Software:Mayu
From SPCTools
Mayu
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
Software
For running Mayu install a perl interpreter and run the software from the unpacked zip file on a command line. See the [ manual] for more details.
Download
- manual
- software package
- example data set
- perl script to create target decoy databases
Features
- 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 Mayu.pl -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
