Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools
Label-free protein quantification
Protein sequence coverage
Fitting four-parameter dose response curves
Perform gene ontology enrichment analysis
Analyse protein interaction network for significant hits
Perform ANOVA
Assignment of missingness types
Assign peptide type
Barcode plot
Calculate scores for each amino acid position in a protein sequence
Calculate differential abundance between conditions
Perform gene ontology enrichment analysis
Sampling of values for imputation
Perform KEGG pathway enrichment analysis
Check treatment enrichment
Protein abundance correction for LiP-data
Creates a mass spectrometer queue for Xcalibur
Creates a contact map of all atoms from a structure file
Creates a synthetic limited proteolysis proteomics dataset
Calculate differential abundance between conditions
Plotting of four-parameter dose response curves
Dose response curve helper function
Extract metal-binding protein information from UniProt
Fetch AlphaFold aligned error
Fetch AlphaFold prediction
Fetch ChEBI database information
Fetch evidence & conclusion ontology
Fetch gene ontology information from geneontology.org
Fetch KEGG pathway data from KEGG
Fetch structural information about protein-metal binding from MetalPDB
Read, clean and convert
Fetch protein disorder and mobility information from MobiDB
Fetch PDB structure atom data from RCSB
Fetch structure information from RCSB
Fetch information from the QuickGO API
Fetch proteome data from UniProt
Fetch protein data from UniProt
Data filtering based on coefficients of variation (CV)
Find all sub IDs of an ID in a network
Find ChEBI IDs for name patterns
Finds peptide positions in a PDB structure based on positional matchin...
Find peptide location
Imputation of missing values
Perform KEGG pathway enrichment analysis
Maps peptides onto a PDB structure or AlphaFold prediction
Intensity normalisation
Analyse protein interaction network for significant hits
Intensity normalisation
Creates a contact map of all atoms from a structure file (using parall...
Fitting four-parameter dose response curves (using parallel processing...
Peptide abundance profile plot
Assign peptide type
Perform gene ontology enrichment analysis
Peptide abundance profile plot
Plot histogram of p-value distribution
Predict protein domains of AlphaFold predictions
Plot histogram of p-value distribution
Check charge state distribution
Percentage of contaminants per sample
Check CV distribution
Data completeness
Check number of precursor, peptide or protein IDs
Check intensity distribution per sample and overall
Median run intensities
Check missed cleavages
Plot principal component analysis
Peak width over retention time
Check peptide type percentage share
Proteome coverage per sample and total
Check ranked intensities
Correlation based hirachical clustering of samples
Protein coverage distribution
Randomise samples in MS queue
Replace identified positions in protein sequence by "x"
Scaling a vector
Protein sequence coverage
Convert metal names to search pattern
Check treatment enrichment
Query from URL
Perform Welch's t-test
Volcano plot
Volcano plot
Woods' plot
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.
Useful links