteins bearing post-translational modifications to support mass spectrometry-based proteomics and histone epigenetics analyses.

Key Features:

• PTM Calculation: Determines type, number, combinations, and corresponding mass changes for post-translational modifications, including methylations (arginines and lysines), acetylations (lysines), and phosphorylations (serines and threonines).
• Charge Calculation: Computes charge states of peptides, proteins, and protein fragments in both modified and unmodified forms for mass spectrometry interpretation.
• Proteolytic Cleavage Analysis: Calculates masses of fragments generated by proteolytic cleavage of PTM-modified proteins to support peptide identification after enzymatic digestion.
• Histone Variant Browser: Provides analysis support for epigenetically modified histone variants by enabling variant-specific mass and modification assessments.
• Fragment Mass Calculation: Calculates masses and charges of fragmented histone variants carrying predefined PTMs for detailed fragment-level analysis.

Scientific Applications:

• Proteomics: Provides theoretical masses and charge states of PTM-bearing peptides and fragments to aid protein and peptide identification and characterization by mass spectrometry.
• Epigenetics / Histone modification analysis: Supports analysis of histone PTMs and histone variant-specific fragmentation to investigate epigenetic regulation and the histone code.

Methodology:

Computes PTM mass shifts, evaluates combinatorial PTM states, calculates peptide/protein and fragment charge states, predicts masses of proteolytic cleavage products, and calculates masses and charges of fragmented histone variants with predefined PTMs.