Installation | The core pipeline | Protein input | Step 1: Digest a protein | Step 1a: Inspect cleavage efficiency | Step 2: Score the peptide set | Scoring model | Known limitations | Scope | Step 2a: Apply a workflow preset | Step 2b: Add proteome-aware uniqueness | Step 3: Evaluate in one call | Step 4: Compare enzymes | Step 5: Get the top model rank | Step 6: Batch across a proteome | Step 6a: Summarize a batch | Step 6b: Triage proteins | Step 6c: Export a peptide list | Step 7: Quick interactive check | Step 8: Report to the console | Additional examples and references | A challenging protein: Histone H3.1 | Amino acid reference data | How pepVet differs from common tools | Related articles | Session info

Installation | Comparison basis | Common ground | How tools differ | Worked comparisons | pepVet scoring in practice | Workflow preset effects | Pipeline with PeptideRanger | Binary versus graded: pepVet and Protein Cleaver | Choosing an output type | References | Session info