Package: protti 1.0.0

Jan-Philipp Quast

protti: Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

Useful functions and workflows for proteomics quality control and data analysis of both limited proteolysis-coupled mass spectrometry (LiP-MS) (Feng et. al. (2014) <doi:10.1038/nbt.2999>) and regular bottom-up proteomics experiments. Data generated with search tools such as 'Spectronaut', 'MaxQuant' and 'Proteome Discover' can be easily used due to flexibility of functions.

Authors:Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

protti_1.0.0.tar.gz
protti_1.0.0.zip(r-4.7)protti_1.0.0.zip(r-4.6)protti_1.0.0.zip(r-4.5)
protti_1.0.0.tgz(r-4.6-any)protti_1.0.0.tgz(r-4.5-any)
protti_1.0.0.tar.gz(r-4.7-any)protti_1.0.0.tar.gz(r-4.6-any)
protti_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
protti/json (API)

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

Bug tracker:https://github.com/jpquast/protti/issues

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

Datasets:

On CRAN:

Conda:

data-analysislip-msmass-spectrometryomicsproteinproteomicssystems-biology

8.11 score 65 stars 160 scripts 836 downloads 78 exports 83 dependencies

Last updated from:ad9c7abf37. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK279
source / vignettesOK246
linux-release-x86_64OK261
macos-release-arm64OK125
macos-oldrel-arm64OK127
windows-develOK183
windows-releaseOK202
windows-oldrelOK174
wasm-releaseOK188

Exports:analyse_functional_networkanova_prottiassign_missingnessassign_peptide_typebarcode_plotcalculate_aa_scorescalculate_diff_abundancecalculate_go_enrichmentcalculate_kegg_enrichmentcalculate_protein_abundancecalculate_sequence_coveragecalculate_treatment_enrichmentcorrect_lip_for_abundancecreate_queuecreate_structure_contact_mapcreate_synthetic_datadiff_abundancedrc_4p_plotextract_metal_bindersfetch_alphafold_aligned_errorfetch_alphafold_predictionfetch_chebifetch_ecofetch_gofetch_interprofetch_keggfetch_metal_pdbfetch_mobidbfetch_pdbfetch_pdb_structurefetch_quickgofetch_uniprotfetch_uniprot_proteomefilter_cvfind_peptidefind_peptide_in_structurefit_drc_4pgo_enrichmentimputeimpute_randomforestkegg_enrichmentmap_peptides_on_structuremedian_normalisationnetwork_analysisnormaliseparallel_create_structure_contact_mapparallel_fit_drc_4ppeptide_profile_plotpeptide_typeplot_drc_4pplot_peptide_profilesplot_pval_distributionpredict_alphafold_domainpval_distribution_plotqc_charge_statesqc_contaminantsqc_cvsqc_data_completenessqc_idsqc_intensity_distributionqc_median_intensitiesqc_missed_cleavagesqc_pcaqc_peak_widthqc_peptide_typeqc_proteome_coverageqc_ranked_intensitiesqc_sample_correlationqc_sequence_coveragerandomise_queueread_prottiscale_prottisequence_coveragetreatment_enrichmentttest_prottivolcano_plotvolcano_prottiwoods_plot

Dependencies:askpassbase64encbitbit64bslibcachemclicliprcpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomeforcatsfsgenericsggplot2ggrepelgluegtablehighrhmshtmltoolshtmlwidgetshttrisobandjanitorjquerylibjsonliteknitrlabelinglaterlazyevallifecyclelubridatemagrittrmemoisemimeopensslotelpillarpkgconfigplotlyprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrlangrmarkdownS7sassscalessnakecasestringistringrsystibbletidyrtidyselecttimechangetinytextzdbutf8vctrsviridisLitevroomwithrxfunyaml

Dose-Response Data Analysis Workflow
Introduction | Getting started | Loading data | Cleaning data | Clustering of samples | Fitting dose-response curves | Model fit plotting | Further analysis | Annotation of data | Enrichment and network analysis
Rendered fromdata_analysis_dose_response_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2021-03-08

Input Preparation Workflow
Introduction | Protein-centric analysis | Loading packages | Spectronaut | MaxQuant | Peptide-centric analysis/LiP-MS analysis | Skyline | Proteome Discoverer | Other search engines and software
Rendered frominput_preparation_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2021-03-11

Protein Structure Analysis Workflow
Introduction | Structural data | Getting started | Loading data | Preparing data | Fetching structural information | Fetching atomic structural information | Fetching atomic structure prediction information from AlphaFold | AlphaFold domain predictions using the predicted aligned error (PAE) | ptsI domain prediction with graph_resolution = 1 | ptsI domain prediction with graph_resolution = 0.5 | Generation of structural contact maps | Mapping of amino acids, peptides or regions on 3D protein structures and predictions | 3D structure mapping in R using r3dmol | PyMOL | ChimeraX | Result | Mapping of amino acid scores
Rendered fromprotein_structure_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2022-03-22

Qualtiy Control (QC) Workflow
Introduction | protti | Getting started | Quality control | Coefficients of variation | Number of identifications (IDs) | Peptide types | Run intensities | Charge states | Missed cleavages | Sequence coverage | Peak width | Data completeness | Log2 Intensity distribution | Sample correlation | Principal component analysis (PCA) | Ranked intensity distribution | Additional QC functions
Rendered fromquality_control_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2021-02-01

