Package: protti 0.9.0

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_0.9.0.tar.gz
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protti.pdf |protti.html✨
protti/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

data-analysislip-msmass-spectrometryomicsproteinproteomicssystems-biology

76 exports 58 stars 3.53 score 89 dependencies 76 scripts 675 downloads

Last updated 2 months agofrom:d5f7503e7b. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 14 2024
R-4.5-winOKSep 14 2024
R-4.5-linuxOKSep 14 2024
R-4.4-winOKSep 14 2024
R-4.4-macOKSep 14 2024
R-4.3-winOKSep 14 2024
R-4.3-macOKSep 14 2024

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_keggfetch_metal_pdbfetch_mobidbfetch_pdbfetch_pdb_structurefetch_quickgofetch_uniprotfetch_uniprot_proteomefilter_cvfind_peptidefind_peptide_in_structurefit_drc_4pgo_enrichmentimputekegg_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:askpassbase64encbitbit64bslibcachemclicliprcolorspacecpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforcatsfsgenericsggplot2ggrepelgluegtablehighrhmshtmltoolshtmlwidgetshttrisobandjanitorjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplotlyprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreadrrlangrmarkdownsassscalessnakecasestringistringrsystibbletidyrtidyselecttimechangetinytextzdbutf8vctrsviridisLitevroomwithrxfunyaml

Dose-Response Data Analysis Workflow

Jan-Philipp Quast

Rendered fromdata_analysis_dose_response_workflow.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2024-07-16
Started: 2021-03-08

Input Preparation Workflow

Dina Schuster

Rendered frominput_preparation_workflow.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2024-02-17
Started: 2021-03-11

Protein Structure Analysis Workflow

Jan-Philipp Quast, Patrick Stalder

Rendered fromprotein_structure_workflow.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2024-02-17
Started: 2022-03-22

Qualtiy Control (QC) Workflow

Dina Schuster

Rendered fromquality_control_workflow.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2024-03-28
Started: 2021-02-01

Single Dose Treatment Data Analysis Workflow

Dina Schuster

Rendered fromdata_analysis_single_dose_treatment_workflow.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2024-02-17
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 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
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