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

## Documentation for package ‘protti’ version 1.0.0

- 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_interpro | Fetch domain and residue information from InterPro
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
impute_randomforest | Imputation of Missing Values Using Random Forest Imputation
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