Param-Medic: breathing new life into MS/MS database search by optimizing parameter settings

This is a set of resources for Param-Medic, a tool that optimizes MS/MS database search parameter settings. Param-Medic infers instrument precursor and fragment error directly from MS/MS experimental data by analyzing pairs of MS/MS spectra that represent the same peptide ion.

This website accompanies the manuscript "Param-Medic Breathes New Life into MS/MS Database Search by Optimizing Parameter Settings", submitted to the Journal of Proteome Research in December 2016. That manuscript describes the training and evaluation of Param-Medic on 11 publicly available datasets (eight training datasets and three test datasets), which are available below.