PepMOD - Peptide Multivariate Outlier Detection
PepMOD is a data filtering tool designed to filter X!tandem search engine results based on p-values calculated from a random score distribution.

Requirements for PepMOD:

  1. X!tandem XML results with all data exported, accomplished by including "<note type="input" label="output, results">all</note>" in the X!tandem parameter file before searching.
  2. Target and Decoy search results are necessary for proper filtering, but a target set can be filtered against itself in the case decoy results are not available.