Single Dose Treatment Data Analysis Workflow
Introduction | How to use protti to analyse your data | Getting started | Data preparation | Log2 transformation, median normalisation and CV filtering | Remove non-proteotypic peptides | Fetching database information and assigning peptide types | Data analysis | Statistical hypothesis test | p-value distribution | Volcano plot | Barcode plot | Wood's plot | Peptide profile plots | Additional helpful functions
Rendered fromdata_analysis_single_dose_treatment_workflow.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2021-03-08

Readme and manuals

Help Manual

Help pageTopics
Analyse protein interaction network for significant hitsanalyse_functional_network
Perform ANOVAanova_protti
Assignment of missingness typesassign_missingness
Assign peptide typeassign_peptide_type
Barcode plotbarcode_plot
Calculate scores for each amino acid position in a protein sequencecalculate_aa_scores
Calculate differential abundance between conditionscalculate_diff_abundance
Perform gene ontology enrichment analysiscalculate_go_enrichment
Sampling of values for imputationcalculate_imputation
Perform KEGG pathway enrichment analysiscalculate_kegg_enrichment
Label-free protein quantificationcalculate_protein_abundance
Protein sequence coveragecalculate_sequence_coverage
Check treatment enrichmentcalculate_treatment_enrichment
Protein abundance correction for LiP-datacorrect_lip_for_abundance
Creates a mass spectrometer queue for Xcaliburcreate_queue
Creates a contact map of all atoms from a structure filecreate_structure_contact_map
Creates a synthetic limited proteolysis proteomics datasetcreate_synthetic_data
Dose response curve helper functiondrc_4p
Plotting of four-parameter dose response curvesdrc_4p_plot
Extract metal-binding protein information from UniProtextract_metal_binders
Fetch AlphaFold aligned errorfetch_alphafold_aligned_error
Fetch AlphaFold predictionfetch_alphafold_prediction
Fetch ChEBI database informationfetch_chebi
Fetch evidence & conclusion ontologyfetch_eco
Fetch gene ontology information from geneontology.orgfetch_go
Fetch domain and residue information from InterProfetch_interpro
Fetch KEGG pathway data from KEGGfetch_kegg
Fetch structural information about protein-metal binding from MetalPDBfetch_metal_pdb
Fetch protein disorder and mobility information from MobiDBfetch_mobidb
Fetch structure information from RCSBfetch_pdb
Fetch PDB structure atom data from RCSBfetch_pdb_structure
Fetch information from the QuickGO APIfetch_quickgo
Fetch protein data from UniProtfetch_uniprot
Fetch proteome data from UniProtfetch_uniprot_proteome
Data filtering based on coefficients of variation (CV)filter_cv
Find all sub IDs of an ID in a networkfind_all_subs
Find ChEBI IDs for name patternsfind_chebis
Find peptide locationfind_peptide
Finds peptide positions in a PDB structure based on positional matchingfind_peptide_in_structure
Fitting four-parameter dose response curvesfit_drc_4p
Imputation of missing valuesimpute
Imputation of Missing Values Using Random Forest Imputationimpute_randomforest
Viridis colour schememako_colours
Maps peptides onto a PDB structure or AlphaFold predictionmap_peptides_on_structure
List of metal-related ChEBI IDs in UniProtmetal_chebi_uniprot
Molecular function gene ontology metal subsetmetal_go_slim_subset
List of metalsmetal_list
Intensity normalisationnormalise
Creates a contact map of all atoms from a structure file (using parallel processing)parallel_create_structure_contact_map
Fitting four-parameter dose response curves (using parallel processing)parallel_fit_drc_4p
Peptide abundance profile plotpeptide_profile_plot
Predict protein domains of AlphaFold predictionspredict_alphafold_domain
Colour scheme for prottiprotti_colours
Structural analysis example dataptsi_pgk
Plot histogram of p-value distributionpval_distribution_plot
Check charge state distributionqc_charge_states
Percentage of contaminants per sampleqc_contaminants
Check CV distributionqc_cvs
Data completenessqc_data_completeness
Check number of precursor, peptide or protein IDsqc_ids
Check intensity distribution per sample and overallqc_intensity_distribution
Median run intensitiesqc_median_intensities
Check missed cleavagesqc_missed_cleavages
Plot principal component analysisqc_pca
Peak width over retention timeqc_peak_width
Check peptide type percentage shareqc_peptide_type
Proteome coverage per sample and totalqc_proteome_coverage
Check ranked intensitiesqc_ranked_intensities
Correlation based hirachical clustering of samplesqc_sample_correlation
Protein coverage distributionqc_sequence_coverage
Randomise samples in MS queuerandomise_queue
Rapamycin 10 uM example datarapamycin_10uM
Rapamycin dose response example datarapamycin_dose_response
Read, clean and convertread_protti
Replace identified positions in protein sequence by "x"replace_identified_by_x
Scaling a vectorscale_protti
Convert metal names to search patternsplit_metal_name
Query from URLtry_query
Perform Welch's t-testttest_protti
Viridis colour schemeviridis_colours
Volcano plotvolcano_plot
Woods' plotwoods_plot