coronaAnalysis.py - Main script that performs quantification and generates figures and tables for the paper
coronaBatcher.py - Batch script that executes external tools (msconvert, MSGF+, Percolator) and prepares the input for KNIME workflow
coronaHelpers.py - Helper data handling functions used by other scripts
coronaPlots.py - Helper graphing functions used by main script
msgf.mods - Modification file used by MSGF+
multiplier.csv - Direction coefficients for alpha-, beta-, and turn propensities
msgf-percolator-lfq.knwf - KNIME workflow that executes OpenMS tools for label-free quantification
parsePPD.py - Script to convert Plasma Proteome Database to FASTA format and extract concentration data
gravy.py - functions to calculate GRAVY and amino acid content
shrinkTest.py - multithreaded permutation test for shrinkage measure
V. Gorshkov, J. A. Bubis, E. M. Solovyeva, M. V. Gorshkov, and F. Kjeldsen Protein corona formed on silver nanoparticles in blood plasma is highly selective and resistant to physicochemical changes of the solution Environ. Sci.: Nano, 2019, 6, 1089-1098; DOI: 10.1039/C8EN01054D