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.

Param-Medic software

Param-Medic is implemented as a standalone tool, and is also integrated into the Crux mass spectrometry toolkit (both as a separate tool and as a method for selecting parameter values for Crux and Tide searches).

The param-medic GitHub repository has all necessary software and documentation for running Param-Medic. It is also easily installed vi PyPi, with the command "pip install param-medic". The standalone version of Param-Medic can process .ms2 and .mzML files, while the Crux version can handle all formats supported by Crux.

LC-MS/MS spectra

The LC-MS/MS spectra used to train and test Param-Medic are available below. Links go to the appropriate projects within the PRIDE or Chorus repositories, and directly to the data files in .ms2 and .mzML format hosted on this server.
2014kim-kidney repository .ms2 .mzML
2014kim-lung repository .ms2 .mzML
2015clark-redefining repository .ms2 .mzML
2015radoshevich-isg15 repository .ms2 .mzML
2015tanca-impact repository .ms2 .mzML
2015uszkoreit-intuitive repository .ms2 .mzML
2016mann-unpublished repository .ms2 .mzML
2016schittmayer-cleaning repository .ms2 .mzML
2016zhong-quantitative repository .ms2 .mzML
2016may-metapeptides repository .ms2 .mzML
2016audain-in-depth repository .ms2 .mzML