Protein Identification False Discovery Rates

Mayu is a software package for the analysis of (large) mass spectrometry-based shotgun proteomics data sets. Mayu determines protein identification false discovery rates (protFDR), peptide identification false discovery rates (pepFDR) and peptide-spectrum match false discovery rates (mFDR) using a novel robust and fast strategy.

Mayu is not a search engine and works with any* peptide-spectrum match discriminant score derived from a database search.

This software is licensed under the CC-GNU GPL version 2.0 or later. This software and associated documentation is provided "as is" and there is no warranty for this software.

*if this discriminant score is compatible with target decoy searching

For running Mayu install a perl interpreter and run the software from the unpacked zip file on a command line. See the manual, pdf for more details.


Mayu source code on GitHub Mayu package v1.08
  • manual
  • software package
  • example data set
  • perl script to create target
    decoy databases
  • provides false discovery rates not only on peptide-spectrum match level (mFDR) but also on protein identification (protFDR) and peptide identification (pepFDR) level
  • false discovery rates for single hits (single peptide-spectrum match protein identifications) and all but single hits (protein identifications with more than one peptide-spectrum match)
  • analysis in dependence of the amount of data
  • R plots
  • provides tables for each input file that relate the discriminant score (e.g. PeptideProphet, xcorr, mascot ion score,...) to a peptide-spectrum match false discovery rate

Example Result Plots

perl -B example.csv -C tardecdb.fa -H 41 -N 4 -O 15 -v -PmFDR -runR

  • graphical characterization of the input search results: discriminant score vs. peptide-spectrum match false discovery rate ds_vs_mFDR.pdf
  • a number of plots helping the user in selecting the appropriate filtering for the desired quality main.pdf
Lukas Reiter
Manfred Claassen

Mayu Software
Lukas Reiter - Hengartner Laboratory
Institute of Molecular Biology
Winterthurerstrasse 190
University of Zürich - Irchel
CH-8057 Zürich
Located at:
Institute for Molecular Systems Biology
Aebersold Laboratory
Wolfgang-Pauli-Str. 16
ETH Hönggerberg, HPT C 75
CH-8093 Zürich
Tel: +41 44 633 39 45