Package index • pepVet

Digest simulation

Cleave protein sequences into peptide fragments using any of 40 cleaver-compatible enzyme rules.

annotate_cleavage_sites(): Annotate cleavage-site efficiency
digest_protein(): Simulate a proteolytic digest

Scoring

Summarise a peptide set into component scores, explicit scoring parameters, and an advisory weighted composite verdict.

score_peptides(): Score digested peptides for pre-acquisition review
pepvet_preset(): Return a named scoring preset

Peptide properties

Calculate peptide mass and isoelectric point annotations used in fractionation-aware planning workflows.

calculate_peptide_mass(): Calculate peptide mass or m/z
calculate_pI(): Calculate peptide isoelectric point

Evaluation and comparison

Combine digest and scoring into a single call, compare enzymes side-by-side, or return the highest-scoring enzyme under the selected settings.

evaluate_digest(): Evaluate a proteolytic digest
compare_digests(): Compare multiple enzymes on a single protein
recommend_enzyme(): Return the highest-scoring enzyme for a single protein
sensitivity_analysis(): Weight sensitivity analysis

Batch workflows

Evaluate all proteins in a multi-FASTA in one call, compare enzymes across a proteome, summarise the score distribution, and triage proteins by difficulty.

batch_evaluate(): Batch-evaluate multiple proteins
batch_compare_enzymes(): Compare multiple enzymes across a full proteome
summarize_batch(): Summarize a batch digest evaluation
triage_proteins(): Triage proteins from a batch evaluation

Visualisation

Plot digest quality, score components, enzyme comparisons, residue-level overlap maps, and proteome-level overviews.

plot_digest_profile(): Four-Panel Digest Diagnostic Plot
plot_coverage_map(): Protein Coverage Map
plot_cleavage_map(): Cleavage Site Map
plot_peptide_overlap_map(): Amino-Acid Peptide Overlap Map
plot_length_distribution(): Standalone Peptide Length Distribution
plot_gravy_landscape(): GRAVY Landscape: 2D Scatter of Peptide Length vs. Hydrophobicity
plot_pI_distribution(): pI Distribution: Histogram of Peptide Isoelectric Points
plot_mz_distribution(): Precursor m/z Distribution
plot_missed_cleavage_impact(): Missed Cleavage Impact Plot
plot_enzyme_comparison(): Enzyme Comparison Chart
plot_proteome_overview(): Proteome digest overview
plot_batch_comparison(): Multi-enzyme proteome comparison
plot_weight_sensitivity(): Plot weight sensitivity

Plot Configuration & Output

Customise colours, thresholds, and theme defaults for all pepVet plots, and export figures with publication-ready defaults.

pepvet_plot_config(): Configure pepVet plot appearance
pepvet_plot_config_reset(): Reset pepVet plot configuration to defaults
pepvet_theme_manuscript(): pepVet manuscript theme
pepvet_theme_presentation(): pepVet presentation theme
pepvet_save_figure(): Save a pepVet figure with publication-ready defaults

Sensitivity analysis

Assess verdict and rank stability under weight perturbation via Dirichlet-based Monte Carlo simulation.

sensitivity_analysis(): Weight sensitivity analysis
plot_weight_sensitivity(): Plot weight sensitivity

Score diagnostics

Quantify multicollinearity, dimensionality, and component contributions in the scoring model.

score_diagnostics(): Score diagnostics for pepVet scoring models
plot_score_diagnostics(): Plot score diagnostics

Reporting

Render compact, ASCII-safe console summaries of digest quality. pepvet_check() combines evaluation and reporting in a single call for interactive use.

digest_report(): Print a compact console report for a proteolytic digest
pepvet_check(): Quick digest check for a single protein

Export

Export valid peptide lists to downstream proteomics tools. Supported formats: Skyline transition list, generic annotated CSV, and FASTA.

export_peptide_list(): Export a peptide list for downstream tools

Reference data

Amino acid property table used by the scoring engine.

aa_properties: Amino acid properties

Package

pepVet pepVet-package: pepVet: Evaluate Proteolytic Digests for Proteomics Workflows