BioinformaticsBioinformaticsPeer-reviewed
Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
Ana S. C. Silva, Robbin Bouwmeester, Lennart Martens, Sven Degroeve
The paper shows that using MS2PIP to predict fragment ion intensities and comparing them to experimental spectra improves Percolator's ability to distinguish PSMs while controlling false discovery rates.