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

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Documentation for package ‘protti’ version 0.9.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

analyse_functional_network	Analyse protein interaction network for significant hits
anova_protti	Perform ANOVA
assign_missingness	Assignment of missingness types
assign_peptide_type	Assign peptide type
barcode_plot	Barcode plot
calculate_aa_scores	Calculate scores for each amino acid position in a protein sequence
calculate_diff_abundance	Calculate differential abundance between conditions
calculate_go_enrichment	Perform gene ontology enrichment analysis
calculate_imputation	Sampling of values for imputation
calculate_kegg_enrichment	Perform KEGG pathway enrichment analysis
calculate_protein_abundance	Label-free protein quantification
calculate_sequence_coverage	Protein sequence coverage
calculate_treatment_enrichment	Check treatment enrichment
correct_lip_for_abundance	Protein abundance correction for LiP-data
create_queue	Creates a mass spectrometer queue for Xcalibur
create_structure_contact_map	Creates a contact map of all atoms from a structure file
create_synthetic_data	Creates a synthetic limited proteolysis proteomics dataset
drc_4p	Dose response curve helper function
drc_4p_plot	Plotting of four-parameter dose response curves
extract_metal_binders	Extract metal-binding protein information from UniProt
fetch_alphafold_aligned_error	Fetch AlphaFold aligned error
fetch_alphafold_prediction	Fetch AlphaFold prediction
fetch_chebi	Fetch ChEBI database information
fetch_eco	Fetch evidence & conclusion ontology
fetch_go	Fetch gene ontology information from geneontology.org
fetch_kegg	Fetch KEGG pathway data from KEGG
fetch_metal_pdb	Fetch structural information about protein-metal binding from MetalPDB
fetch_mobidb	Fetch protein disorder and mobility information from MobiDB
fetch_pdb	Fetch structure information from RCSB
fetch_pdb_structure	Fetch PDB structure atom data from RCSB
fetch_quickgo	Fetch information from the QuickGO API
fetch_uniprot	Fetch protein data from UniProt
fetch_uniprot_proteome	Fetch proteome data from UniProt
filter_cv	Data filtering based on coefficients of variation (CV)
find_all_subs	Find all sub IDs of an ID in a network
find_chebis	Find ChEBI IDs for name patterns
find_peptide	Find peptide location
find_peptide_in_structure	Finds peptide positions in a PDB structure based on positional matching
fit_drc_4p	Fitting four-parameter dose response curves
impute	Imputation of missing values
mako_colours	Viridis colour scheme
map_peptides_on_structure	Maps peptides onto a PDB structure or AlphaFold prediction
metal_chebi_uniprot	List of metal-related ChEBI IDs in UniProt
metal_go_slim_subset	Molecular function gene ontology metal subset
metal_list	List of metals
normalise	Intensity normalisation
parallel_create_structure_contact_map	Creates a contact map of all atoms from a structure file (using parallel processing)
parallel_fit_drc_4p	Fitting four-parameter dose response curves (using parallel processing)
peptide_profile_plot	Peptide abundance profile plot
predict_alphafold_domain	Predict protein domains of AlphaFold predictions
protti_colours	Colour scheme for protti
ptsi_pgk	Structural analysis example data
pval_distribution_plot	Plot histogram of p-value distribution
qc_charge_states	Check charge state distribution
qc_contaminants	Percentage of contaminants per sample
qc_cvs	Check CV distribution
qc_data_completeness	Data completeness
qc_ids	Check number of precursor, peptide or protein IDs
qc_intensity_distribution	Check intensity distribution per sample and overall
qc_median_intensities	Median run intensities
qc_missed_cleavages	Check missed cleavages
qc_pca	Plot principal component analysis
qc_peak_width	Peak width over retention time
qc_peptide_type	Check peptide type percentage share
qc_proteome_coverage	Proteome coverage per sample and total
qc_ranked_intensities	Check ranked intensities
qc_sample_correlation	Correlation based hirachical clustering of samples
qc_sequence_coverage	Protein coverage distribution
randomise_queue	Randomise samples in MS queue
rapamycin_10uM	Rapamycin 10 uM example data
rapamycin_dose_response	Rapamycin dose response example data
read_protti	Read, clean and convert
replace_identified_by_x	Replace identified positions in protein sequence by "x"
scale_protti	Scaling a vector
split_metal_name	Convert metal names to search pattern
try_query	Query from URL
ttest_protti	Perform Welch's t-test
viridis_colours	Viridis colour scheme
volcano_plot	Volcano plot
woods_plot	Woods' plot