ProteomeDigestSim

ProteomeDigestSim predicts proteome coverage by simulating iterative multi-enzyme digestion using the MED-FASP (Multiple Enzyme Digestion - Filter Aided Sample Preparation) methodology to evaluate sequence coverage and protein identification.

Key Features:

• Iterative Multi-Enzyme Digestion: Simulates consecutive digestion with two or three endoproteinases, typically LysC and trypsin, to increase sequence coverage.
• FASP Integration: Models digestion of samples dissolved in sodium dodecyl sulfate (SDS) within an ultrafiltration unit according to the FASP protocol.
• Efficient Peptide Separation: Represents separation of orthogonal peptide populations via ultrafiltration devices for downstream analysis.
• Enhanced Protein Identification: Estimates increases in protein and phosphorylation site identification, reported up to 40% relative to one-step tryptic digestion.
• Optimized Use of Sample Material: Accounts for sequential use of previously unused sample material across digestion steps to maximize proteomic depth.

Scientific Applications:

• Phosphorylation Site Mapping: Supports analyses that increase identification of phosphorylation sites for post-translational modification studies.
• Proteomic Depth Exploration: Enables prediction of enhanced sequence coverage for comprehensive proteome analysis from low microgram sample inputs.

Methodology:

Simulates MED-FASP sample preparation (SDS solubilization and ultrafiltration), sequential digestion with multiple enzymes, and ultrafiltration-based peptide separation as described.