This R package implements statistical modelling of affinity purification–mass spectrometry (AP-MS) data to compute confidence scores to identify bona fide protein-protein interactions (PPI).
Installation The development version can be installed through github:
devtools::install_github(repo="zqzneptune/SMAD") library(SMAD) Input Data A demo data.frame was provided as a hint how the input data should strcutured in order to run the scoring functions:
data(TestDatInput) colnames(TestDataInput) [1] "idRun" "idBait" "idPrey" "countPrey" "lenPrey" idRun idBait idPrey countPrey lenPrey Unique ID of one AP-MS run Bait ID Prey ID Prey peptide count Protein sequence length of the prey In case of duplcates, a suffix or prefix of e.
A collection of resources regarding affinity purification mass spectrometry proteomics for the identification of protein-protein interactions.
Algorithms Year Algorithm Publication Implementation 2006 SAI (socio-affinity index) Anne-Claude Gavin et al., Nature 2007 partial least squares based regression model Rob M Ewing et al., Mol Syst Biol 2007 PE (purification enrichment) Sean R. Collins et al., Molecular & Cellular Proteomics SMAD 2007 Hart G Traver Hart et al.