Package: pepVet 0.99.1

Enes K. Ergin

pepVet: Evaluate Proteolytic Digests for Proteomics Workflows

Simulates proteolytic digestion, scores the resulting peptides for LC-MS/MS suitability, compares candidate enzymes, and reports digest quality at the protein level. Supports 40 cleaver-compatible enzyme rules, workflow presets, peptide mass and pI calculations, sequence-local cleavage-efficiency annotations, and proteome-aware uniqueness scoring. Evaluates multi-FASTA files in batches with per-protein triage and proteome-level summaries. Exports peptide lists for Skyline and generic downstream tools and prints styled console reports.

Authors:Enes K. Ergin [aut, cre]

pepVet_0.99.1.tar.gz
pepVet_0.99.1.zip(r-4.7-any)pepVet_0.99.1.zip(r-4.6-any)pepVet_0.99.1.zip(r-4.5-any)
pepVet_0.99.1.tgz(r-4.6-any)pepVet_0.99.1.tgz(r-4.5-any)
pepVet_0.99.1.tar.gz(r-4.7-any)pepVet_0.99.1.tar.gz(r-4.6-any)
pepVet_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
pepVet/json (API)

# Install 'pepVet' in R:
install.packages('pepVet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/langelab/pepvet/issues

Pkgdown/docs site:https://langelab.github.io

Datasets:

On BioConductor:pepVet-0.99.1(bioc 3.24)

proteomicsmassspectrometryqualitycontrolbioinformaticscomparisondigestenzymequality-assurance

5.56 score 3 stars 12 scripts 212 downloads 37 exports 19 dependencies

Last updated from:6582caf217. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE170
linux-develOK394
source / vignettesOK198
linux-releaseOK364
macos-releaseOK288
macos-oldrelOK217
windows-develOK284
windows-releaseOK247
windows-oldrelOK284
wasm-releaseOK98

Exports:annotate_cleavage_sitesbatch_compare_enzymesbatch_evaluatecalculate_peptide_masscalculate_pIcompare_digestsdigest_proteindigest_reportevaluate_digestexport_peptide_listpepvet_checkpepvet_plot_configpepvet_plot_config_resetpepvet_presetpepvet_save_figurepepvet_theme_manuscriptpepvet_theme_presentationplot_batch_comparisonplot_cleavage_mapplot_coverage_mapplot_digest_profileplot_enzyme_comparisonplot_gravy_landscapeplot_length_distributionplot_missed_cleavage_impactplot_mz_distributionplot_peptide_overlap_mapplot_pI_distributionplot_proteome_overviewplot_score_diagnosticsplot_weight_sensitivityrecommend_enzymescore_diagnosticsscore_peptidessensitivity_analysissummarize_batchtriage_proteins

Dependencies:BiocGenericsBiostringscleaverclicrayongenericsglueIRangeslifecyclemagrittrpillarpkgconfigrlangS4VectorsSeqinfotibbleutf8vctrsXVector

Getting Started with pepVet
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
Rendered frompepVet-introduction.Rmdusingknitr::rmarkdown

Last update: 2026-07-30
Started: 2026-03-20

pepVet Compared to Other Tools
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
Rendered frompepVet-tool-comparison.Rmdusingknitr::rmarkdown

Last update: 2026-07-30
Started: 2026-06-16

Readme and manuals

Help Manual

Help pageTopics
Amino acid propertiesaa_properties
Annotate cleavage-site efficiencyannotate_cleavage_sites
Compare multiple enzymes across a full proteomebatch_compare_enzymes
Batch-evaluate multiple proteinsbatch_evaluate
Calculate peptide mass or m/zcalculate_peptide_mass
Calculate peptide isoelectric pointcalculate_pI
Compare multiple enzymes on a single proteincompare_digests
Simulate a proteolytic digestdigest_protein
Print a compact console report for a proteolytic digestdigest_report
Evaluate a proteolytic digestevaluate_digest
Export a peptide list for downstream toolsexport_peptide_list
Quick digest check for a single proteinpepvet_check
Configure pepVet plot appearancepepvet_plot_config
Reset pepVet plot configuration to defaultspepvet_plot_config_reset
Return a named scoring presetpepvet_preset
Save a pepVet figure with publication-ready defaultspepvet_save_figure
pepVet manuscript themepepvet_theme_manuscript
pepVet presentation themepepvet_theme_presentation
Multi-enzyme proteome comparisonplot_batch_comparison
Cleavage Site Mapplot_cleavage_map
Protein Coverage Mapplot_coverage_map
Four-Panel Digest Diagnostic Plotplot_digest_profile
Enzyme Comparison Chartplot_enzyme_comparison
GRAVY Landscape: 2D Scatter of Peptide Length vs. Hydrophobicityplot_gravy_landscape
Standalone Peptide Length Distributionplot_length_distribution
Missed Cleavage Impact Plotplot_missed_cleavage_impact
Precursor m/z Distributionplot_mz_distribution
Amino-Acid Peptide Overlap Mapplot_peptide_overlap_map
pI Distribution: Histogram of Peptide Isoelectric Pointsplot_pI_distribution
Proteome digest overviewplot_proteome_overview
Plot score diagnosticsplot_score_diagnostics
Plot weight sensitivityplot_weight_sensitivity
Return the highest-scoring enzyme for a single proteinrecommend_enzyme
Score diagnostics for pepVet scoring modelsscore_diagnostics
Score digested peptides for pre-acquisition reviewscore_peptides
Weight sensitivity analysissensitivity_analysis
Summarize a batch digest evaluationsummarize_batch
Triage proteins from a batch evaluationtriage_proteins